1
|
Zhang W, Yang Z, Wang W, Sun Q. Primase promotes the competition between transcription and replication on the same template strand resulting in DNA damage. Nat Commun 2024; 15:73. [PMID: 38168108 PMCID: PMC10761990 DOI: 10.1038/s41467-023-44443-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
Transcription-replication conflicts (TRCs), especially Head-On TRCs (HO-TRCs) can introduce R-loops and DNA damage, however, the underlying mechanisms are still largely unclear. We previously identified a chloroplast-localized RNase H1 protein AtRNH1C that can remove R-loops and relax HO-TRCs for genome integrity. Through the mutagenesis screen, we identify a mutation in chloroplast-localized primase ATH that weakens the binding affinity of DNA template and reduces the activities of RNA primer synthesis and delivery. This slows down DNA replication, and reduces competition of transcription-replication, thus rescuing the developmental defects of atrnh1c. Strand-specific DNA damage sequencing reveals that HO-TRCs cause DNA damage at the end of the transcription unit in the lagging strand and overexpression of ATH can boost HO-TRCs and exacerbates DNA damage. Furthermore, mutation of plastid DNA polymerase Pol1A can similarly rescue the defects in atrnh1c mutants. Taken together these results illustrate a potentially conserved mechanism among organisms, of which the primase activity can promote the occurrence of transcription-replication conflicts leading to HO-TRCs and genome instability.
Collapse
Affiliation(s)
- Weifeng Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, 100084, Beijing, China
| | - Zhuo Yang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, 100084, Beijing, China
| | - Wenjie Wang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, 100084, Beijing, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, 100084, Beijing, China.
| |
Collapse
|
2
|
Köhler M, Reginato M, Jin JJ, Majure LC. More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae). ANNALS OF BOTANY 2023; 132:771-786. [PMID: 37467174 PMCID: PMC10799996 DOI: 10.1093/aob/mcad098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages, including gene losses, inversions, boundary movements or loss of the canonical inverted repeat (IR) region. However, only a small fraction of cactus diversity has been analysed so far. METHODS Here, we investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent one of the most diverse and important lineages of Cactaceae. We assembled de novo the plastome of 43 species, representing a comprehensive sampling of the tribe, including all seven genera, and analysed their evolution in a phylogenetic comparative framework. Phylogenomic analyses with different datasets (full plastome sequences and genes only) were performed, followed by congruence analyses to assess signals underlying contentious nodes. KEY RESULTS Plastomes varied considerably in length, from 121 to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including a lack of the canonical IR in some lineages and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported, deviating in the presence of the IR region or the genes contained in the IR. Overall, plastome sequences resolved phylogenetic relationships within major clades of Opuntieae with high bootstrap values but presented some contentious nodes depending on the dataset analysed (e.g. whole plastome vs. genes only). Congruence analyses revealed that most plastidial regions lack phylogenetic resolution, while few markers are supporting the most likely topology. Likewise, alternative topologies are driven by a handful of plastome markers, suggesting recalcitrant nodes in the phylogeny. CONCLUSIONS Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure and content and can be important for the recognition of species in some major clades. Unravelling connections between the causes of plastome variation and the consequences for species biology, physiology, ecology, diversification and adaptation is a promising and ambitious endeavour in cactus research. Although plastome data resolved major phylogenetic relationships, the generation of nuclear genomic data is necessary to confront these hypotheses and assess the recalcitrant nodes further.
Collapse
Affiliation(s)
- Matias Köhler
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marcelo Reginato
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Jian-Jun Jin
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Lucas C Majure
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
| |
Collapse
|
3
|
Wang X, Dorjee T, Chen Y, Gao F, Zhou Y. The complete chloroplast genome sequencing analysis revealed an unusual IRs reduction in three species of subfamily Zygophylloideae. PLoS One 2022; 17:e0263253. [PMID: 35108324 PMCID: PMC8809528 DOI: 10.1371/journal.pone.0263253] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 01/17/2022] [Indexed: 11/18/2022] Open
Abstract
Tetraena mongolica, Zygophyllum xanthoxylon, and Z. fabago are three typical dryland plants with important ecological values in subfamily Zygophylloideae of Zygophyllaceae. Studies on the chloroplast genomes of them are favorable for understanding the diversity and phylogeny of Zygophyllaceae. Here, we sequenced and assembled the whole chloroplast genomes of T. mongolica, Z. xanthoxylon, and Z. fabago, and performed comparative genomic and phylogenetic analysis. The total size, structure, gene content and orders of these three chloroplast genomes were similar, and the three chloroplast genomes exhibited a typical quadripartite structure with a large single-copy region (LSC; 79,696–80,291 bp), a small single-copy region (SSC; 16,462–17,162 bp), and two inverted repeats (IRs; 4,288–4,413 bp). A total of 107 unique genes were identified from the three chloroplast genomes, including 70 protein-coding genes, 33 tRNAs, and 4 rRNAs. Compared with other angiosperms, the three chloroplast genomes were significantly reduced in overall length due to an unusual 16–24 kb shrinkage of IR regions and loss of the 11 genes which encoded subunits of NADH dehydrogenase. Genome-wide comparisons revealed similarities and variations between the three species and others. Phylogenetic analysis based on the three chloroplast genomes supported the opinion that Zygophyllaceae belonged to Zygophyllales in Fabids, and Z. xanthoxylon and Z. fabago belonged to Zygophyllum. The genome-wide comparisons revealed the similarity and variations between the chloroplast genomes of the three Zygophylloideae species and other plant species. This study provides a valuable molecular biology evidence for further studies of phylogenetic status of Zygophyllaceae.
Collapse
Affiliation(s)
- Xiaoyang Wang
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Tashi Dorjee
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Yiru Chen
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Fei Gao
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
- * E-mail: (FG); (YZ)
| | - Yijun Zhou
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
- * E-mail: (FG); (YZ)
| |
Collapse
|
4
|
Occhialini A, Pfotenhauer AC, Li L, Harbison SA, Lail AJ, Burris JN, Piasecki C, Piatek AA, Daniell H, Stewart CN, Lenaghan SC. Mini-synplastomes for plastid genetic engineering. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:360-373. [PMID: 34585834 PMCID: PMC8753362 DOI: 10.1111/pbi.13717] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/08/2021] [Accepted: 09/25/2021] [Indexed: 05/19/2023]
Abstract
In the age of synthetic biology, plastid engineering requires a nimble platform to introduce novel synthetic circuits in plants. While effective for integrating relatively small constructs into the plastome, plastid engineering via homologous recombination of transgenes is over 30 years old. Here we show the design-build-test of a novel synthetic genome structure that does not disturb the native plastome: the 'mini-synplastome'. The mini-synplastome was inspired by dinoflagellate plastome organization, which is comprised of numerous minicircles residing in the plastid instead of a single organellar genome molecule. The first mini-synplastome in plants was developed in vitro to meet the following criteria: (i) episomal replication in plastids; (ii) facile cloning; (iii) predictable transgene expression in plastids; (iv) non-integration of vector sequences into the endogenous plastome; and (v) autonomous persistence in the plant over generations in the absence of exogenous selection pressure. Mini-synplastomes are anticipated to revolutionize chloroplast biotechnology, enable facile marker-free plastid engineering, and provide an unparalleled platform for one-step metabolic engineering in plants.
Collapse
Affiliation(s)
- Alessandro Occhialini
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Alexander C. Pfotenhauer
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Li Li
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Stacee A. Harbison
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Andrew J. Lail
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Jason N. Burris
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | | | | | - Henry Daniell
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - C. Neal Stewart
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Scott C. Lenaghan
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
| |
Collapse
|
5
|
Abstract
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.
Collapse
Affiliation(s)
- Tracey A Ruhlman
- Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Robert K Jansen
- Integrative Biology, University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
6
|
Sugimoto H, Hirano M, Tanaka H, Tanaka T, Kitagawa-Yogo R, Muramoto N, Mitsukawa N. Plastid-targeted forms of restriction endonucleases enhance the plastid genome rearrangement rate and trigger the reorganization of its genomic architecture. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:1042-1057. [PMID: 31925982 DOI: 10.1111/tpj.14687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/25/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
Plant cells have acquired chloroplasts (plastids) with a unique genome (ptDNA), which developed during the evolution of endosymbiosis. The gene content and genome structure of ptDNAs in land plants are considerably stable, although those of algal ptDNAs are highly varied. Plant cells seem, therefore, to be intolerant of any structural or organizational changes in the ptDNA. Genome rearrangement functions as a driver of genomic evolutionary divergence. Here, we aimed to create various types of rearrangements in the ptDNA of Arabidopsis genomes using plastid-targeted forms of restriction endonucleases (pREs). Arabidopsis plants expressing each of the three specific pREs, i.e., pTaqI, pHinP1I, and pMseI, were generated; they showed the leaf variegation phenotypes associated with impaired chloroplast development. We confirmed that these pREs caused double-stranded breaks (DSB) at their recognition sites in ptDNAs. Genome-wide analysis of ptDNAs revealed that the transgenic lines exhibited a large number of rearrangements such as inversions and deletions/duplications, which were dominantly repaired by microhomology-mediated recombination and microhomology-mediated end-joining, and less by non-homologous end-joining. Notably, pHinP1I, which recognized a small number of sites in ptDNA, induced drastic structural changes, including regional copy number variations throughout ptDNAs. In contrast, the transient expression of either pTaqI or pMseI, whose recognition site numbers were relatively larger, resulted in small-scale changes at the whole genome level. These results indicated that DSB frequencies and their distribution are major determinants in shaping ptDNAs.
Collapse
Affiliation(s)
- Hiroki Sugimoto
- Genome Engineering Program, Strategic Research Division, Toyota Central R&D Laboratories, Inc., Nagakute, Aichi, 480-1192, Japan
| | - Minoru Hirano
- Bio System Engineering Program, Strategic Research Division, Toyota Central R&D Laboratories, Inc., Nagakute, Aichi, 480-1192, Japan
| | - Hidenori Tanaka
- Genome Engineering Program, Strategic Research Division, Toyota Central R&D Laboratories, Inc., Nagakute, Aichi, 480-1192, Japan
| | - Tomoko Tanaka
- Genome Engineering Program, Strategic Research Division, Toyota Central R&D Laboratories, Inc., Nagakute, Aichi, 480-1192, Japan
| | - Ritsuko Kitagawa-Yogo
- Genome Engineering Program, Strategic Research Division, Toyota Central R&D Laboratories, Inc., Nagakute, Aichi, 480-1192, Japan
| | - Nobuhiko Muramoto
- Genome Engineering Program, Strategic Research Division, Toyota Central R&D Laboratories, Inc., Nagakute, Aichi, 480-1192, Japan
| | - Norihiro Mitsukawa
- Genome Engineering Program, Strategic Research Division, Toyota Central R&D Laboratories, Inc., Nagakute, Aichi, 480-1192, Japan
| |
Collapse
|
7
|
Abstract
While the model bacteria Escherichia coli and Bacillus subtilis harbor single chromosomes, which is known as monoploidy, some freshwater cyanobacteria contain multiple chromosome copies per cell throughout their cell cycle, which is known as polyploidy. In the model cyanobacteria Synechococcus elongatus PCC 7942 and Synechocystis sp. PCC 6803, chromosome copy number (ploidy) is regulated in response to growth phase and environmental factors. In S. elongatus 7942, chromosome replication is asynchronous both among cells and chromosomes. Comparative analysis of S. elongatus 7942 and S. sp. 6803 revealed a variety of DNA replication mechanisms. In this review, the current knowledge of ploidy and DNA replication mechanisms in cyanobacteria is summarized together with information on the features common with plant chloroplasts. It is worth noting that the occurrence of polyploidy and its regulation are correlated with certain cyanobacterial lifestyles and are shared between some cyanobacteria and chloroplasts. ABBREVIATIONS NGS: next-generation sequencing; Repli-seq: replication sequencing; BrdU: 5-bromo-2'-deoxyuridine; TK: thymidine kinase; GCSI: GC skew index; PET: photosynthetic electron transport; RET: respiration electron transport; Cyt b6f complex: cytochrome b6f complex; PQ: plastoquinone; PC: plastocyanin.
Collapse
Affiliation(s)
- Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture , Tokyo, Japan
| |
Collapse
|
8
|
Choi IS, Jansen R, Ruhlman T. Lost and Found: Return of the Inverted Repeat in the Legume Clade Defined by Its Absence. Genome Biol Evol 2019; 11:1321-1333. [PMID: 31046101 PMCID: PMC6496590 DOI: 10.1093/gbe/evz076] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2019] [Indexed: 12/23/2022] Open
Abstract
The plant genome comprises a coevolving, integrated genetic system housed in three subcellular compartments: the nucleus, mitochondrion, and the plastid. The typical land plant plastid genome (plastome) comprises the sum of repeating units of 130–160 kb in length. The plastome inverted repeat (IR) divides each plastome monomer into large and small single copy regions, an architecture highly conserved across land plants. There have been varying degrees of expansion or contraction of the IR, and in a few distinct lineages, including the IR-lacking clade of papilionoid legumes, one copy of the IR has been lost. Completion of plastome sequencing and assembly for 19 Medicago species and Trigonella foenum-graceum and comparative analysis with other IR-lacking clade taxa revealed modest divergence with regard to structural organization overall. However, one clade contained unique variation suggesting an ancestor had experienced repeat-mediated changes in plastome structure. In Medicago minima, a novel IR of ∼9 kb was confirmed and the role of repeat-mediated, recombination-dependent replication in IR reemergence is discussed.
Collapse
Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin
| | - Robert Jansen
- Department of Integrative Biology, University of Texas at Austin.,Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Tracey Ruhlman
- Department of Integrative Biology, University of Texas at Austin
| |
Collapse
|
9
|
Wang W, Schalamun M, Morales-Suarez A, Kainer D, Schwessinger B, Lanfear R. Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case. BMC Genomics 2018; 19:977. [PMID: 30594129 PMCID: PMC6311037 DOI: 10.1186/s12864-018-5348-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 12/03/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Chloroplasts are organelles that conduct photosynthesis in plant and algal cells. The information chloroplast genome contained is widely used in agriculture and studies of evolution and ecology. Correctly assembling chloroplast genomes can be challenging because the chloroplast genome contains a pair of long inverted repeats (10-30 kb). Typically, it is simply assumed that the gross structure of the chloroplast genome matches the most commonly observed structure of two single-copy regions separated by a pair of inverted repeats. The advent of long-read sequencing technologies should remove the need to make this assumption by providing sufficient information to completely span the inverted repeat regions. Yet, long-reads tend to have higher error rates than short-reads, and relatively little is known about the best way to combine long- and short-reads to obtain the most accurate chloroplast genome assemblies. Using Eucalyptus pauciflora, the snow gum, as a test case, we evaluated the effect of multiple parameters, such as different coverage of long-(Oxford nanopore) and short-(Illumina) reads, different long-read lengths, different assembly pipelines, with a view to determining the most accurate and efficient approach to chloroplast genome assembly. RESULTS Hybrid assemblies combining at least 20x coverage of both long-reads and short-reads generated a single contig spanning the entire chloroplast genome with few or no detectable errors. Short-read-only assemblies generated three contigs (the long single copy, short single copy and inverted repeat regions) of the chloroplast genome. These contigs contained few single-base errors but tended to exclude several bases at the beginning or end of each contig. Long-read-only assemblies tended to create multiple contigs with a much higher single-base error rate. The chloroplast genome of Eucalyptus pauciflora is 159,942 bp, contains 131 genes of known function. CONCLUSIONS Our results suggest that very accurate assemblies of chloroplast genomes can be achieved using a combination of at least 20x coverage of long- and short-reads respectively, provided that the long-reads contain at least ~5x coverage of reads longer than the inverted repeat region. We show that further increases in coverage give little or no improvement in accuracy, and that hybrid assemblies are more accurate than long-read-only or short-read-only assemblies.
Collapse
Affiliation(s)
- Weiwen Wang
- Research School of Biology, Australian National University, Canberra, Australia.
| | - Miriam Schalamun
- Research School of Biology, Australian National University, Canberra, Australia.,Institute of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - David Kainer
- Research School of Biology, Australian National University, Canberra, Australia
| | | | - Robert Lanfear
- Research School of Biology, Australian National University, Canberra, Australia
| |
Collapse
|
10
|
Le Ret M, Belcher S, Graindorge S, Wallet C, Koechler S, Erhardt M, Williams-Carrier R, Barkan A, Gualberto JM. Efficient Replication of the Plastid Genome Requires an Organellar Thymidine Kinase. PLANT PHYSIOLOGY 2018; 178:1643-1656. [PMID: 30305373 PMCID: PMC6288739 DOI: 10.1104/pp.18.00976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/01/2018] [Indexed: 05/17/2023]
Abstract
Thymidine kinase (TK) is a key enzyme of the salvage pathway that recycles thymidine nucleosides to produce deoxythymidine triphosphate. Here, we identified the single TK of maize (Zea mays), denoted CPTK1, as necessary in the replication of the plastidial genome (cpDNA), demonstrating the essential function of the salvage pathway during chloroplast biogenesis. CPTK1 localized to both plastids and mitochondria, and its absence resulted in an albino phenotype, reduced cpDNA copy number and a severe deficiency in plastidial ribosomes. Mitochondria were not affected, indicating they are less reliant on the salvage pathway. Arabidopsis (Arabidopsis thaliana) TKs, TK1A and TK1B, apparently resulted from a gene duplication after the divergence of monocots and dicots. Similar but less-severe effects were observed for Arabidopsis tk1a tk1b double mutants in comparison to those in maize cptk1 TK1B was important for cpDNA replication and repair in conditions of replicative stress but had little impact on the mitochondrial phenotype. In the maize cptk1 mutant, the DNA from the small single-copy region of the plastidial genome was reduced to a greater extent than other regions, suggesting preferential abortion of replication in this region. This was accompanied by the accumulation of truncated genomes that resulted, at least in part, from unfaithful microhomology-mediated repair. These and other results suggest that the loss of normal cpDNA replication elicits the mobilization of new replication origins around the rpoB (beta subunit of plastid-encoded RNA polymerase) transcription unit and imply that increased transcription at rpoB is associated with the initiation of cpDNA replication.
Collapse
Affiliation(s)
- Monique Le Ret
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Susan Belcher
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Stéfanie Graindorge
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Clémentine Wallet
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Sandrine Koechler
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Mathieu Erhardt
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| | | | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - José M Gualberto
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR2357, Université de Strasbourg, 67084 Strasbourg, France
| |
Collapse
|
11
|
Ayala-García VM, Baruch-Torres N, García-Medel PL, Brieba LG. Plant organellar DNA polymerases paralogs exhibit dissimilar nucleotide incorporation fidelity. FEBS J 2018; 285:4005-4018. [PMID: 30152200 DOI: 10.1111/febs.14645] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/27/2018] [Accepted: 08/24/2018] [Indexed: 01/06/2023]
Abstract
The coding sequences of plant mitochondrial and chloroplast genomes present a lower mutation rate than the coding sequences of animal mitochondria. However, plant mitochondrial genomes frequently rearrange and present high mutation rates in their noncoding sequences. DNA replication in plant organelles is carried out by two DNA polymerases (DNAP) paralogs. In Arabidopsis thaliana at least one DNAP paralog (AtPolIA or AtPolIB) is necessary for plant viability, suggesting that both genes are partially redundant. To understand how AtPolIs replicate genomes that present low and high mutation rates, we measured their nucleotide incorporation for all 16-base pair combinations in vitro. AtPolIA presents an error rate of 7.26 × 10-5 , whereas AtPolIB has an error rate of 5.45 × 10-4 . Thus, AtPolIA and AtPolIB are 3.5 and 26-times less accurate than human mitochondrial DNAP γ. The 8-fold difference in fidelity between both AtPolIs results from a higher catalytic efficiency in AtPolIA. Both AtPolIs extend from mismatches and the fidelity of AtPolIs ranks between high fidelity and lesion bypass DNAPs. The different nucleotide incorporation fidelity between AtPolIs predicts a prevalent role of AtPolIA in DNA replication and AtPolIB in DNA repair. We hypothesize that in plant organelles, DNA mismatches generated during DNA replication are repaired via recombination-mediated or DNA mismatch repair mechanisms that selectively target the coding region and that the mismatches generated by AtPolIs may result in the frequent expansion and rearrangements present in plant mitochondrial genomes.
