Plant Organelle DNA Maintenance

Ahmad, Niaz; Nielsen, Brent L.

doi:10.3390/plants9060683

Cited by 4 publications

(7 citation statements)

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“…Chloroplast and mitochondrial genes are preferred over nuclear genes because most of the genes lack introns, and they are generally haploid [ 40 ]. Furthermore, each cell has many chloroplasts and mitochondria, and each one can contain several copies of the respective genome [ 41 , 42 , 43 ]. Thus, when sample tissue is limited, the chloroplast and the mitochondrion offer relatively abundant sources of DNA.…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales

Mäder¹,

Schroeder²,

Schott³

et al. 2020

Plants

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European beech, Fagus sylvatica L., is one of the most important and widespread deciduous tree species in Central Europe and is widely managed for its hard wood. The complete DNA sequence of the mitochondrial genome of Fagus sylvatica L. was assembled and annotated based on Illumina MiSeq reads and validated using long reads from nanopore MinION sequencing. The genome assembled into a single DNA sequence of 504,715 bp in length containing 58 genes with predicted function, including 35 protein-coding, 20 tRNA and three rRNA genes. Additionally, 23 putative protein-coding genes were predicted supported by RNA-Seq data. Aiming at the development of taxon-specific mitochondrial genetic markers, the tool SNPtax was developed and applied to select genic SNPs potentially specific for different taxa within the Fagales. Further validation of a small SNP set resulted in the development of four CAPS markers specific for Fagus, Fagaceae, or Fagales, respectively, when considering over 100 individuals from a total of 69 species of deciduous trees and conifers from up to 15 families included in the marker validation. The CAPS marker set is suitable to identify the genus Fagus in DNA samples from tree tissues or wood products, including wood composite products.

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Section: Introductionmentioning

confidence: 99%

Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales

Mäder¹,

Schroeder²,

Schott³

et al. 2020

Plants

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“…Therefore, maintenance of the stability of the organellar genome along with the nuclear genome is an absolute requirement for plants for sustaining their normal growth and development. Thus, as like the nuclear genome, faithful replication and repair of organellar genomes are also crucial to avoid genome instability, which may eventually cause potentially detrimental effects on phenotypes ( Ahmad and Nielsen, 2020 ). To maintain genome integrity under adverse conditions, plant mitochondria and chloroplast have evolved with an extensive regulatory mechanisms to counteract the deleterious effects of DNA damage ( Maréchal and Brisson, 2010 ; Oldenburg and Bendich, 2015 ; Ahmad and Nielsen, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

“…Thus, as like the nuclear genome, faithful replication and repair of organellar genomes are also crucial to avoid genome instability, which may eventually cause potentially detrimental effects on phenotypes ( Ahmad and Nielsen, 2020 ). To maintain genome integrity under adverse conditions, plant mitochondria and chloroplast have evolved with an extensive regulatory mechanisms to counteract the deleterious effects of DNA damage ( Maréchal and Brisson, 2010 ; Oldenburg and Bendich, 2015 ; Ahmad and Nielsen, 2020 ). Plant mitochondria and chloroplast have been found to possess well-developed base excision repair (BER) pathways, comparable to the nuclear genome to cope up with different forms of oxidative DNA damages ( Boesch et al, 2009 ; Peralta-Castro et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

“…The endosymbiotic origin of mitochondria and chloroplast from cyanobacteria and α-proteobacteria, respectively has indicated the presence of prokaryotic mode of replication and repair machineries in both the organelles ( Ahmad and Nielsen, 2020 ). However, these replication or recombination/repair proteins, which participate in genome stability maintenance mechanisms in mitochondria and chloroplast, are encoded by either of these organellar genomes ( