Identification of the entire set of transferred chloroplast DNA sequences in the mitochondrial genome of rice

Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years

The first complete chloroplast genome of rice (Oryza sativa) was published in 1989, ushering in a new era of studies of chloroplast genomics in Poaceae. Progresses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologiesand in the development of genome assembly software, have significantly advanced chloroplast genomics research. Poaceae is one of the most targeted families in chloroplast genome research because of its agricultural, ecological, and economic importance. Over the last 30 years, 2,050 complete chloroplast genome sequences from 40 tribes and 282 genera have been generated, most (97%) of them in the recent ten years. The wealth of data provides the groundwork for studies on species evolution, phylogeny, genetic transformation, and other aspects of Poaceae chloroplast genomes. As a result, we have gained a deeper understanding of the properties of Poaceae chloroplast genomes. Here, we summarize the achievements of the studies of the Poaceae chloroplast genomes and envision the challenges for moving the area ahead.

Comparative analysis of nuclear, chloroplast, and mitochondrial genomes of watermelon and melon provides evidence of gene transfer

During plant evolution, there is genetic communication between organelle and nuclear genomes. A comparative analysis was performed on the organelle and nuclear genomes of the watermelon and melon. In the watermelon, chloroplast-derived sequences accounted for 7.6% of the total length of the mitochondrial genome. In the melon, chloroplast-derived sequences accounted for approximately 2.73% of the total mitochondrial genome. In watermelon and melon, the chloroplast-derived small-fragment sequences are either a subset of large-fragment sequences or appeared multiple times in the mitochondrial genome, indicating that these fragments may have undergone multiple independent migration integrations or emerged in the mitochondrial genome after migration, replication, and reorganization. There was no evidence of migration from the mitochondria to chloroplast genome. A sequence with a total length of about 73 kb (47%) in the watermelon chloroplast genome was homologous to a sequence of about 313 kb in the nuclear genome. About 33% of sequences in the watermelon mitochondrial genome was homologous with a 260 kb sequence in the nuclear genome. A sequence with a total length of about 38 kb (25%) in the melon chloroplast genome was homologous with 461 sequences in the nuclear genome, with a total length of about 301 kb. A 3.4 Mb sequence in the nuclear genome was homologous with a melon mitochondrial sequence. These results indicate that, during the evolution of watermelon and melon, a large amount of genetic material was exchanged between the nuclear genome and the two organelle genomes in the cytoplasm.

Plastid Genomes of Flowering Plants: Essential Principles

The plastid genome (plastome ) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy, and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations is allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter, we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and the tools of plastid genetic engineering.

Translocation from the chloroplast stroma into the thylakoid lumen allows expression of recombinant epidermal growth factor in transplastomic tobacco plants

Chloroplast transformation has many potential advantages for the production of recombinant proteins in plants. However, it has been reported that chloroplast expression of many proteins, such as human epidermal growth factor (hEGF), results hindered by post-transcriptional mechanisms. hEGF degradation has been related to the redox potential of the stroma and protein misfolding. To solve this problem, we proposed the redirection of hEGF into the thylakoid lumen where the environment could improve disulfide bonds formation stabilizing the functional conformation of the protein. We generated transplastomic tobacco plants targeting hEGF protein to the thylakoid lumen by adding a transit peptide (Str). Following this approach, we could detect thylakoid lumen-targeted hEGF by western blotting while stromal accumulation of hEGF remained undetectable. Southern blot analysis confirmed the integration of the transgene through homologous recombination into the plastome. Northern blot analysis showed similar levels of egf transcripts in the EGF and StrEGF lines. These results suggest that higher stability of the hEGF peptide in the thylakoid lumen is the primary cause of the increased accumulation of the recombinant protein observed in StrEGF lines. They also highlight the necessity of exploring different sub-organellar destinations to improve the accumulation levels of a specific recombinant protein in plastids.

Cytosine methylation of rice mitochondrial DNA from grain and leaf tissues

The rice leaf mitochondrial DNA is  more methylated compared to the rice grain mitochondrial DNA. The old rice leaf mitochondrial DNA has also a higher methylation level than the young rice leaf mitochondrial DNA. The presence of DNA methylation in rice organelles has not been well characterized. We have previously shown that cytosine methylation of chloroplast DNA is different between leaf and grain, and varies between young and old leaves in rice. However, the variation in cytosine methylation of mitochondrial DNA is still poorly characterized. In this study, we have investigated cytosine methylation of mitochondrial DNA in the rice grain and leaf. Based on CpG, CHG, and CHH methylation analyses, the leaf mitochondrial DNA was found to be  more methylated compared to the grain mitochondrial DNA. The methylation of the leaf mitochondrial DNA was also higher in old compared to young leaves. Differences in methylation were observed at different cytosine positions of the mitochondrial DNA between grain and leaf, although there were also positions with a similar level of high methylation in all the tissues examined. The differentially methylated cytosine positions in rice mitochondrial DNA were observed mostly in the intergenic region and in some mitochondrial-specific genes involved in ATP production, transcription, and translation. The functional importance of cytosine methylation in the life cycle of rice mitochondria is still to be determined.

Ancient Mitochondrial Gene Transfer between Fungi and the Orchids

The mitochondrial genomes (mitogenomes) of plants are known to incorporate and accumulate DNA from intra- and extracellular donors. Despite the intimate relationships formed between flowing plants (angiosperms) and fungi, lengthy fungal-like sequence has not been identified in angiosperm mitogenomes to date. Here, we present multiple lines of evidence documenting horizontal gene transfer (HGT) between the mitogenomes of fungi and the ancestors of the orchids, plants that are obligate parasites of fungi during their early development. We show that the ancestor of the orchids acquired an ∼270-bp fungal mitogenomic region containing three transfer RNA genes. We propose that the short HGT was later replaced by a second HGT event transferring >8 kb and 14 genes from a fungal mitogenome to that of the ancestor of the largest orchid subfamily, Epidendroideae. Our results represent the first evidence of genomic-scale HGT between fungal and angiosperm mitogenomes and demonstrate that the length intergenic spacer regions of angiosperm mitogenomes can effectively fossilize the genomic remains of ancient, nonplant organisms.

Comparative sequence and methylation analysis of chloroplast and amyloplast genomes from rice

Grain amyloplast and leaf chloroplast DNA sequences are identical in rice plants but are differentially methylated. The leaf chloroplast DNA becomes more methylated as the rice plant ages. Rice is an important crop worldwide. Chloroplasts and amyloplasts are critical organelles but the amyloplast genome is poorly studied. We have characterised the sequence and methylation of grain amyloplast DNA and leaf chloroplast DNA in rice. We have also analysed the changes in methylation patterns in the chloroplast DNA as the rice plant ages. Total genomic DNA from grain, old leaf and young leaf tissues were extracted from the Oryza sativa ssp. indica cv. MR219 and sequenced using Illumina Miseq. Sequence variant analysis revealed that the amyloplast and chloroplast DNA of MR219 were identical to each other. However, comparison of CpG and CHG methylation between the identical amyloplast and chloroplast DNA sequences indicated that the chloroplast DNA from rice leaves collected at early ripening stage was more methylated than the amyloplast DNA from the grains of the same plant. The chloroplast DNA became more methylated as the plant ages so that chloroplast DNA from young leaves was less methylated overall than amyloplast DNA. These differential methylation patterns were primarily observed in organelle-encoded genes related to photosynthesis followed by those involved in transcription and translation.

Evidence of mitochondrial DNA in the chloroplast genome of Convallaria keiskei and its subsequent evolution in the Asparagales

DNA transfer between internal organelles such as the nucleus, mitochondrion, and plastid is a well-known phenomenon in plant evolution, and DNA transfer from the plastid and mitochondrion to the nucleus, from the plastid to the mitochondrion, and from the nucleus to the mitochondrion has been well-documented in angiosperms. However, evidence of the transfer of mitochondrial DNA (mtDNA) to the plastid has only been found in three dicotyledons and one monocotyledon. In the present study, we characterised and analysed two chloroplast (cp) genome sequences of Convallaria keiskei and Liriope spicata, and found that C. keiskei has the largest cp genome (162,109 bp) in the Asparagaceae. Interestingly, C. keiskei had a ~3.3-kb segment of mtDNA in its cp genome and showed similarity with the mt gene rpl10 as a pseudogene. Further analyses revealed that mtDNA transfer only occurred in C. keiskei in the Nolinoideae, which diverged very recently (7.68 million years ago (mya); 95% highest posterior density (HPD): 14.55–2.97 mya). These findings indicate that the C. keiskei cp genome is unique amongst monocotyledon land plants, but further work is necessary to understand the direction and mechanism involved in the uptake of mtDNA by the plastid genome of C. keiskei.

The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family

The NAD(P)H dehydrogenase complex is encoded by 11 ndh genes in plant chloroplast (cp) genomes. However, ndh genes are truncated or deleted in some autotrophic Epidendroideae orchid cp genomes. To determine the evolutionary timing of the gene deletions and the genomic locations of the various ndh genes in orchids, the cp genomes of Vanilla planifolia, Paphiopedilum armeniacum, Paphiopedilum niveum, Cypripedium formosanum, Habenaria longidenticulata, Goodyera fumata and Masdevallia picturata were sequenced; these genomes represent Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae subfamilies. Four orchid cp genome sequences were found to contain a complete set of ndh genes. In other genomes, ndh deletions did not correlate to known taxonomic or evolutionary relationships and deletions occurred independently after the orchid family split into different subfamilies. In orchids lacking cp encoded ndh genes, non cp localized ndh sequences were identified. In Erycina pusilla, at least 10 truncated ndh gene fragments were found transferred to the mitochondrial (mt) genome. The phenomenon of orchid ndh transfer to the mt genome existed in ndh-deleted orchids and also in ndh containing species.

Translational fusion and redirection to thylakoid lumen as strategies to enhance accumulation of human papillomavirus E7 antigen in tobacco chloroplasts

Human papillomavirus (HPV) is the causal agent of cervical cancer, one of the most common causes of death in women worldwide, and its E7 antigen is the major candidate for a therapeutic vaccine. The large scale production of E7 by molecular farming that would lead to the development of a safe and inexpensive vaccine is impaired by its low accumulation level in the plant cell. To enhance antigen production in the plastids, two alternative strategies were carried out: the expression of E7 as a translational fusion to β-glucuronidase enzyme and redirection of E7 into the thylakoid lumen. The use of the β-glucuronidase as a partner protein turned out to be a successful strategy, antigen expression levels were enhanced between 30 and 40 times relative to unfused E7. Moreover, best accumulation, albeit at a high metabolic cost that compromised biomass production, was obtained redirecting E7 into the thylakoid lumen by the incorporation of the N-terminal transit peptide, Str. Following this approach lumenal E7 production exceeded the stromal by two orders of magnitude. Our results highlight the relevance of exploring different strategies to improve recombinant protein stability for certain transgenes in order to exploit potential advantages of recombinant protein accumulation in chloroplasts.

A sequence-based approach for prediction of CsrA/RsmA targets in bacteria with experimental validation in Pseudomonas aeruginosa

CsrA/RsmA homologs are an extensive family of ribonucleic acid (RNA)-binding proteins that function as global post-transcriptional regulators controlling important cellular processes such as secondary metabolism, motility, biofilm formation and the production and secretion of virulence factors in diverse bacterial species. While direct messenger RNA binding by CsrA/RsmA has been studied in detail for some genes, it is anticipated that there are numerous additional, as yet undiscovered, direct targets that mediate its global regulation. To assist in the discovery of these targets, we propose a sequence-based approach to predict genes directly regulated by these regulators. In this work, we develop a computer code (CSRA_TARGET) implementing this approach, which leads to predictions for several novel targets in Escherichia coli and Pseudomonas aeruginosa. The predicted targets in other bacteria, specifically Salmonella enterica serovar Typhimurium, Pectobacterium carotovorum and Legionella pneumophila, also include global regulators that control virulence in these pathogens, unraveling intricate indirect regulatory roles for CsrA/RsmA. We have experimentally validated four predicted RsmA targets in P. aeruginosa. The sequence-based approach developed in this work can thus lead to several testable predictions for direct targets of CsrA homologs, thereby complementing and accelerating efforts to unravel global regulation by this important family of proteins.

The plastid genomes of flowering plants

The plastid genome (plastome) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations are allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and tools of plastid genetic engineering.

Complete chloroplast genome sequence of an orchid model plant candidate: Erycina pusilla apply in tropical Oncidium breeding

Oncidium is an important ornamental plant but the study of its functional genomics is difficult. Erycina pusilla is a fast-growing Oncidiinae species. Several characteristics including low chromosome number, small genome size, short growth period, and its ability to complete its life cycle in vitro make E. pusilla a good model candidate and parent for hybridization for orchids. Although genetic information remains limited, systematic molecular analysis of its chloroplast genome might provide useful genetic information. By combining bacterial artificial chromosome (BAC) clones and next-generation sequencing (NGS), the chloroplast (cp) genome of E. pusilla was sequenced accurately, efficiently and economically. The cp genome of E. pusilla shares 89 and 84% similarity with Oncidium Gower Ramsey and Phalanopsis aphrodite, respectively. Comparing these 3 cp genomes, 5 regions have been identified as showing diversity. Using PCR analysis of 19 species belonging to the Epidendroideae subfamily, a conserved deletion was found in the rps15-trnN region of the Cymbidieae tribe. Because commercial Oncidium varieties in Taiwan are limited, identification of potential parents using molecular breeding method has become very important. To demonstrate the relationship between taxonomic position and hybrid compatibility of E. pusilla, 4 DNA regions of 36 tropically adapted Oncidiinae varieties have been analyzed. The results indicated that trnF-ndhJ and trnH-psbA were suitable for phylogenetic analysis. E. pusilla proved to be phylogenetically closer to Rodriguezia and Tolumnia than Oncidium, despite its similar floral appearance to Oncidium. These results indicate the hybrid compatibility of E. pusilla, its cp genome providing important information for Oncidium breeding.

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors. We provide an overview on the structure and composition of the plastid genome of land plants as well as the functions of its genes in an explicit phylogenetic and evolutionary context. We will discuss the architecture of land plant plastid chromosomes, including gene content and synteny across land plants. Moreover, we will explore the functions and roles of plastid encoded genes in metabolism and their evolutionary importance regarding gene retention and conservation. We suggest that the slow mode at which the plastome typically evolves is likely to be influenced by a combination of different molecular mechanisms. These include the organization of plastid genes in operons, the usually uniparental mode of plastid inheritance, the activity of highly effective repair mechanisms as well as the rarity of plastid fusion. Nevertheless, structurally rearranged plastomes can be found in several unrelated lineages (e.g. ferns, Pinaceae, multiple angiosperm families). Rearrangements and gene losses seem to correlate with an unusual mode of plastid transmission, abundance of repeats, or a heterotrophic lifestyle (parasites or myco-heterotrophs). While only a few functional gene gains and more frequent gene losses have been inferred for land plants, the plastid Ndh complex is one example of multiple independent gene losses and will be discussed in detail. Patterns of ndh-gene loss and functional analyses indicate that these losses are usually found in plant groups with a certain degree of heterotrophy, might rendering plastid encoded Ndh1 subunits dispensable.

Interorganellar DNA transfer in wheat: dynamics and phylogenetic origin

A homology search of wheat chloroplast (ct) and mitochondrial (mt) genomes identified 54 ctDNA segments that have homology with 66 mtDNA segments. The mtDNA segments were classified according to their origin: orthologs (prokaryotic origin), xenologs (interorganellar DNA transfer origin) and paralogs (intraorganellar DNA amplification origin). The 66 mtDNA sequences with homology to ctDNA segments included 14 paralogs, 18 orthologs and 34 xenologs. Analysis of the xenologs indicated that the DNA transfer occurred unidirectionally from the ct genome to the mt genome. The evolutionary timing of each interorganellar DNA transfer that generated a xenolog was estimated. This analysis showed that 2 xenologs originated early in green plant evolution, 4 in angiosperm evolution, 3 in monocotyledon evolution, 9 during cereal diversification and 8 in the evolution of wheat. Six other xenologs showed recurrent transfer from the ct to mt genomes in more than one taxon. The two remaining xenologs were uninformative on the evolutionary timing of their transfer. The wheat mt nad9 gene was found to be chimeric, consisting of the cereal nad9 gene and its 291 bp 5'-flanking region that included a 58 bp xenolog of the ct-ndhC origin.