Collapse
|
12
|
Yang Z, Hou Q, Cheng L, Xu W, Hong Y, Li S, Sun Q. RNase H1 Cooperates with DNA Gyrases to Restrict R-Loops and Maintain Genome Integrity in Arabidopsis Chloroplasts. THE PLANT CELL 2017; 29:2478-2497. [PMID: 28939594 PMCID: PMC5774575 DOI: 10.1105/tpc.17.00305] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/05/2017] [Accepted: 09/20/2017] [Indexed: 05/19/2023]
Abstract
Maintaining organellar genome integrity is essential for eukaryotic cells, and many factors can threaten genome integrity. R-loops are DNA:RNA duplexes produced during transcription, with the nontemplated DNA forming a single-stranded region. R-loops function in the regulation of transcription, DNA replication, and DNA repair, but can also be susceptible to lesions that form double-stranded breaks and thus induce genome instability. From investigating the function of a plant chloroplast-localized R-loop removing enzyme AtRNH1C, we have found that it is responsible for plastid R-loop homeostasis, chloroplast genome instability, and development. Interactome analysis revealed that AtRNH1C associates with multiple chloroplast-localized DNA and RNA metabolism-related proteins, including the core DNA gyrases complex. The interaction between AtRNH1C and AtGyrases was critical for R-loop homeostasis in chloroplast and important to release the transcription-replication conflicts in the highly transcribed and replication originated cp-rDNA regions and thus to reduce the DNA damage. Our results reveal the plastid R-loop accumulation leads to chloroplast DNA instability and provide insight into the maintenance of genome integrity in chloroplasts, in which the evolutionarily conserved RNase H1 and DNA gyrase proteins are involved.
Collapse
Affiliation(s)
- Zhuo Yang
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Quancan Hou
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lingling Cheng
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xu
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yantao Hong
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shuai Li
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qianwen Sun
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| |
Collapse
|
13
|
Tonti-Filippini J, Nevill PG, Dixon K, Small I. What can we do with 1000 plastid genomes? THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:808-818. [PMID: 28112435 DOI: 10.1111/tpj.13491] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/17/2017] [Accepted: 01/17/2017] [Indexed: 05/21/2023]
Abstract
The plastid genome of plants is the smallest and most gene-rich of the three genomes in each cell and the one generally present in the highest copy number. As a result, obtaining plastid DNA sequence is a particularly cost-effective way of discovering genetic information about a plant. Until recently, the sequence information gathered in this way was generally limited to small portions of the genome amplified by polymerase chain reaction, but recent advances in sequencing technology have stimulated a substantial rate of increase in the sequencing of complete plastid genomes. Within the last year, the number of complete plastid genomes accessible in public sequence repositories has exceeded 1000. This sudden flood of data raises numerous challenges in data analysis and interpretation, but also offers the keys to potential insights across large swathes of plant biology. We examine what has been learnt so far, what more could be learnt if we look at the data in the right way, and what we might gain from the tens of thousands more genome sequences that will surely arrive in the next few years. The most exciting new discoveries are likely to be made at the interdisciplinary interfaces between molecular biology and ecology.
Collapse
Affiliation(s)
- Julian Tonti-Filippini
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Paul G Nevill
- Department of Environment and Agriculture, ARC Centre for Mine Site Restoration, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Kingsley Dixon
- Department of Environment and Agriculture, ARC Centre for Mine Site Restoration, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| |
Collapse
|
14
|
Ruhlman TA, Zhang J, Blazier JC, Sabir JSM, Jansen RK. Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure. AMERICAN JOURNAL OF BOTANY 2017; 104:559-572. [PMID: 28400415 DOI: 10.3732/ajb.1600453] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 02/23/2017] [Indexed: 05/21/2023]
Abstract
PREMISE OF THE STUDY There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. METHODS We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. RESULTS Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. CONCLUSION We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats.
Collapse
Affiliation(s)
- Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA
| | - Jin Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA
| | - John C Blazier
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA
| | - Jamal S M Sabir
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589 Saudi Arabia
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589 Saudi Arabia
| |
Collapse
|
15
|
Yu J, Wang C, Gong X. Degeneration of photosynthetic capacity in mixotrophic plants, Chimaphila japonica and Pyrola decorata (Ericaceae). PLANT DIVERSITY 2017; 39:80-88. [PMID: 30159495 PMCID: PMC6112300 DOI: 10.1016/j.pld.2016.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 05/25/2023]
Abstract
The evolution of photosynthesis is an important feature of mixotrophic plants. Previous inferences proposed that mixotrophic taxa tend to retain most genes relating to photosynthetic functions but vary in plastid gene content. However, no sequence data are available to test this hypothesis in Ericaceae. To investigate changes in plastid genomes that may result from a transition from autotrophy to mixotrophy, the plastomes of two mixotrophic plants, Pyrola decorata and Chimaphila japonica, were sequenced at Illumina's Genome Analyzer and compared to the published plastome of the autotrophic plant Rhododendron simsii, which also belongs to Ericaceae. The greatest discrepancy between mixotrophic and autotrophic plants was that ndh genes for both P. decorata and C. japonica plastomes have nearly all become pseudogenes. P. decorata and C. japonica also retained all genes directly involved in photosynthesis under strong selection. The calculated rate of nonsynonymous nucleotide substitutions and synonymous substitutions of protein-coding genes (dN/dS) showed that substitution rates in shade plants were apparently higher than those in sunlight plants. The two mixotrophic plastomes were generally very similar to that of non-parasitic plants, although ndh genes were largely pseudogenized. Photosynthesis genes under strong selection were retained in the two mixotrophs, however, with greatly increased substitution rates. Further research is needed to gain a clearer understanding of the evolution of autotrophy and mixotrophy in Ericaceae.
Collapse
Affiliation(s)
- Jiaojun Yu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, PR China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Kunming, PR China
| | - Chaobo Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, PR China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Kunming, PR China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, PR China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Kunming, PR China
| |
Collapse
|
16
|
Blazier JC, Jansen RK, Mower JP, Govindu M, Zhang J, Weng ML, Ruhlman TA. Variable presence of the inverted repeat and plastome stability in Erodium. ANNALS OF BOTANY 2016; 117:1209-20. [PMID: 27192713 PMCID: PMC4904181 DOI: 10.1093/aob/mcw065] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/05/2016] [Accepted: 02/22/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Several unrelated lineages such as plastids, viruses and plasmids, have converged on quadripartite genomes of similar size with large and small single copy regions and a large inverted repeat (IR). Except for Erodium (Geraniaceae), saguaro cactus and some legumes, the plastomes of all photosynthetic angiosperms display this structure. The functional significance of the IR is not understood and Erodium provides a system to examine the role of the IR in the long-term stability of these genomes. We compared the degree of genomic rearrangement in plastomes of Erodium that differ in the presence and absence of the IR. METHODS We sequenced 17 new Erodium plastomes. Using 454, Illumina, PacBio and Sanger sequences, 16 genomes were assembled and categorized along with one incomplete and two previously published Erodium plastomes. We conducted phylogenetic analyses among these species using a dataset of 19 protein-coding genes and determined if significantly higher evolutionary rates had caused the long branch seen previously in phylogenetic reconstructions within the genus. Bioinformatic comparisons were also performed to evaluate plastome evolution across the genus. KEY RESULTS Erodium plastomes fell into four types (Type 1-4) that differ in their substitution rates, short dispersed repeat content and degree of genomic rearrangement, gene and intron content and GC content. Type 4 plastomes had significantly higher rates of synonymous substitutions (dS) for all genes and for 14 of the 19 genes non-synonymous substitutions (dN) were significantly accelerated. We evaluated the evidence for a single IR loss in Erodium and in doing so discovered that Type 4 plastomes contain a novel IR. CONCLUSIONS The presence or absence of the IR does not affect plastome stability in Erodium. Rather, the overall repeat content shows a negative correlation with genome stability, a pattern in agreement with other angiosperm groups and recent findings on genome stability in bacterial endosymbionts.
Collapse
Affiliation(s)
- John C Blazier
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Madhu Govindu
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Jin Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Mao-Lun Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
17
|
Abstract
Codon adaptation is codon usage bias that results from selective pressure to increase the translation efficiency of a gene. Codon adaptation has been studied across a wide range of genomes and some early analyses of plastids have shown evidence for codon adaptation in a limited set of highly expressed plastid genes. Here we study codon usage bias across all fully sequenced plastid genomes which includes representatives of the Rhodophyta, Alveolata, Cryptophyta, Euglenozoa, Glaucocystophyceae, Rhizaria, Stramenopiles and numerous lineages within the Viridiplantae, including Chlorophyta and Embryophyta. We show evidence that codon adaptation occurs in all genomes except for two, Theileria parva and Heicosporidium sp., both of which have highly reduced gene contents and no photosynthesis genes. We also show evidence that selection for codon adaptation increases the representation of the same set of codons, which we refer to as the adaptive codons, across this wide range of taxa, which is probably due to common features descended from the initial endosymbiont. We use various measures to estimate the relative strength of selection in the different lineages and show that it appears to be fairly strong in certain Stramenopiles and Chlorophyta lineages but relatively weak in many members of the Rhodophyta, Euglenozoa and Embryophyta. Given these results we propose that codon adaptation in plastids is widespread and displays the same general features as adaptation in eubacterial genomes.
Collapse
Affiliation(s)
- Haruo Suzuki
- Graduate School of Science and Engineering, Yamaguchi University, Yamaguchi, Japan
| | - Brian R. Morton
- Department of Biology, Barnard College, Columbia University, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
18
|
Morley SA, Nielsen BL. Chloroplast DNA Copy Number Changes during Plant Development in Organelle DNA Polymerase Mutants. FRONTIERS IN PLANT SCIENCE 2016; 7:57. [PMID: 26870072 PMCID: PMC4740508 DOI: 10.3389/fpls.2016.00057] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/14/2016] [Indexed: 05/18/2023]
Abstract
Chloroplast genome copy number is very high in leaf tissue, with upwards of 10,000 or more copies of the chloroplast DNA (ctDNA) per leaf cell. This is often promoted as a major advantage for engineering the plastid genome, as it provides high gene copy number and thus is expected to result in high expression of foreign proteins from integrated genes. However, it is also known that ctDNA copy number and ctDNA integrity decrease as cells age. Quantitative PCR (qPCR) allows measurement of organelle DNA levels relative to a nuclear gene target. We have used this approach to determine changes in copy number of ctDNA relative to the nuclear genome at different ages of Arabidopsis plant growth and in organellar DNA polymerase mutants. The mutant plant lines have T-DNA insertions in genes encoding the two organelle localized DNA polymerases (PolIA and PolIB). Each of these mutant lines exhibits some delay in plant growth and development as compared to wild-type plants, with the PolIB plants having a more pronounced delay. Both mutant lines develop to maturity and produce viable seeds. Mutants for both proteins were observed to have a reduction in ctDNA and mtDNA copy number relative to wild type plants at all time points as measured by qPCR. Both DNA polymerase mutants had a fairly similar decrease in ctDNA copy number, while the PolIB mutant had a greater effect of reduction in mtDNA levels. However, despite similar decreases in genome copy number, RT-PCR analysis of PolIA mutants show that PolIB expression remains unchanged, suggesting that PolIA may not be essential to plant survival. Furthermore, genotypic analysis of plants from heterozygous parents display a strong pressure to maintain two functioning copies of PolIB. These results indicate that the two DNA polymerases are both important in ctDNA replication, and they are not fully redundant to each other, suggesting each has a specific function in plant organelles.
