Special Issue "Plant Organelle DNA Maintenance"

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Molecular Botany".

Deadline for manuscript submissions: 31 December 2019.

Special Issue Editors

Prof. Dr. Brent L. Nielsen
E-Mail Website
Guest Editor
Department of Microbiology & Molecular Biology, Brigham Young University, Provo, UT 84602, USA
Tel. +801-422-1102
Interests: plant molecular biology; DNA replication and recombination; plant mitochondrial and chloroplast genomes; salt-tolerant microbiomes
Dr. Niaz Ahmad
E-Mail Website
Guest Editor
Agricultural Biotechnology Division, National Institute for Biotechnology & Genetic Engineering (NIBGE), 38000 Faisalabad, Pakistan
Tel. +92-412-9201316-20 Ext 243
Interests: chloroplast biotechnology; biopharming; stress physiology; improving photosynthesis

Special Issue Information

Dear Colleagues,

In addition to the nuclear genome, plant cells also contain DNA in two of their organelles—plastids and mitochondria. These double-membrane-bound organelles are considered to have originated through endosymbiosis. Over the course of evolution, the modern-day plant organelle genomes have considerably shrunk compared to their progenitors, as genes move from the organelles to the nuclear genomes. This provides additional control points for the nucleus over plant and organelle development, physiology, and maintenance. Consequently, the products of genes that have migrated to the nucleus have to be imported into their corresponding organelle destination, which has resulted in the evolution of a sophisticated signaling network between the nucleus and the organelles for synthesis and quality control. Both the plastids and the mitochondria house important biochemical reactions, namely, photosynthesis and respiration, respectively. In addition to photosynthesis and respiration, these organelles play a central role in various metabolic reactions, such as amino acid synthesis, sucrose metabolism, nitrogen assimilation, sulphur metabolism, steroid synthesis, and apoptosis. Both the organelles and their genomes are present in high copy number. Depending upon the plant age and tissue type, their number, morphology, and genomic content vary considerably during cell division as well as in response to different stresses, reflecting the diversity of organelles’ functions. For example, the DNA copy number in plastids and mitochondria can reach very high levels in rapidly growing plant tissues, such as young leaves for plastid DNA and shoot and root meristems for mitochondrial DNA. Likewise, the DNA in both organelles is degraded in aging leaves, and the components are recycled. The mechanisms that control copy number and DNA replication are poorly understood. Displacement loop replication origins have been mapped and studied in plant chloroplast DNA, and the major proteins involved in replication have been identified. The situation is more complex for plant mitochondrial genomes, which appear to replicate by a recombination-dependent mechanism without any known origin of replication. The link between the metabolic needs of a cell and the capacity of organelles to fulfil this demand is thought to act as a selective force on the number of organelles in a cell. Many questions, including why the DNA and the organelles themselves exist in high copy number and how the organelles’ genomes are maintained through different developmental stages, remain yet to be fully understood.

This Special Issue of Plants is poised to address these questions. The issue focuses on organelle DNA dynamics in plants, with particular emphasis on fluctuations in organelle DNA, mechanisms to maintain DNA copy number, and its degradation.

Prof. Brent L. Nielsen
Dr. Niaz Ahmad
Guest Editors

Manuscript Submission Information

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Keywords

  • Plant mitochondrial genomes
  • chloroplast genomes
  • recombination-dependent DNA replication
  • organelle DNA maintenance

Published Papers (3 papers)