A one-megabase physical map provides insights on gene organization in the enormous mitochondrial genome of cucumber

Cucumber ( Cucumis sativus ) has one of the largest mitochondrial genomes known among all eukaryotes, due in part to the accumulation of short 20 to 60 bp repetitive DNA motifs. Recombination among these repetitive DNAs produces rearrangements affecting organization and expression of mitochondrial genes. To more efficiently identify rearrangements in the cucumber mitochondrial DNA, we built two nonoverlapping 800 and 220 kb BAC contigs and assigned major mitochondrial genes to these BACs. Polymorphism carried on the largest BAC contig was used to confirm paternal transmission. Mitochondrial genes were distributed across BACs and physically distant, although occasional clustering was observed. Introns in the nad1, nad4, and nad7 genes were larger than those reported in other plants, due in part to accumulation of short repetitive DNAs and indicating that increased intron sizes contributed to mitochondrial genome expansion in cucumber. Mitochondrial genes atp6 and atp9 are physically close to each other and cotranscribed. These physical contigs will be useful for eventual sequencing of the cucumber mitochondrial DNA, which can be exploited to more efficiently screen for unique rearrangements affecting mitochondrial gene expression.

Evolution of Buchloë dactyloides based on cloning and sequencing of matK, rbcL, and cob genes from plastid and mitochondrial genomes

Buffalograss (Buchloë dactyloides (Nutt.) Englem), a C4 turfgrass species, is native to the Great Plains region of North America. The evolutionary implications of buffalograss are unclear. Sequencing of rbcL and matK genes from plastid and the cob gene from mitochondrial genomes was examined to elucidate buffalo grass evolution. This study is the first to report sequencing of these genes from organelle genomes in the genus Buchloë. Comparisons of sequence data from the mitochondrial and plastid genome revealed that all genotypes contained the same cytoplasmic origin. There were some rearrangements detected in mitochondrial genome. The buffalograss genome appears to have evolved through the rearrangements of convergent subgenomic domains. Combined analyses of plastid genes suggest that the evolutionary process in Buchloë accessions studied was monophyletic rather than polyphyletic. However, since plastid and mitochondrial genomes are generally uniparentally inherited, the evolutionary history of these genomes may not reflect the evolutionary history of the organism, especially in a species in which out-crossing is common. The sequence information obtained from this study can be used as a genome-specific marker for investigation of the buffalograss polyploidy complex and testing of the mode of plastid and mitochondrial transmission in genus Buchloë.

Efficient and stable transformation of Lactuca sativa L. cv. Cisco (lettuce) plastids

Transgenic plastids offer unique advantages in plant biotechnology, including high-level foreign protein expression. However, broad application of plastid genome engineering in biotechnology has been largely hampered by the lack of plastid transformation systems for major crops. Here we describe the development of a plastid transformation system for lettuce, Lactuca sativa L. cv. Cisco. The transforming DNA carries a spectinomycin-resistance gene (aadA) under the control of lettuce chloroplast regulatory expression elements, flanked by two adjacent lettuce plastid genome sequences allowing its targeted insertion between the rbcL and accD genes. On average, we obtained 1 transplastomic lettuce plant per bombardment. We show that lettuce leaf chloroplasts can express transgene-encoded GFP to approximately 36% of the total soluble protein. All transplastomic T0 plants were fertile and the T1 progeny uniformly showed stability of the transgene in the chloroplast genome. This system will open up new possibilities for the efficient production of edible vaccines, pharmaceuticals, and antibodies in plants.

Extensive intraindividual variation in plastid rDNA sequences from the holoparasite Cynomorium coccineum (Cynomoriaceae)

Ribosomal genes are considered to have a high degree of sequence conservation between species and also at higher taxonomic levels. In this paper we document a case where a single individual of Cynomorium coccineum (Cynomoriaceae), a nonphotosynthetic holoparasitic plant, contains highly divergent plastid ribosomal genes. PCR amplification a nearly complete ribosomal DNA cistron was performed using genomic DNA, the products cloned, and the 23S rDNA genes were sequenced from 19 colonies. Of these, five distinct types were identified. Fifteen of the sequences were nearly identical (11 or fewer differences) and these were designated Type I. The remaining types (II-V) were each represented by a single clone and differed from Type I by 93 to 255 changes. Compared with green vascular plants, we found that there are more substitutional differences in the 23S rDNA sequences within a single individual of Cynomorium than among all sequenced photosynthetic vascular plants. Several trends of molecular evolution observed in 16S rDNA from other holoparasitic angiosperms and heterotrophic green algae have been also observed in Cynomorium 23S rDNA. Higher-order structures were constructed for representatives of the five clone types, and in all cases these possessed complete complements of the major structural elements present in functional plastid 23S rRNAs. These data indicate that such molecules may be subject to purifying selection, thus providing indirect evidence that they have retained some degree of functionality. This intraindividual polymorphism is probably a case of plastid heteroplasmy but translocation of ribosomal cistrons to the nucleus or mitochondria has not been tested and therefore cannot be ruled out.