Collapse
|
19
|
Romani I, Manavski N, Morosetti A, Tadini L, Maier S, Kühn K, Ruwe H, Schmitz-Linneweber C, Wanner G, Leister D, Kleine T. A Member of the Arabidopsis Mitochondrial Transcription Termination Factor Family Is Required for Maturation of Chloroplast Transfer RNAIle(GAU). PLANT PHYSIOLOGY 2015; 169:627-46. [PMID: 26152711 PMCID: PMC4577433 DOI: 10.1104/pp.15.00964] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/07/2015] [Indexed: 05/20/2023]
Abstract
Plastid gene expression is crucial for organelle function, but the factors that control it are still largely unclear. Members of the so-called mitochondrial transcription termination factor (mTERF) family are found in metazoans and plants and regulate organellar gene expression at different levels. Arabidopsis (Arabidopsis thaliana) mTERF6 is localized in chloroplasts and mitochondria, and its knockout perturbs plastid development and results in seedling lethality. In the leaky mterf6-1 mutant, a defect in photosynthesis is associated with reduced levels of photosystem subunits, although corresponding messenger RNA levels are unaffected, whereas translational capacity and maturation of chloroplast ribosomal RNAs (rRNAs) are perturbed in mterf6-1 mutants. Bacterial one-hybrid screening, electrophoretic mobility shift assays, and coimmunoprecipitation experiments reveal a specific interaction between mTERF6 and an RNA sequence in the chloroplast isoleucine transfer RNA gene (trnI.2) located in the rRNA operon. In vitro, recombinant mTERF6 bound to its plastid DNA target site can terminate transcription. At present, it is unclear whether disturbed rRNA maturation is a primary or secondary defect. However, it is clear that mTERF6 is required for the maturation of trnI.2. This points to an additional function of mTERFs.
Collapse
MESH Headings
- 5' Untranslated Regions/genetics
- Aminoacylation
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Base Sequence
- Basic-Leucine Zipper Transcription Factors/genetics
- Basic-Leucine Zipper Transcription Factors/metabolism
- Chloroplasts/metabolism
- DNA, Bacterial/genetics
- Gene Expression Regulation, Plant
- Genetic Loci
- Mitochondria/metabolism
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Molecular Sequence Data
- Mutagenesis, Insertional/genetics
- Mutation
- Phenotype
- Photosynthesis
- Protein Binding
- Protein Transport
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/genetics
- RNA, Transfer, Ile/chemistry
- RNA, Transfer, Ile/genetics
- RNA, Transfer, Ile/metabolism
- Ribosomes/metabolism
- Seedlings/metabolism
- Seeds/ultrastructure
- Transcription Termination, Genetic
Collapse
Affiliation(s)
- Isidora Romani
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Nikolay Manavski
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Arianna Morosetti
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Luca Tadini
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Swetlana Maier
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Kristina Kühn
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Hannes Ruwe
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Christian Schmitz-Linneweber
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Gerhard Wanner
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Dario Leister
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Department Biology I (I.R., N.M., A.M., L.T., D.L., T.K.), and Ultrastrukturforschung, Department Biology I (G.W.), Ludwig-Maximilians-Universität München, 81252 Planegg-Martinsried, Germany;Mathematisch-Naturwissenschaftliche Fakultät I/Biologie, Molekulare Zellbiologie der Pflanzen, Humboldt-Universität zu Berlin, 10099 Berlin, Germany (S.M., K.K.); andInstitute of Biology, Molecular Genetics, Humboldt-University of Berlin, 10115 Berlin, Germany (H.R., C.S.-L.)
| |
Collapse
|
20
|
Comparative genomics of ten solanaceous plastomes. Adv Bioinformatics 2014; 2014:424873. [PMID: 25477958 PMCID: PMC4248371 DOI: 10.1155/2014/424873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 10/14/2014] [Indexed: 11/17/2022] Open
Abstract
Availability of complete plastid genomes of ten solanaceous species, Atropa belladonna, Capsicum annuum, Datura stramonium, Nicotiana sylvestris, Nicotiana tabacum, Nicotiana tomentosiformis, Nicotiana undulata, Solanum bulbocastanum, Solanum lycopersicum, and Solanum tuberosum provided us with an opportunity to conduct their in silico comparative analysis in depth. The size of complete chloroplast genomes and LSC and SSC regions of three species of Solanum is comparatively smaller than that of any other species studied till date (exception: SSC region of A. belladonna). AT content of coding regions was found to be less than noncoding regions. A duplicate copy of trnH gene in C. annuum and two alternative tRNA genes for proline in D. stramonium were observed for the first time in this analysis. Further, homology search revealed the presence of rps19 pseudogene and infA genes in A. belladonna and D. stramonium, a region identical to rps19 pseudogene in C. annum and orthologues of sprA gene in another six species. Among the eighteen intron-containing genes, 3 genes have two introns and 15 genes have one intron. The longest insertion was found in accD gene in C. annuum. Phylogenetic analysis using concatenated protein coding sequences gave two clades, one for Nicotiana species and another for Solanum, Capsicum, Atropa, and Datura.
Collapse
|
21
|
Wu Z, Gui S, Quan Z, Pan L, Wang S, Ke W, Liang D, Ding Y. A precise chloroplast genome of Nelumbo nucifera (Nelumbonaceae) evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicots. BMC PLANT BIOLOGY 2014; 14:289. [PMID: 25407166 PMCID: PMC4245832 DOI: 10.1186/s12870-014-0289-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 10/15/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND The chloroplast genome is important for plant development and plant evolution. Nelumbo nucifera is one member of relict plants surviving from the late Cretaceous. Recently, a new sequencing platform PacBio RS II, known as 'SMRT (Single Molecule, Real-Time) sequencing', has been developed. Using the SMRT sequencing to investigate the chloroplast genome of N. nucifera will help to elucidate the plastid evolution of basal eudicots. RESULTS The sizes of the de novo assembled complete chloroplast genome of N. nucifera were 163,307 bp, 163,747 bp and 163,600 bp with average depths of coverage of 7×, 712× and 105× sequenced by Sanger, Illumina MiSeq and PacBio RS II, respectively. The precise chloroplast genome of N. nucifera was obtained from PacBio RS II data proofread by Illumina MiSeq reads, with a quadripartite structure containing a large single copy region (91,846 bp) and a small single copy region (19,626 bp) separated by two inverted repeat regions (26,064 bp). The genome contains 113 different genes, including four distinct rRNAs, 30 distinct tRNAs and 79 distinct peptide-coding genes. A phylogenetic analysis of 133 taxa from 56 orders indicated that Nelumbo with an age of 177 million years is a sister clade to Platanus, which belongs to the basal eudicots. Basal eudicots began to emerge during the early Jurassic with estimated divergence times at 197 million years using MCMCTree. IR expansions/contractions within the basal eudicots seem to have occurred independently. CONCLUSIONS Because of long reads and lack of bias in coverage of AT-rich regions, PacBio RS II showed a great promise for highly accurate 'finished' genomes, especially for a de novo assembly of genomes. N. nucifera is one member of basal eudicots, however, evolutionary analyses of IR structural variations of N. nucifera and other basal eudicots suggested that IR expansions/contractions occurred independently in these basal eudicots or were caused by independent insertions and deletions. The precise chloroplast genome of N. nucifera will present new information for structural variation of chloroplast genomes and provide new insight into the evolution of basal eudicots at the primary sequence and structural level.
Collapse
Affiliation(s)
- Zhihua Wu
- />State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072 Republic of China
| | - Songtao Gui
- />State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072 Republic of China
| | | | - Lei Pan
- />College of Life Sciences, Jianghan University, Wuhan, 430056 China
| | - Shuzhen Wang
- />College of Life Sciences, Huanggang Normal University, Huanggang, 438000 Hubei China
| | - Weidong Ke
- />Wuhan Vegetable Scientific Research Institute, Wuhan National Field Observation & Research Station for Aquatic Vegetables, Wuhan, 430065 China
| | - Dequan Liang
- />Nextomics Biosciences Co., Ltd., Wuhan, 430075 China
| | - Yi Ding
- />State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072 Republic of China
| |
Collapse
|
22
|
Sanchez-Puerta MV, Abbona CC. The chloroplast genome of Hyoscyamus niger and a phylogenetic study of the tribe Hyoscyameae (Solanaceae). PLoS One 2014; 9:e98353. [PMID: 24851862 PMCID: PMC4031233 DOI: 10.1371/journal.pone.0098353] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 05/01/2014] [Indexed: 12/04/2022] Open
Abstract
The tribe Hyoscyameae (Solanaceae) is restricted to Eurasia and includes the genera Archihyoscyamus, Anisodus, Atropa, Atropanthe, Hyoscyamus, Physochlaina, Przewalskia and Scopolia. Even though the monophyly of Hyoscyameae is strongly supported, the relationships of the taxa within the tribe remain unclear. Chloroplast markers have been widely used to elucidate plant relationships at low taxonomic levels. Identification of variable chloroplast intergenic regions has been developed based on comparative genomics of chloroplast genomes, but these regions have a narrow phylogenetic utility. In this study, we present the chloroplast genome sequence of Hyoscyamus niger and make comparisons to other solanaceous plastid genomes in terms of gene order, gene and intron content, editing sites, origins of replication, repeats, and hypothetical open reading frames. We developed and sequenced three variable plastid markers from eight species to elucidate relationships within the tribe Hyoscyameae. The presence of a horizontally transferred intron in the mitochondrial cox1 gene of some species of the tribe is considered here a likely synapomorphy uniting five genera of the Hyoscyameae. Alternatively, the cox1 intron could be a homoplasious character acquired twice within the tribe. A homoplasious inversion in the intergenic plastid spacer trnC-psbM was recognized as a source of bias and removed from the data set used in the phylogenetic analyses. Almost 12 kb of plastid sequence data were not sufficient to completely resolve relationships among genera of Hyoscyameae but some clades were identified. Two alternative hypotheses of the evolution of the genera within the tribe are proposed.