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Research

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Open AccessArticle
Organization Features of the Mitochondrial Genome of Sunflower (Helianthus annuus L.) with ANN2-Type Male-Sterile Cytoplasm
Plants 2019, 8(11), 439; https://doi.org/10.3390/plants8110439 (registering DOI) - 23 Oct 2019
Abstract
This study provides insights into the flexibility of the mitochondrial genome in sunflower (Helianthus annuus L.) as well as into the causes of ANN2-type cytoplasmic male sterility (CMS). De novo assembly of the mitochondrial genome of male-sterile HA89(ANN2) sunflower line was performed [...] Read more.
This study provides insights into the flexibility of the mitochondrial genome in sunflower (Helianthus annuus L.) as well as into the causes of ANN2-type cytoplasmic male sterility (CMS). De novo assembly of the mitochondrial genome of male-sterile HA89(ANN2) sunflower line was performed using high-throughput sequencing technologies. Analysis of CMS ANN2 mitochondrial DNA sequence revealed the following reorganization events: twelve rearrangements, seven insertions, and nine deletions. Comparisons of coding sequences from the male-sterile line with the male-fertile line identified a deletion of orf777 and seven new transcriptionally active open reading frames (ORFs): orf324, orf327, orf345, orf558, orf891, orf933, orf1197. Three of these ORFs represent chimeric genes involving atp6 (orf1197), cox2 (orf558), and nad6 (orf891). In addition, orf558, orf891, orf1197, as well as orf933, encode proteins containing membrane domain(s), making them the most likely candidate genes for CMS development in ANN2. Although the investigated CMS phenotype may be caused by simultaneous action of several candidate genes, we assume that orf1197 plays a major role in developing male sterility in ANN2. Comparative analysis of mitogenome organization in sunflower lines representing different CMS sources also allowed identification of reorganization hot spots in the mitochondrial genome of sunflower. Full article
(This article belongs to the Special Issue Plant Organelle DNA Maintenance)
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Open AccessArticle
De Novo Assembly Discovered Novel Structures in Genome of Plastids and Revealed Divergent Inverted Repeats in Mammillaria (Cactaceae, Caryophyllales)
Plants 2019, 8(10), 392; https://doi.org/10.3390/plants8100392 - 01 Oct 2019
Abstract
The complete sequence of chloroplast genome (cpDNA) has been documented for single large columnar species of Cactaceae, lacking inverted repeats (IRs). We sequenced cpDNA for seven species of the short-globose cacti of Mammillaria and de novo assembly revealed three novel structures in land [...] Read more.
The complete sequence of chloroplast genome (cpDNA) has been documented for single large columnar species of Cactaceae, lacking inverted repeats (IRs). We sequenced cpDNA for seven species of the short-globose cacti of Mammillaria and de novo assembly revealed three novel structures in land plants. These structures have a large single copy (LSC) that is 2.5 to 10 times larger than the small single copy (SSC), and two IRs that contain strong differences in length and gene composition. Structure 1 is distinguished by short IRs of <1 kb composed by rpl23-trnI-CAU-ycf2; with a total length of 110,189 bp and 113 genes. In structure 2, each IR is approximately 7.2 kb and is composed of 11 genes and one Intergenic Spacer-(psbK-trnQ)-trnQ-UUG-rps16-trnK-UUU-matK-trnK-UUU-psbA-trnH-GUG-rpl2-rpl23-trnI-CAU-ycf2; with a total size of 116,175 bp and 120 genes. Structure 3 has divergent IRs of approximately 14.1 kb, where IRA is composed of 20 genes: psbA-trnH-GUG-rpl23-trnI-CAU-ycf2-ndhB-rps7-rps12-trnV-GAC-rrn16-ycf68-trnI-GAU-trnA-AGC-rrn23-rrn4.5-rrn5-trnR-ACG-trnN-GUU-ndhF-rpl32; and IRB is identical to the IRA, but lacks rpl23. This structure has 131 genes and, by pseudogenization, it is shown to have the shortest cpDNA, of just 107,343 bp. Our findings show that Mammillaria bears an unusual structural diversity of cpDNA, which supports the elucidation of the evolutionary processes involved in cacti lineages. Full article
(This article belongs to the Special Issue Plant Organelle DNA Maintenance)
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Review

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Open AccessReview
Plant Organelle Genome Replication
Plants 2019, 8(10), 358; https://doi.org/10.3390/plants8100358 - 21 Sep 2019
Abstract
Mitochondria and chloroplasts perform essential functions in respiration, ATP production, and photosynthesis, and both organelles contain genomes that encode only some of the proteins that are required for these functions. The proteins and mechanisms for organelle DNA replication are very similar to bacterial [...] Read more.
Mitochondria and chloroplasts perform essential functions in respiration, ATP production, and photosynthesis, and both organelles contain genomes that encode only some of the proteins that are required for these functions. The proteins and mechanisms for organelle DNA replication are very similar to bacterial or phage systems. The minimal replisome may consist of DNA polymerase, a primase/helicase, and a single-stranded DNA binding protein (SSB), similar to that found in bacteriophage T7. In Arabidopsis, there are two genes for organellar DNA polymerases and multiple potential genes for SSB, but there is only one known primase/helicase protein to date. Genome copy number varies widely between type and age of plant tissues. Replication mechanisms are only poorly understood at present, and may involve multiple processes, including recombination-dependent replication (RDR) in plant mitochondria and perhaps also in chloroplasts. There are still important questions remaining as to how the genomes are maintained in new organelles, and how genome copy number is determined. This review summarizes our current understanding of these processes. Full article
(This article belongs to the Special Issue Plant Organelle DNA Maintenance)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Manuscript type: Review

Title: Maintenance of organelle genome stability in the moss Physcomitrella patens

Author: Masaki Odahara (Biomacromolecules Research Team, CSRS, RIKEN)

Abstract: Organelle genomes are essential for plants, however, the mechanism for the maintenance of organelle genomes is largely unknown. By using a basal land plant Physcomitrella patens as a model, nuclear-encoded homologs of bacterial-type homologous recombination repair factors have been shown to play an important role in the maintenance of organelle stability by suppressing recombination between short dispersed repeats. In this review, I summarize the factors and pathways for the maintenance mechanisms as well as the repeats that cause genome instability, and compare them with the findings from other plants. I also discuss the relationship between HRR factors and the structure of organelle genomes from the viewpoint of evolution.

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