The evolutionary processes of mitochondrial and chloroplast genomes differ from those of nuclear genomes

This paper first introduces our present knowledge of the origin of mitochondria and chloroplasts, and the organization and inheritance patterns of their genomes, and then carries on to review the evolutionary processes influencing mitochondrial and chloroplast genomes. The differences in evolutionary phenomena between the nuclear and cytoplasmic genomes are highlighted. It is emphasized that varying inheritance patterns and copy numbers among different types of genomes, and the potential advantage achieved through the transfer of many cytoplasmic genes to the nucleus, have important implications for the evolution of nuclear, mitochondrial and chloroplast genomes. Cytoplasmic genes transferred to the nucleus have joined the more strictly controlled genetic system of the nuclear genome, including also sexual recombination, while genes retained within the cytoplasmic organelles can be involved in selection and drift processes both within and among individuals. Within-individual processes can be either intra- or intercellular. In the case of heteroplasmy, which is attributed to mutations or biparental inheritance, within-individual selection on cytoplasmic DNA may provide a mechanism by which the organism can adapt rapidly. The inheritance of cytoplasmic genomes is not universally maternal. The presence of a range of inheritance patterns indicates that different strategies have been adopted by different organisms. On the other hand, the variability occasionally observed in the inheritance mechanisms of cytoplasmic genomes reduces heritability and increases environmental components in phenotypic features and, consequently, decreases the potential for adaptive evolution.

A comparison of rice chloroplast genomes

Using high quality sequence reads extracted from our whole genome shotgun repository, we assembled two chloroplast genome sequences from two rice (Oryza sativa) varieties, one from 93-11 (a typical indica variety) and the other from PA64S (an indica-like variety with maternal origin of japonica), which are both parental varieties of the super-hybrid rice, LYP9. Based on the patterns of high sequence coverage, we partitioned chloroplast sequence variations into two classes, intravarietal and intersubspecific polymorphisms. Intravarietal polymorphisms refer to variations within 93-11 or PA64S. Intersubspecific polymorphisms were identified by comparing the major genotypes of the two subspecies represented by 93-11 and PA64S, respectively. Some of the minor genotypes occurring as intravarietal polymorphisms in one variety existed as major genotypes in the other subspecific variety, thus giving rise to intersubspecific polymorphisms. In our study, we found that the intersubspecific variations of 93-11 (indica) and PA64S (japonica) chloroplast genomes consisted of 72 single nucleotide polymorphisms and 27 insertions or deletions. The intersubspecific polymorphism rates between 93-11 and PA64S were 0.05% for single nucleotide polymorphisms and 0.02% for insertions or deletions, nearly 8 and 10 times lower than their respective nuclear genomes. Based on the total number of nucleotide substitutions between the two chloroplast genomes, we dated the divergence of indica and japonica chloroplast genomes as occurring approximately 86,000 to 200,000 years ago.

Plastid transformation in higher plants

Plastids of higher plants are semi-autonomous organelles with a small, highly polyploid genome and their own transcription-translation machinery. This review provides an overview of the technology for the genetic modification of the plastid genome including: vectors, marker genes and gene design, the use of gene knockouts and over-expression to probe plastid function and the application of site-specific recombinases for excision of target DNA. Examples for applications in basic science include the study of plastid gene transcription, mRNA editing, photosynthesis and evolution. Examples for biotechnological applications are incorporation of transgenes in the plastid genome for containment and high-level expression of recombinant proteins for pharmaceutical and industrial applications. Plastid transformation is routine only in tobacco. Progress in implementing the technology in other crops is discussed.

Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiosperms

We used the chloroplast gene rbcL as a model to study the frequency and relative timing of transfer of chloroplast sequences to the mitochondrial genome. Southern blot survey of 20 mitochondrial DNAs confirmed three previously reported groups of plants containing rbcL in their mitochondrion, while PCR studies identified a new mitochondrial rbcL. Published and newly determined mitochondrial and chloroplast rbcL sequences were used to reconstruct rbcL phylogeny. The results imply five or six separate interorganellar transfers of rbcL among the angiosperms examined, and hundreds of successful transfers across all flowering plants. By taxonomic criteria, the crucifer transfer is the most ancient, two separate transfers within the grass family are of intermediate ancestry, and the morning-glory transfer is most recent. All five mitochondrial copies of rbcL examined exhibit insertion and/or deletion events that disrupt the reading frame (three are grossly truncated); and all are elevated in the proportion of nonsynonymous substitutions, providing clear evidence that these sequences are pseudogenes.

The obligate root parasite Orobanche cumana exhibits several rbcL sequences

Orobanche species characterization using plastid sequences as molecular markers revealed that O. cumana contains at least two distinct rbcL sequences: one similar in size to the truncated rbcL pseudogene from O. cernua, a closely related species, and another with a size comparable to that of rbcL plastid genes from autotrophic plants. In this work, the nucleotide sequences of these two copies are reported and analysed. The organization of the O. cumana plastid genome was investigated using a long-distance PCR strategy in order to determine their localization. Because of the non-plastid localization of the rbcL larger copy, Southern blot and PCR chromosome-walking experiments were carried out to better characterize this transferred sequence and to identify its localization. Then the mode of multiple transfer of genetic information from plastid to nucleus and the concomitant plastid sequence disorganization and migration during parasitic plant evolution are discussed.

A small chloroplast-encoded protein as a novel architectural component of the light-harvesting antenna

A small conserved open reading frame in the plastid genome, ycf9, encodes a putative membrane protein of 62 amino acids. To determine the function of this reading frame we have constructed a knockout allele for targeted disruption of ycf9. This allele was introduced into the tobacco plastid genome by biolistic transformation to replace the wild-type ycf9 allele. Homoplasmic ycf9 knockout plants displayed no phenotype under normal growth conditions. However, under low light conditions, their growth rate was significantly reduced as compared with the wild-type, due to a lowered efficiency of the light reaction of photosynthesis. We show that this phenotype is caused by the deficiency in a pigment-protein complex of the light-harvesting antenna of photosystem II and hence by a reduced efficiency of photon capture when light availability is limiting. Our results indicate that, in contrast to the current view, light-harvesting complexes do not only consist of the classical pigment-binding proteins, but may contain small structural subunits in addition. These subunits appear to be crucial architectural factors for the assembly and/or maintenance of stable light-harvesting complexes.