Collapse
Affiliation(s)
- M. Virginia Sanchez-Puerta
- Facultad de Ciencias Exactas y Naturales, IBAM-CONICET and Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Chacras de Coria, Mendoza, Argentina
- * E-mail:
| | - Cinthia Carolina Abbona
- IBAM-CONICET and Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Chacras de Coria, Mendoza, Argentina
| |
Collapse
|
23
|
Abstract
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.
Collapse
Affiliation(s)
- Tracey A Ruhlman
- Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | |
Collapse
|
24
|
Plastid trnF pseudogenes are present in Jaltomata, the sister genus of Solanum (Solanaceae): molecular evolution of tandemly repeated structural mutations. Gene 2013; 530:143-50. [PMID: 23962687 DOI: 10.1016/j.gene.2013.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/05/2013] [Accepted: 08/06/2013] [Indexed: 11/24/2022]
Abstract
Extensive gene duplication arranged in a tandem array is rare in the plastome of embryophytes. Interestingly, we found pseudogene copies of the trnF gene in the genus Jaltomata, the sister genus of Solanum where such gene duplication has been previously reported. In each Jaltomata sequence available we found two pseudogene copies in close 5'-proximity to the original functional gene. The size of each pseudogene copy ranged between 17 and 48 bp and the anticodon domain was identified as the most conserved element. A common ATT(G)n motif is particularly interesting and its modifications were found to border the 3' of the duplicated regions. Other motifs were partial residues, or entire parts of the T- and D-domains, and both domains proved to be variable in length among the pseudogenes identified. The residues of the 3' and 5' acceptor stem were not found among the copies. We further compared the newly discovered copies of Jaltomata with those ones previously described from Solanum and inferred phylogenetic relationships of the copies aligned. The evolution of Solanum copies, in contrast to Jaltomata, is hard to explain as resulting only in parsimonious changes since reticulate evolutionary patterns were detected among the copies. The dynamic evolutionary patterns of Solanum might be explained by possible inter- or intrachromosomal recombination.
Collapse
|
25
|
Udy DB, Belcher S, Williams-Carrier R, Gualberto JM, Barkan A. Effects of reduced chloroplast gene copy number on chloroplast gene expression in maize. PLANT PHYSIOLOGY 2012; 160:1420-31. [PMID: 22977281 PMCID: PMC3490597 DOI: 10.1104/pp.112.204198] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/12/2012] [Indexed: 05/18/2023]
Abstract
Chloroplasts and other members of the plastid organelle family contain a small genome of bacterial ancestry. Young chloroplasts contain hundreds of genome copies, but the functional significance of this high genome copy number has been unclear. We describe molecular phenotypes associated with mutations in a nuclear gene in maize (Zea mays), white2 (w2), encoding a predicted organellar DNA polymerase. Weak and strong mutant alleles cause a moderate (approximately 5-fold) and severe (approximately 100-fold) decrease in plastid DNA copy number, respectively, as assayed by quantitative PCR and Southern-blot hybridization of leaf DNA. Both alleles condition a decrease in most chloroplast RNAs, with the magnitude of the RNA deficiencies roughly paralleling that of the DNA deficiency. However, some RNAs are more sensitive to a decrease in genome copy number than others. The rpoB messenger RNA (mRNA) exhibited a unique response, accumulating to dramatically elevated levels in response to a moderate reduction in plastid DNA. Subunits of photosynthetic enzyme complexes were reduced more severely than were plastid mRNAs, possibly because of impaired translation resulting from limiting ribosomal RNA, transfer RNA, and ribosomal protein mRNA. These results indicate that chloroplast genome copy number is a limiting factor for the expression of a subset of chloroplast genes in maize. Whereas in Arabidopsis (Arabidopsis thaliana) a pair of orthologous genes function redundantly to catalyze DNA replication in both mitochondria and chloroplasts, the w2 gene is responsible for virtually all chloroplast DNA replication in maize. Mitochondrial DNA copy number was reduced approximately 2-fold in mutants harboring strong w2 alleles, suggesting that w2 also contributes to mitochondrial DNA replication.
Collapse
|
26
|
Alkatib S, Fleischmann TT, Scharff LB, Bock R. Evolutionary constraints on the plastid tRNA set decoding methionine and isoleucine. Nucleic Acids Res 2012; 40:6713-24. [PMID: 22553362 PMCID: PMC3413147 DOI: 10.1093/nar/gks350] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 03/27/2012] [Accepted: 03/31/2012] [Indexed: 12/31/2022] Open
Abstract
The plastid (chloroplast) genomes of seed plants typically encode 30 tRNAs. Employing wobble and superwobble mechanisms, most codon boxes are read by only one or two tRNA species. The reduced set of plastid tRNAs follows the evolutionary trend of organellar genomes to shrink in size and coding capacity. A notable exception is the AUN codon box specifying methionine and isoleucine, which is decoded by four tRNA species in nearly all seed plants. However, three of these four tRNA genes were lost from the genomes of some parasitic plastid-containing lineages, possibly suggesting that less than four tRNA species could be sufficient to decode the triplets in the AUN box. To test this hypothesis, we have performed knockout experiments for the four AUN-decoding tRNAs in tobacco (Nicotiana tabacum) plastids. We find that all four tRNA genes are essential under both autotrophic and heterotrophic growth conditions, possibly suggesting tRNA import into plastids of parasitic plastid-bearing species. Phylogenetic analysis of the four plastid tRNA genes reveals striking conservation of all those bacterial features that are involved in discrimination between the different tRNA species containing CAU anticodons.
Collapse
Affiliation(s)
| | | | | | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| |
Collapse
|
27
|
Shah K, Krishnamachari A. Nucleotide correlation based measure for identifying origin of replication in genomic sequences. Biosystems 2012; 107:52-5. [PMID: 21945744 DOI: 10.1016/j.biosystems.2011.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 08/30/2011] [Accepted: 09/10/2011] [Indexed: 12/18/2022]
Abstract
Computational prediction of the origin of replication is a challenging problem and of immense interest to biologists. Several methods have been proposed for identifying the replicon site for various classes of organisms. However, these methods have limited applicability since the replication mechanism is different in different organisms. We propose a correlation measure and show that it is correctly able to predict the origin of replication in most of the bacterial genomes. When applied to Methanocaldococcus jannaschii, Plasmodium falciparum apicoplast and Nicotiana tabacum plastid, this correlation based method is able to correctly predict the origin of replication whereas the generally used GC skew measure fails. Thus, this correlation based measure is a novel and promising tool for predicting the origin of replication in a wide class of organisms. This could have important implications in not only gaining a deeper understanding of the replication machinery in higher organisms, but also for drug discovery.
Collapse
Affiliation(s)
- Kushal Shah
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
| | | |
Collapse
|
28
|
Lassen MG, Kochhar S, Kocchar S, Nielsen BL. Identification of a soybean chloroplast DNA replication origin-binding protein. PLANT MOLECULAR BIOLOGY 2011; 76:463-71. [PMID: 21264493 DOI: 10.1007/s11103-011-9736-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 01/10/2011] [Indexed: 05/04/2023]
Abstract
Replication of chloroplast DNA (ctDNA) in several plants and in Chlamydomonas reinhardii has been shown to occur by a double displacement loop (D-loop) mechanism and potentially also by a rolling circle mechanism. D-loop replication origins have been mapped in several species. Minimal replication origin sequences used as probes identified two potential binding proteins by southwestern blot analysis. A 28 kDa (apparent molecular weight by SDS-PAGE analysis) soybean protein has been isolated by origin sequence-specific DNA affinity chromatography from total chloroplast proteins. Mass spectrometry analysis identified this protein as the product of the soybean C6SY33 gene (accession number ACU14156), which is annotated as encoding a putative uncharacterized protein with a molecular weight of 25,897 Da, very near the observed molecular weight of the purified protein based on gel electrophoresis. Western blot analysis using an antibody against a homologous Arabidopsis protein indicates that this soybean protein is localized specifically in chloroplasts. The soybean protein shares some homology within a single-stranded DNA binding (SSB) domain of E. coli SSB and an Arabidopsis thaliana mitochondrial-localized SSB of about 21 kDa (mtSSB). However, the soybean protein induces a specific electrophoretic mobility shift only when incubated with a double-stranded fragment containing the previously mapped ctDNA replication oriA region. This protein has no electrophoretic mobility shift activity when incubated with single-stranded DNA. In contrast, the Arabidopsis mtSSB causes a mobility shift only with single-stranded DNA but not with the oriA fragment or with control dsDNA of unrelated sequence. These results suggest that the 26 kDa soybean protein is a specific origin binding protein that may be involved in initiation of ctDNA replication.
Collapse
Affiliation(s)
- Matthew G Lassen
- Department of Microbiology and Molecular Biology, Brigham Young University, 775 WIDB, Provo, UT 84602, USA
| | | | | | | |
Collapse
|
29
|
Wicke S, Schneeweiss GM, dePamphilis CW, Müller KF, Quandt D. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. PLANT MOLECULAR BIOLOGY 2011; 76:273-97. [PMID: 21424877 PMCID: PMC3104136 DOI: 10.1007/s11103-011-9762-4] [Citation(s) in RCA: 825] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2010] [Accepted: 02/19/2011] [Indexed: 05/18/2023]
Abstract
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.