GSP-dependent protein secretion in gram-negative bacteria: the Xcp system of Pseudomonas aeruginosa

Bacteria have evolved several secretory pathways to release proteins into the extracellular medium. In Gram-negative bacteria, the exoproteins cross a cell envelope composed of two successive hydrophobic barriers, the cytoplasmic and outer membranes. In some cases, the protein is translocated in a single step across the cell envelope, directly from the cytoplasm to the extracellular medium. In other cases, outer membrane translocation involves an extension of the signal peptide-dependent pathway for translocation across the cytoplasmic membrane via the Sec machinery. By analogy with the so-called general export pathway (GEP), this latter route, including two separate steps across the inner and the outer membrane, was designated as the general secretory pathway (GSP) and is widely conserved among Gram-negative bacteria. In their great majority, exoproteins use the main terminal branch (MTB) of the GSP, namely the Xcp machinery in Pseudomonas aeruginosa, to reach the extracellular medium. In this review, we will use the P. aeruginosa Xcp system as a basis to discuss multiple aspects of the GSP mechanism, including machinery assembly, exoprotein recognition, energy requirement and pore formation for driving through the outer membrane.

Analysis of RNA editing in plastids

Chloroplast mRNAs can be subject to posttranscriptional pyrimidine-to-pyrimidine conversions at highly specific sites. This RNA modification mechanism shows a high degree of similarity to plant mitochondrial editing but differs markedly from, and is most likely evolutionarily unrelated to, all other RNA editing systems. The study of RNA editing processes in chloroplasts has been largely hampered by the lack of in vitro editing systems; however, considerable insights into the recognition mechanisms of individual editing sites have come from in vivo approaches. Chloroplast transformation proved to be a particularly useful tool to study plastid RNA editing. In this article, specific methods for the analysis of chloroplast RNA editing are discussed. Detailed experimental procedures are provided for (i) the purification of chloroplasts and (ii) the stable genetic transformation of higher plant plastids.

Molecular evolution of angiosperm mitochondrial introns and exons

Numbers of substitutions per site for 15 protein-coding genes and six introns of the plant mitochondria were estimated to compare modes and tempos of evolution between exons and introns, and numbers of insertions-deletions per site also were investigated in introns. Intra-gene homogeneity of numbers of substitutions per site was assessed further among different taxa and between mitochondrial and nuclear paralogs translocated from the mitochondrial genome. Gene-to-gene differences in numbers of substitutions per site were found to be higher for nonsynonymous than synonymous sites, and this could be due to differential selection if mutation rate is assumed constant for the genome. Some mitochondrial genes have evolved as fast as chloroplast genes, thus faster than previously thought. For coxI, relative rate tests showed that woody taxa evolved slower than annuals at synonymous sites. Generation time, population size, and speciation rate are likely factors involved in this rate heterogeneity. Introns were less constrained than their adjacent exons for both overall numbers of substitutions per site and indels, but, on average, overall numbers of substitutions per site for introns were similar to numbers of synonymous substitutions per site for exons. Correlations were generally high between numbers of substitutions and numbers of indels per site for the same intron. Mitochondrial genes transferred to the nucleus had an accelerated rate of substitution per site, which was most significant at synonymous sites. These differences between paralogs in two different genomes are likely the result of different mutation rates.

S-formylglutathione hydrolase of Paracoccus denitrificans is homologous to human esterase D: a universal pathway for formaldehyde detoxification?

Downstream of flhA, the Paracoccus denitrificans gene encoding glutathione-dependent formaldehyde dehydrogenase, an open reading frame was identified and called fghA. The gene product of fghA showed appreciable similarity with human esterase D and with the deduced amino acid sequences of open reading frames found in Escherichia coli, Haemophilus influenzae, and Saccharomyces cerevisiae. Mutating fghA strongly reduced S-formylglutathione hydrolase activity. The mutant was unable to grow on methanol and methylamine, indicating that the enzyme is essential for methylotrophic growth. S-Formylglutathione hydrolase appears to be part of a formaldehyde detoxification pathway that is universal in nature.

A chloroplast-derived sequence is utilized as a source of promoter sequences for the gene for subunit 9 of NADH dehydrogenase (nad9) in rice mitochondria

The chloroplast-derived sequence trnS-rps4/ 3'trnL-trnF-ndhJ-ndhK (4066 bases in length) is present in a region that starts 355 bases upstream of the gene for subunit 9 of NADH dehydrogenase (nad9) in the mitochondrial genome of rice. Northern blot hybridization revealed that three large transcripts of 3.05, 1.62 and 1.05 kb hybridized to strand-specific probes for both the nad9 gene and the chloroplast-derived sequence, indicating that the nad9 gene was transcribed together with the chloroplast-derived sequence. From the results of in vitro capping and ribonuclease protection experiments, as well as primer extension analysis, we identified at least seven sites for the initiation of transcription of nad9 in the chloroplast-derived sequence. All of the initiation sites for transcription of the nad9 gene were located in sequences homologous to chloroplast DNA. Two of seven initiation sites were flanked by a sequence homologous to the consensus promoter motif that includes the CRTA motif (where R is A or G) of the rice mitochondrion. However, the sequences surrounding the other five sites showed only limited similarity to the conserved sequence. It is suggested that all the promoters of the rice nad9 gene exist in a sequence that was transferred from the chloroplast during evolution. Thus, the chloroplast-derived sequence has a novel, significant function in the mitochondrial genome of this higher plant.