Collapse
Affiliation(s)
- Susann Wicke
- Department of Biogeography and Botanical Garden, University of Vienna, Rennweg 14, 1030 Vienna, Austria.
| | | | | | | | | |
Collapse
|
30
|
Brouard JS, Otis C, Lemieux C, Turmel M. The chloroplast genome of the green alga Schizomeris leibleinii (Chlorophyceae) provides evidence for bidirectional DNA replication from a single origin in the chaetophorales. Genome Biol Evol 2011; 3:505-15. [PMID: 21546564 PMCID: PMC3138424 DOI: 10.1093/gbe/evr037] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In the Chlorophyceae, the chloroplast genome is extraordinarily fluid in architecture and displays unique features relative to other groups of green algae. For the Chaetophorales, 1 of the 5 major lineages of the Chlorophyceae, it has been shown that the distinctive architecture of the 223,902-bp genome of Stigeoclonium helveticum is consistent with bidirectional DNA replication from a single origin. Here, we report the 182,759-bp chloroplast genome sequence of Schizomeris leibleinii, a member of the earliest diverging lineage of the Chaetophorales. Like its Stigeoclonium homolog, the Schizomeris genome lacks a large inverted repeat encoding the rRNA operon and displays a striking bias in coding regions that is associated with a bias in base composition along each strand. Our results support the notion that these two chaetophoralean genomes replicate bidirectionally from a putative origin located in the vicinity of the small subunit ribosomal RNA gene. Their shared structural characteristics were most probably inherited from the common ancestor of all chaetophoralean algae. Short dispersed repeats account for most of the 41-kb size variation between the Schizomeris and Stigeoclonium genomes, and there is no indication that homologous recombination between these repeated elements led to the observed gene rearrangements. A comparison of the extent of variation sustained by the Stigeoclonium and Schizomeris chloroplast DNAs (cpDNAs) with that observed for the cpDNAs of the chlamydomonadalean Chlamydomonas and Volvox suggests that gene rearrangements as well as changes in the abundance of intergenic and intron sequences occurred at a slower pace in the Chaetophorales than in the Chlamydomonadales.
Collapse
Affiliation(s)
- Jean-Simon Brouard
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Ville de Québec, Québec, Canada
| | | | | | | |
Collapse
|
31
|
Nielsen BL, Cupp JD, Brammer J. Mechanisms for maintenance, replication, and repair of the chloroplast genome in plants. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:2535-7. [PMID: 20513654 DOI: 10.1093/jxb/erq163] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- Brent L Nielsen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA.
| | | | | |
Collapse
|
32
|
Abstract
Maintenance of genome stability is essential for the accurate propagation of genetic information and cell growth and survival. Organisms have therefore developed efficient strategies to prevent DNA lesions and rearrangements. Much of the information concerning these strategies has been obtained through the study of bacterial and nuclear genomes. Comparatively, little is known about how organelle genomes maintain a stable structure. Here, we report that the plastid-localized Whirly ssDNA-binding proteins are required for plastid genome stability in Arabidopsis. We show that a double KO of the genes AtWhy1 and AtWhy3 leads to the appearance of plants with variegated green/white/yellow leaves, symptomatic of nonfunctional chloroplasts. This variegation is maternally inherited, indicating defects in the plastid genome. Indeed, in all variegated lines examined, reorganized regions of plastid DNA are amplified as circular and/or head-tail concatemers. All amplified regions are delimited by short direct repeats of 10-18 bp, strongly suggesting that these regions result from illegitimate recombination between repeated sequences. This type of recombination occurs frequently in plants lacking both Whirlies, to a lesser extent in single KO plants and rarely in WT individuals. Maize mutants for the ZmWhy1 Whirly protein also show an increase in the frequency of illegitimate recombination. We propose a model where Whirlies contribute to plastid genome stability by protecting against illegitimate repeat-mediated recombination.
Collapse
|
33
|
Krishnan NM, Rao BJ. A comparative approach to elucidate chloroplast genome replication. BMC Genomics 2009; 10:237. [PMID: 19457260 PMCID: PMC2695485 DOI: 10.1186/1471-2164-10-237] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Accepted: 05/20/2009] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Electron microscopy analyses of replicating chloroplast molecules earlier predicted bidirectional Cairns replication as the prevalent mechanism, perhaps followed by rounds of a rolling circle mechanism. This standard model is being challenged by the recent proposition of homologous recombination-mediated replication in chloroplasts. RESULTS We address this issue in our current study by analyzing nucleotide composition in genome regions between known replication origins, with an aim to reveal any adenine to guanine deamination gradients. These gradual linear gradients typically result from the accumulation of deaminations over the time spent single-stranded by one of the strands of the circular molecule during replication and can, therefore, be used to model the course of replication. Our linear regression analyses on the nucleotide compositions of the non-coding regions and the synonymous third codon position of coding regions, between pairs of replication origins, reveal the existence of significant adenine to guanine deamination gradients in portions overlapping the Small Single Copy (SSC) and the Large Single Copy (LSC) regions between inverted repeats. These gradients increase bi-directionally from the center of each region towards the respective ends, suggesting that both the strands were left single-stranded during replication. CONCLUSION Single-stranded regions of the genome and gradients in time that these regions are left single-stranded, as revealed by our nucleotide composition analyses, appear to converge with the original bi-directional dual displacement loop model and restore evidence for its existence as the primary mechanism. Other proposed faster modes such as homologous recombination and rolling circle initiation could exist in addition to this primary mechanism to facilitate homoplasmy among the intra-cellular chloroplast population.
Collapse
Affiliation(s)
- Neeraja M Krishnan
- B-202, Department of Biological Sciences, Tata Institute of Fundamental Research, 1 Homi Bhabha road, Colaba, Mumbai 400 005, India
- Current address: Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560 012, India
| | - Basuthkar J Rao
- B-202, Department of Biological Sciences, Tata Institute of Fundamental Research, 1 Homi Bhabha road, Colaba, Mumbai 400 005, India
| |
Collapse
|
34
|
Shaver JM, Oldenburg DJ, Bendich AJ. The structure of chloroplast DNA molecules and the effects of light on the amount of chloroplast DNA during development in Medicago truncatula. PLANT PHYSIOLOGY 2008; 146:1064-74. [PMID: 18218970 PMCID: PMC2259089 DOI: 10.1104/pp.107.112946] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Accepted: 01/12/2008] [Indexed: 05/18/2023]
Abstract
We used pulsed-field gel electrophoresis and restriction fragment mapping to analyze the structure of Medicago truncatula chloroplast DNA (cpDNA). We find most cpDNA in genome-sized linear molecules, head-to-tail genomic concatemers, and complex branched forms with ends at defined sites rather than at random sites as expected from broken circles. Our data suggest that cpDNA replication is initiated predominantly on linear DNA molecules with one of five possible ends serving as putative origins of replication. We also used 4',6-diamidino-2-phenylindole staining of isolated plastids to determine the DNA content per plastid for seedlings grown in the dark for 3 d and then transferred to light before being returned to the dark. The cpDNA content in cotyledons increased after 3 h of light, decreased with 9 h of light, and decreased sharply with 24 h of light. In addition, we used real-time quantitative polymerase chain reaction to determine cpDNA levels of cotyledons in dark- and light-grown (low white, high white, blue, and red light) seedlings, as well as in cotyledons and leaves from plants grown in a greenhouse. In white, blue, and red light, cpDNA increased initially and then declined, but cpDNA declined further in white and blue light while remaining constant in red light. The initial decline in cpDNA occurred more rapidly with increased white light intensity, but the final DNA level was similar to that in less intense light. The patterns of increase and then decrease in cpDNA level during development were similar for cotyledons and leaves. We conclude that the absence in M. truncatula of the prominent inverted repeat cpDNA sequence found in most plant species does not lead to unusual properties with respect to the structure of plastid DNA molecules, cpDNA replication, or the loss of cpDNA during light-stimulated chloroplast development.
Collapse
Affiliation(s)
- Jeffrey M Shaver
- Department of Biology, University of Washington, Seattle, WA 98195-5325, USA
| | | | | |
Collapse
|
35
|
Abstract
Several major costs associated with the production of biopharmaceuticals or vaccines in fermentation-based systems could be minimized by using plant chloroplasts as bioreactors, which facilitates rapid scale-up. Oral delivery of chloroplast-derived therapeutic proteins through plant cells eliminates expensive purification steps, low temperature storage, transportation and sterile injections for their delivery. Chloroplast transformation technology (CTT) has also been successfully used to engineer valuable agronomic traits and for the production of industrial enzymes and biomaterials. Here, we provide a detailed protocol for the construction of chloroplast expression and integration vectors, selection and regeneration of transformants, evaluation of transgene integration and inheritance, confirmation of transgene expression and extraction, and quantitation and purification of foreign proteins. Integration of appropriate transgenes into chloroplast genomes and the resulting high levels of functional protein expression can be achieved in approximately 6 months in lettuce and tobacco. CTT is eco-friendly because transgenes are maternally inherited in most crop plants.
Collapse
Affiliation(s)
- Dheeraj Verma
- Department of Molecular Biology and Microbiology, College of Medicine, University of Central Florida, Biomolecular Science, Building #20, Room 336, Orlando, Florida 32816-2364, USA
| | | | | | | |
Collapse
|
36
|
Verma D, Daniell H. Chloroplast vector systems for biotechnology applications. PLANT PHYSIOLOGY 2007; 145:1129-43. [PMID: 18056863 PMCID: PMC2151729 DOI: 10.1104/pp.107.106690] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Accepted: 09/30/2007] [Indexed: 05/19/2023]
Affiliation(s)
- Dheeraj Verma
- Department of Molecular Biology and Microbiology, College of Medicine, University of Central Florida, Orlando, Florida 32816-2364, USA
| | | |
Collapse
|
37
|
Wang D, Wu YW, Shih ACC, Wu CS, Wang YN, Chaw SM. Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA. Mol Biol Evol 2007; 24:2040-8. [PMID: 17609537 DOI: 10.1093/molbev/msm133] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
With the completion of the first gymnosperm mitochondrial genome (mtDNA) from Cycas taitungensis and the availability of more mtDNA taxa in the past 5 years, we have conducted a systematic analysis of DNA transfer from chloroplast genomes (cpDNAs) to mtDNAs (mtpts) in 11 plants, including 2 algae, 1 liverwort, 1 moss, 1 gymnosperm, 3 monocots, and 3 eudicots. By using shared gene order and boundaries between different mtpts as the criterion, the timing of cpDNA transfer during plant evolution was estimated from the phylogenetic tree reconstructed independently from concatenated protein-coding genes of 11 available mtDNAs. Several interesting findings emerged. First, frequent DNA transfer from cpDNA to mtDNA occurred at least as far back as the common ancestor of extant gymnosperms and angiosperms, about 300 MYA. The oldest mtpt is trnV(uac)-trnM(cau)-atpE-atpB-rbcL. Three other mtpts--psaA-psaB, rps19-trnH(gug)-rpl2-rpl23, and psbE-psbF--were dated to the common ancestor of extant angiosperms, at least 150 MYA. However, all protein-coding genes of mtpts have degenerated since their first transfer. Therefore, mtpts contribute nothing to the functioning of mtDNA but junk sequences. We discovered that the cpDNA transfers have occurred randomly at any positions of the cpDNAs. We provide strong evidence that the cp-derived tRNA-trnM(cau) is the only mtpt (1 out of 3 cp-derived tRNA shared by seed plants) truly transferred from cpDNA to mtDNA since the time of the common ancestor of extant gymnosperms and angiosperms. Our observations support the proposition of Richly and Leister (2004) that "primary insertions of organellar DNAs are large and then diverge and fragment over evolutionary time."