A ribosomal protein L2 gene is transcribed, spliced, and edited at one site in rice mitochondria

The mitochondrial ribosomal protein L2 gene (rpl2) is coded by two exons of 840 and 669 bp separated by an intron sequence of 1481 bp in the rice mitochondrial genome. The rpl2 gene is located three nucleotides upstream of the ribosomal protein S19 gene (rps19) and both genes are co-transcribed. cDNA sequence analysis identified splicing of the intron sequence from the rpl2 mRNA as well as RNA editing events. The deduced secondary structure of the rpl2 intron sequence shows the characteristic features of a group-II intron. A single RNA editing site is identified in rpl2 and six editing sites in rps19 transcripts. In addition, one editing site is observed in the 3 nucleotide intergenic region. Analysis of individual cDNA clones showed a different extent of RNA editing. The rice rpl2 intron is located at a different site and shows no significant nucleotide sequence similarity with the rpl2 intron of liverwort. However, 60% nucleotide sequence identity is observed between the rice rpl2 intron and the Oenothera nad5 intron in a 234 nucleotide region. The mitochondrial rpl2 sequence is absent from the pea mitochondrial genome and we consequently propose that the mitochondrial RPL2 protein is encoded by a nuclear gene in pea.

A promiscuous chloroplast DNA fragment is transcribed in plant mitochondria but the encoded RNA is not edited

The RNA editing processes in chloroplasts and mitochondira of higher plants show several similarities which are suggestive of common components and/or biochemical steps between the two plant organelles. The existence of various promiscuous DNA fragments of chloroplast origin in plant mitochondrial genomes allowed us to test the possibility that chloroplast sequences are also edited in mitochondria. An rpoB fragment transferred from chloroplasts to mitochondria in rice was chosen as it contains several editing sites, two of which match sequence motifs surrounding even non-homologous editing sites in both chloroplast and mitochondrial transcripts. Rice chloroplast and mitochondrial rpoB DNA and cDNA sequences were selectively amplified and the editing status of the cDNA sequences was determined. Three of the four potential rpoB editing sites previously detected in maize were found to be edited in the rice chloroplast rpoB transcript, whereas the fourth was found to remain unedited. In mitochondria, however, all four editing sites remain unmodified at the cDNA level. This indicates that the editing processes of higher plant mitochondria and chloroplasts are not identical and that organelle-specific factors are required for eliciting the respective editing events.

The gene for a subunit of an ABC-type heme transporter is transcribed together with the gene for subunit 6 of NADH dehydrogenase in rice mitochondria

We previously identified a chloroplast-derived (ct-derived) sequence of 32 base pairs (bp) in rice mitochondrial DNA that includes a part (30 bp; psitrnI) of a gene for isoleucine tRNA (CAU) of the chloroplast. Analyzing the ct-derived psitrnI, we found that an open reading frame (orf240), which was homologous to the gene for a subunit of an ATP-binding cassette-type (ABC-type) heme transporter, namely helC, of Rhodobacter capsulatus, and a gene for subunit 6 of NADH dehydrogenase (nad6) were located upstream of and downstream from the ct-derived psitrnI, respectively. Northern-blot hybridization and analysis by reverse transcription-polymerase chain reaction (RT-PCR) revealed that both orf240 and nad6 were co-transcribed in rice mitochondria. An analysis of PCR-amplified fragments of the region of orf240/nad6 from the DNA of some Gramineae suggests that the arrangement of orf240/nad6 was generated in the mitochondrial genome of the genus Oryza during evolution after its divergence from the other Gramineae. Most of the transcripts of orf240 are edited, with a change from cytidine to uridine, at 35 positions. Editing of the RNA changes 33 amino-acid residues among the 240 encoded amino-acid residues, suggesting that the orf240 gene is functional in rice mitochondria.

Pervasive migration of organellar DNA to the nucleus in plants

A surprisingly large number of plant nuclear DNA sequences inferred to be remnants of chloroplast and mitochondrial DNA migration events were detected through computer-assisted database searches. Nineteen independent organellar DNA insertions, with a median size of 117 bp (range of 38 to > 785 bp), occur in the proximity of 15 nuclear genes. One fragment appears to have been passed through a RNA intermediate, based on the presence of an edited version of the mitochondrial gene in the nucleus. Tandemly arranged fragments from disparate regions of organellar genomes and from different organellar genomes indicate that the fragments joined together from an intracellular pool of RNA and/or DNA before they integrated into the nuclear genome. Comparisons of integrated sequences to genes lacking the insertions, as well as the occurrence of coligated fragments, support a model of random integration by end joining. All transferred sequences were found in noncoding regions, but the positioning of organellar-derived DNA in introns, as well as regions 5' and 3' to nuclear genes, suggests that the random integration of organellar DNA has the potential to influence gene expression patterns. A semiquantitative estimate was performed on the amount of organellar DNA being transferred and assimilated into the nucleus. Based on this database survey, we estimate that 3-7% of the plant nuclear genomic sequence files contain organellar-derived DNA. The timing and the magnitude of genetic flux to the nuclear genome suggest that random integration is a substantial and ongoing process for creating sequence variation.