Collapse
Affiliation(s)
- Daryi Wang
- Research Center for Biodiversity, Academia Sinica, Taipei, Taiwan
| | | | | | | | | | | |
Collapse
|
38
|
Scharff LB, Koop HU. Targeted inactivation of the tobacco plastome origins of replication A and B. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 50:782-94. [PMID: 17470061 DOI: 10.1111/j.1365-313x.2007.03087.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
According to the Kolodner and Tewari model [Kolodner, R.D. and Tewari, K.K. (1975) Nature, 256, 708.], plastid DNA replication involves displacement-loop and rolling-circle modes of replication, which are initiated on a pair of origins of replication (ori). In accordance with the model, such a pair of oris -oriA and oriB- was described in Nicotiana tabacum [Kunnimalaiyaan, M. and Nielsen B.L. (1997b) Nucl. Acids Res. 25, 3681.]. However, as reported previously, both copies of oriA can be deleted without abolishing replication. Deletion of both oriBs was not found [Mühlbauer, S.K. et al. (2002) Plant J. 32, 175.]. Here we describe new ori inactivation lines, in which one oriB is deleted and the other copy is strongly mutated. In addition, lines oriA and oriB were deleted from the same inverted repeat. In contrast to the expectations of the model, neither oriA nor oriB is essential. Some of the deletions led to reduced growth of plants and reduced plastid DNA copy number in later stages of leaf development. The gross structure of plastid DNA was unchanged; however, the location of the ends of branched plastid DNA complexes was different in the inactivation mutants. Taken together, the results indicate that there are additional mechanisms of plastid DNA replication and/or additional origins of replication. These mechanisms seem to be different from those found in eubacteria, which, according to the endosymbiont theory, are the progenitors of plastids.
Collapse
Affiliation(s)
- Lars B Scharff
- Department I - Botany, Faculty of Biology, Ludwig-Maximilians-Universität, Menzinger Str. 67, D-80638 München, Germany
| | | |
Collapse
|
39
|
DNA replication, recombination, and repair in plastids. CELL AND MOLECULAR BIOLOGY OF PLASTIDS 2007. [DOI: 10.1007/4735_2007_0231] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
40
|
McNutt PM, Dehart MJ, Matej LA. Characterization of the 16S-23S internal transcribed spacer among 34 higher plants: suitability for interspecific plastid transformation. PLANT CELL REPORTS 2007; 26:47-60. [PMID: 16912867 DOI: 10.1007/s00299-006-0203-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2006] [Revised: 06/03/2006] [Accepted: 06/18/2006] [Indexed: 05/11/2023]
Abstract
Biomanufacturing by chloroplast transgene expression has the potential to produce significant amounts of biopharmaceuticals, endow plants with novel commercial or humanitarian capabilities, enhance phytoremediation methods and harden plants against adverse environments. Plastid bioengineering exploits the phenomenon of homologous recombination to specifically integrate heterologous sequences into the plastid genome. Previous research suggests the plastid genome 16S-23S internal transcribed spacer provides an advantageous integration site for transgene expression. To characterize the suitability of the 16S-23S region for interspecific recombination, we developed primers against conserved plastid sequences and amplified approximately 2.6 kb from 25 plant species. We analyzed the amplicons with nine species from Genbank for homeology, phylogenetic relationships, potential to form chimeric rDNA elements disruptive to translational/replication systems, and the potential number of recombination events for various minimal essential processing segments (MEPS) lengths. Multiple sequence alignment of the 34 species revealed considerable conservation, with identities exceeding 95% among the angiosperms. Substitutions were statistically clustered, generally in noncoding sites, although proposed functional elements such as the OriA region and 3' terminus of the 16S rRNA exhibited unexpected variation. The nonrandom distribution of substitutions undermines the established, statistical method of estimating the number of recombination initiation sites. This finding is further substantiated by comparing statistical estimates of the number of MEPS sites to a direct count at three different MEPS lengths. We frame this in silico analysis in terms of the potential of the 16S-23S region as a target for interspecific transformation, and describe a 'primer-to-plastid' system to rapidly generate species-specific flanking regions for transformation vectors.
Collapse
MESH Headings
- Base Sequence
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- Plants/classification
- Plants/genetics
- Plastids/genetics
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- Sequence Alignment
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- Patrick M McNutt
- Department of Clinical Investigation, Madigan Army Medical Center, Fort Lewis, WA 98327, USA.
| | | | | |
Collapse
|
41
|
Scharff LB, Koop HU. Linear molecules of tobacco ptDNA end at known replication origins and additional loci. PLANT MOLECULAR BIOLOGY 2006; 62:611-21. [PMID: 16897466 DOI: 10.1007/s11103-006-9042-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 06/28/2006] [Indexed: 05/10/2023]
Abstract
Higher plant plastid DNA (ptDNA) is generally described as a double-stranded circular molecule of the size of the monomer of the plastid genome. Also, the substrates and products of ptDNA replication are generally assumed to be circular molecules. Linear or partly linear ptDNA molecules were detected in our present study using pulsed-field gel electrophoresis and Southern blotting of ptDNA restricted with 'single cutter' restriction enzymes. These linear DNA molecules show discrete end points which were mapped using appropriate probes. One possible explanation of discrete ends would be that they represent origins of replication. Indeed, some of the mapped ends correlate well with the known origins of replication of tobacco plastids, i.e. both of the oriA sequences and--less pronouncedly--with the oriB elements. Other ends correspond to replication origins that were described for Oenothera hookeri, Zea mays, Glycine max and Chlamydomonas reinhardtii, respectively, while some of the mapped ends were not described previously and might therefore represent additional origins of replication.
Collapse
Affiliation(s)
- Lars B Scharff
- Department of Biology I - Botany, University of Munich, Menzinger Str. 67, D-80638 München, Germany
| | | |
Collapse
|
42
|
Daniell H, Kumar S, Dufourmantel N. Breakthrough in chloroplast genetic engineering of agronomically important crops. Trends Biotechnol 2005; 23:238-45. [PMID: 15866001 PMCID: PMC3486632 DOI: 10.1016/j.tibtech.2005.03.008] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Chloroplast genetic engineering offers several unique advantages, including high-level transgene expression, multi-gene engineering in a single transformation event and transgene containment by maternal inheritance, as well as a lack of gene silencing, position and pleiotropic effects and undesirable foreign DNA. More than 40 transgenes have been stably integrated and expressed using the tobacco chloroplast genome to confer desired agronomic traits or express high levels of vaccine antigens and biopharmaceuticals. Despite such significant progress, this technology has not been extended to major crops. However, highly efficient soybean, carrot and cotton plastid transformation has recently been accomplished through somatic embryogenesis using species-specific chloroplast vectors. This review focuses on recent exciting developments in this field and offers directions for further research and development.
Collapse
Affiliation(s)
- Henry Daniell
- Department of Molecular Biology and Microbiology, University of Central Florida, Biomolecular Science, Orlando, FL 32816-2364, USA.
| | | | | |
Collapse
|
43
|
Singh D, Kumar A, Raghu Ram EVS, Habib S. Multiple replication origins within the inverted repeat region of the Plasmodium falciparum apicoplast genome are differentially activated. Mol Biochem Parasitol 2005; 139:99-106. [PMID: 15610824 DOI: 10.1016/j.molbiopara.2004.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Revised: 08/07/2004] [Accepted: 09/13/2004] [Indexed: 10/26/2022]
Abstract
The 35 kb circular genome (plDNA) of the Plasmodium falciparum apicoplast replicates by the bidirectional ori/D-loop mechanism. PlDNA replication was previously shown to initiate within the inverted repeat (IR) region of the apicoplast genome [Williamson DH, Preiser PR, Moore PW, McCready S, Strath M, Wilson RJM (Iain). The plastid DNA of the malaria parasite Plasmodium falciparum is replicated by two mechanisms. Mol Microbiol 2002;45:533-42; Singh D, Chaubey S, Habib S. Replication of the Plasmodium falciparum apicoplast DNA initiates within the inverted repeat region. Mol Biochem Parasitol 2003;126:9-14.] and the presence of at least two ori within each segment of the IR was postulated. Using 5' end-labelled nascent DNA as probe, we now demonstrate the utilization of several putative ori located within the IR for plDNA replication. Quantitation of signals obtained for different segments of the IR as well as determination of the number of molecules emanating from two ori regions by competitive PCR analysis indicated differential strengths of ori during plDNA replication prior to schizogony.
Collapse
Affiliation(s)
- Divya Singh
- Division of Molecular and Structural Biology, Central Drug Research Institute, P.O. Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow 226001, India
| | | | | | | |
Collapse
|
44
|
Kumar S, Dhingra A, Daniell H. Stable transformation of the cotton plastid genome and maternal inheritance of transgenes. PLANT MOLECULAR BIOLOGY 2004; 56:203-16. [PMID: 15604738 PMCID: PMC3481848 DOI: 10.1007/s11103-004-2907-y] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Chloroplast genetic engineering overcomes concerns of gene containment, low levels of transgene expression, gene silencing, positional and pleiotropic effects or presence of vector sequences in transformed genomes. Several therapeutic proteins and agronomic traits have been highly expressed via the tobacco chloroplast genome but extending this concept to important crops has been a major challenge; lack of 100 homologous species-specific chloroplast transformation vectors containing suitable selectable markers, ability to regulate transgene expression in developing plastids and inadequate tissue culture systems via somatic embryogenesis are major challenges. We employed a 'Double Gene/Single Selection (DGSS)' plastid transformation vector that harbors two selectable marker genes (aph A-6 and npt II) to detoxify the same antibiotic by two enzymes, irrespective of the type of tissues or plastids; by combining this with an efficient regeneration system via somatic embryogenesis, cotton plastid transformation was achieved for the first time. The DGSS transformation vector is at least 8-fold (1 event/2.4 bombarded plates) more efficient than 'Single Gene/Single Selection (SGSS)' vector (aph A-6; 1 event per 20 bombarded plates). Chloroplast transgenic lines were fertile, flowered and set seeds similar to untransformed plants. Transgenes stably integrated into the cotton chloroplast genome were maternally inherited and were not transmitted via pollen when out-crossed with untransformed female plants. Cotton is one of the most important genetically modified crops (120 billion US dollars US annual economy). Successful transformation of the chloroplast genome should address concerns about transgene escape, insects developing resistance, inadequate insect control and promote public acceptance of genetically modified cotton.
Collapse
Affiliation(s)
- Shashi Kumar
- Department ofMolecular Biology and Microbiology, University of Central Florida, Biomolecular Science, Bldg # 20, Room 336, Orlando FL 32816-2364, USA
| | - Amit Dhingra
- Department ofMolecular Biology and Microbiology, University of Central Florida, Biomolecular Science, Bldg # 20, Room 336, Orlando FL 32816-2364, USA
| | - Henry Daniell
- Department ofMolecular Biology and Microbiology, University of Central Florida, Biomolecular Science, Bldg # 20, Room 336, Orlando FL 32816-2364, USA
| |
Collapse
|
45
|
Oldenburg DJ, Bendich AJ. Most chloroplast DNA of maize seedlings in linear molecules with defined ends and branched forms. J Mol Biol 2004; 335:953-70. [PMID: 14698291 DOI: 10.1016/j.jmb.2003.11.020] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We used pulsed-field gel electrophoresis, restriction fragment mapping, and fluorescence microscopy of individual DNA molecules to analyze the structure of chloroplast DNA (cpDNA) from shoots of ten to 14 day old maize seedlings. We find that most of the cpDNA is in linear and complex branched forms, with only 3-4% as circles. We find the ends of linear genomic monomers and head-to-tail (h-t) concatemers within inverted repeat sequences (IRs) near probable origins of replication, not at random sites as expected from broken circles. Our results predict two major and three minor populations of linear molecules, each with different ends and putative origins of replication. Our mapping data predict equimolar populations of h-t linear concatemeric molecules differing only in the relative orientation (inversion) of the single copy regions. We show how recombination during replication can produce h-t linear concatemers containing an inversion of single copy sequences that has for 20 years been attributed to recombinational flipping between IRs in a circular chromosome. We propose that replication is initiated predominantly on linear, not circular, DNA, producing multi-genomic branched chromosomes and that most replication involves strand invasion of internal regions by the ends of linear molecules, rather than the generally accepted D-loop-to-theta mechanism. We speculate that if the minor amount of cpDNA in circular form is useful to the plant, its contribution to chloroplast function does not depend on the circularity of these cpDNA molecules.
Collapse
MESH Headings
- Chloroplasts/genetics
- Chromosomes, Plant/chemistry
- Chromosomes, Plant/metabolism
- DNA Replication
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/metabolism
- DNA, Concatenated/chemistry
- DNA, Concatenated/metabolism
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/metabolism
- DNA, Viral/chemistry
- DNA, Viral/metabolism
- Electrophoresis, Gel, Pulsed-Field
- Genome
- Microscopy, Fluorescence
- Models, Genetic
- Nucleic Acid Conformation
- Recombination, Genetic
- Restriction Mapping
- Seedlings/cytology
- Seedlings/genetics
- Simplexvirus/genetics
- Zea mays/cytology
- Zea mays/genetics
Collapse
Affiliation(s)
- Delene J Oldenburg
- Department of Biology, University of Washington, Seattle, WA 98195-5325, USA
| | | |
Collapse
|
46
|
Jeong SY, Rose A, Meier I. MFP1 is a thylakoid-associated, nucleoid-binding protein with a coiled-coil structure. Nucleic Acids Res 2003; 31:5175-85. [PMID: 12930969 PMCID: PMC212795 DOI: 10.1093/nar/gkg693] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Plastid DNA, like bacterial and mitochondrial DNA, is organized into protein-DNA complexes called nucleoids. Plastid nucleoids are believed to be associated with the inner envelope in developing plastids and the thylakoid membranes in mature chloroplasts, but the mechanism for this re-localization is unknown. Here, we present the further characterization of the coiled-coil DNA-binding protein MFP1 as a protein associated with nucleoids and with the thylakoid membranes in mature chloroplasts. MFP1 is located in plastids in both suspension culture cells and leaves and is attached to the thylakoid membranes with its C-terminal DNA-binding domain oriented towards the stroma. It has a major DNA-binding activity in mature Arabidopsis chloroplasts and binds to all tested chloroplast DNA fragments without detectable sequence specificity. Its expression is tightly correlated with the accumulation of thylakoid membranes. Importantly, it is associated in vivo with nucleoids, suggesting a function for MFP1 at the interface between chloroplast nucleoids and the developing thylakoid membrane system.
Collapse
Affiliation(s)
- Sun Yong Jeong
- Department of Plant Biology and Plant Biotechnology Center, Ohio State University, 244 Rightmire Hall, 1060 Carmack Road, Columbus, OH 43210, USA
| | | | | |
Collapse
|
47
|
Wang Y, Saitoh Y, Sato T, Hidaka S, Tsutsumi KI. Comparison of plastid DNA replication in different cells and tissues of the rice plant. PLANT MOLECULAR BIOLOGY 2003; 52:905-913. [PMID: 13677476 DOI: 10.1023/a:1025093528174] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In a previous study, we mapped replication origin regions of the plastid DNA around the 3' end of the 23S rRNA gene in rice suspension-cultured cells. Here, we examined initiation of the plastid DNA replication in different rice cells by two-dimensional agarose gel electrophoresis. We show for the first time, to our knowledge, that the replication origin region of the plastid DNA differs among cultured cells, coleoptiles and mature leaves. In addition, digestion of the replication intermediates from the rice cultured cells with mung bean nuclease, a single-strand-specific nuclease, revealed that both two single strands of the double-stranded parental DNA were simultaneously replicated in the origin region. This was further confirmed by two-dimensional agarose gel analysis with single-stranded RNA probes. Thus, the mode of plastid DNA replication presented here differs from the unidirectional replication started by forming displacement loops (D-loops), in which the two D-loops on the opposite strands expand toward each other and only one parental strand serves as a template.
Collapse
Affiliation(s)
- Ying Wang
- United Graduate School of Agricultural Sciences, Iwate University, Ueda, Morioka, Iwate 020-8550, Japan
| | | | | | | | | |
Collapse
|
48
|
Singh D, Chaubey S, Habib S. Replication of the Plasmodium falciparum apicoplast DNA initiates within the inverted repeat region. Mol Biochem Parasitol 2003; 126:9-14. [PMID: 12554079 DOI: 10.1016/s0166-6851(02)00251-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The 35kb apicoplast genomes (plDNA) of Plasmodium falciparum and Toxoplasma gondii share close sequence similarity but differ in their in vivo topologies. Although sequence analysis of tandem repeats of T. gondii plDNA has suggested the presence of replication initiation sites within the inverted repeat region, the replication origins (ori) of the P. falciparum circular plDNA have not been identified. Using 5' end-labelled nascent DNA as probe, we demonstrate that the ori of P. falciparum plDNA is localised within the inverted repeat region. Our results also indicate the presence of two initiation sites within each inverted repeat segment of the circular plDNA of P. falciparum suggestive of a four D-loop/bi-directional ori mechanism of DNA replication.
Collapse
Affiliation(s)
- Divya Singh
- Molecular and Structural Biology Division, Central Drug Research Institute, Post Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow 226001, India
| | | | | |
Collapse
|
49
|
Sato N, Terasawa K, Miyajima K, Kabeya Y. Organization, Developmental Dynamics, and Evolution of Plastid Nucleoids. INTERNATIONAL REVIEW OF CYTOLOGY 2003; 232:217-62. [PMID: 14711120 DOI: 10.1016/s0074-7696(03)32006-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The plastid is a semiautonomous organelle essential in photosynthesis and other metabolic activities of plants and algae. Plastid DNA is organized into the nucleoid with various proteins and RNA, and the nucleoid is subject to dynamic changes during the development of plant cells. Characterization of the major DNA-binding proteins of nucleoids revealed essential differences in the two lineages of photosynthetic eukaryotes, namely nucleoids of green plants contain sulfite reductase as a major DNA-binding protein that represses the genomic activity, whereas the prokaryotic DNA-binding protein HU is abundant in plastid nucleoids of the rhodophyte lineage. In addition, current knowledge on DNA-binding proteins, as well as the replication and transcription systems of plastids, is reviewed from comparative and evolutionary points of view. A revised hypothesis on the discontinuous evolution of plastid genomic machinery is presented: despite the cyanobacterial origin of plastids, the genomic machinery of the plastid genome is fundamentally different from its counterpart in cyanobacteria.
Collapse
Affiliation(s)
- Naoki Sato
- Department of Molecular Biology, Faculty of Science, Saitama University, Saitama 338-8570, Japan
| | | | | | | |
Collapse
|
50
|
Mühlbauer SK, Lössl A, Tzekova L, Zou Z, Koop HU. Functional analysis of plastid DNA replication origins in tobacco by targeted inactivation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 32:175-84. [PMID: 12383083 DOI: 10.1046/j.1365-313x.2002.01408.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Sequences described as chloroplast DNA replication origins were analysed in vivo by creating deletion and insertion mutants via plastid transformation in tobacco. Deletion of the described oriA sequence, which is located within the intron of the trnI gene, resulted in heteroplastomic transformants, when the selection marker was inserted within the intron. Removal of the complete intron sequence together with the oriA sequence, however, yielded homoplastomic transformants of normal phenotype, in which wild-type signals were no longer detectable through Southern analysis, thus bringing the role of the described oriA sequence for plastome replication into question. Similarly, deletion of sequence elements upstream of trnI, which have a possible ori function in Oenothera, did not show any effect in tobacco. The two copies of oriB, which are located at the very end of the plastome Inverted Repeats, were targeted with two different transformation vectors in a cotransformation approach. While in initial transformants integration of the selection marker could be detected at both sites, the transgene was found exclusively at one site or the other after additional rounds of regeneration. Whereas the copy of oriB in Inverted Repeat B could be completely deleted, targeting of the copy in Inverted Repeat A resulted in heteroplastomic lines, as the essential ycf1 gene was also affected. Due to the strong selection against cotransformants we conclude that at least one copy of the oriB sequence is essential for plastome replication, whereas replication appears possible without oriA elements.
Collapse
Affiliation(s)
- Stefan K Mühlbauer
- University of Munich, Department of Biology I - Botany, Menzinger Str. 67, D-80638, München, Germany
| | | | | | | | | |
Collapse
|