The chloroplast trnP-trnW-petG gene cluster in the mitochondrial genomes of Beta vulgaris, B. trigyna and B. webbiana: evolutionary aspects

The chloroplast trnP-trnW-petG gene cluster has been identified in the mitochondrial DNA (mtDNA) of sugar beet (Beta vulgaris). The chloroplast-derived trnW gene is transcribed in the mitochondria; the other two genes, however, do not seem to be transcribed. This gene cluster is also present in the mitochondrial genomes of two wild Beta species, B. trigyna and B. webbiana. Sugar beet and the two wild relatives share 100% sequence identity in the coding regions of both the mitochondrial trnP and trnW genes. On the other hand, the petG genes from the wild Beta mtDNAs were found to be disrupted either by a 5-bp duplication (B. trigyna) or by a deletion of the 5' region (B. webbiana). A data-base search revealed that a conserved sequence of 60 bp is present in the trnP-trnW intergenic region of the mitochondrial genomes of the three Beta species as well as in other higher plants, including wheat and maize, and that the conserved sequence is absent from the chloroplast counterpart. Our results thus favour the hypothesis of a monophyletic origin of the trnP-trnW-petG cluster found in the plant mitochondrial genomes examined.

orf250 encodes a second subunit of an ABC-type heme transporter in Oenothera mitochondria

A highly transcribed region in Oenothera mitochondria codes for an open reading frame comprising 250 condons (orf250). This open reading frame shows high sequence similarity to the helC gene of Rhodobacter capsulatus which encodes a subunit of a proposed ABC-type heme transporter. Transcripts of orf250 are edited by cytidine to uridine transitions at 29 sites, altering 10% of all encoded amino acids. Genes homologous to helC have also been found in the bacteria Bradyrhizobium japonicum and Escherichia coli, and are conserved in mitochondria of Marchantia polymorpha, Daucus carota, and Arabidopsis thaliana. In bacteria these genes belong to operons that are involved in the biogenesis of c-type cytochromes. The bacterial gene organization is partly conserved in Marchantia, but altered in the mitochondrial genome of Oenothera.

Evolutionary variations in DNA sequences transferred from chloroplast genomes to mitochondrial genomes in the Gramineae

The transfer of fragments of DNA from chloroplast genomes to mitochondrial genomes is considered to be a general phenomenon in higher plants. In the present study, Southern hybridization, together with amplification by PCR and DNA sequencing techniques, was used to examine the regions homologous to chloroplast rps19 in the mitochondrial genomes of several gramineous plants. In all the mitochondrial DNAs from the gramineous plants examined, except for that from wheat, the transferred fragments of chloroplast DNA were found to be maintained and the same junctions of mitochondrion-specific and chloroplast-like sequences were found at one terminus. This finding indicates that the transfer of the chloroplast sequence occurred in the distant past during the evolution of gramineous plants. Subsequent analysis revealed that the fragments had been variously rearranged among species with respect to the other terminus. Considering the current diversity of this one particular transferred fragment of chloroplast DNA, we propose that chloroplast-derived DNA sequences that have lost their original functions tend to be rearranged during evolution in mitochondrial genomes.

Palindromic repeated sequences (PRSs) in the mitochondrial genome of rice: evidence for their insertion after divergence of the genus Oryza from the other Gramineae

We have identified a family of small repeated sequences (from 60 to 66 bp in length) in the mitochondrial genome of rice (Oryza sativa cv. Nipponbare). There are at least ten copies of these sequences and they are distributed throughout the mitochondrial genome. Each is potentially capable of forming a stem-and-loop structure and we have designated them PRSs (palindromic repeated sequences). Their features are reminiscent of the small dispersed repeats in the mitochondrial DNA (mtDNA) of some lower eukaryotes, such as Saccharomyces cerevisiae, Neurospora crassa and Chlamydomonas reinhardtii. Some of the PRSs of rice mtDNA are located in the intron of the gene for ribosomal protein S3 (rps3) and in the flanking sequence of the gene for chloroplast-like tRNA(Asn) (trnN). analysis of PCR-amplified fragments of these regions from the DNA of some Gramineae suggests that the PRSs were inserted into these regions of the Oryza mtDNA after the divergence of Oryza from the other Gramineae.

A tRNA(Val) (GAC) gene of chloroplast origin in sunflower mitochondria is not transcribed

A tRNA(Val) (GAC) gene is located in opposite orientation 552 nucleotides (nt) down-stream of the cytochrome oxidase subunit III (coxIII) gene in sunflower mitochondria. The comparison with the homologous chloroplast DNA revealed that the tRNA(Val) gene is part of a 417 nucleotides DNA insertion of chloroplast origin in the mitochondrial genome. No tRNA(Val) is encoded in monocot mitochondrial DNA (mtDNA), whereas two tRNA(Val) species are coded for by potato mtDNA. The mitochondrial genomes of different plant species thus seem to encode unique sets of tRNAs and must thus be competent in importing the missing differing sets of tRNAs.

RNA editing in plant mitochondria and chloroplasts

In the mitochondria and chloroplasts of flowering plants (angiosperms), transcripts of protein-coding genes are altered after synthesis so that their final primary nucleotide sequence differs from that of the corresponding DNA sequence. This posttranscriptional mRNA editing consists almost exclusively of C-to-U substitutions. Editing occurs predominantly within coding regions, mostly at isolated C residues, and usually at first or second positions of codons, thereby almost always changing the amino acid from that specified by the unedited codon. Editing may also create initiation and termination codons. The net effect of C-to-U RNA editing in plants is to make proteins encoded by plant organelles more similar in sequence to their nonplant homologs. In a few cases, a strong argument can be made that specific C-to-U editing events are essential for the production of functional plant mitochondrial proteins. Although the phenomenon of RNA editing in plants is now well documented, fundamental questions remain to be answered: What determines the specificity of editing? What is the biochemical mechanism (deamination, base exchange, or nucleotide replacement)? How did the system evolve? RNA editing in plants, as in other organisms, challenges our traditional notions of genetic information transfer.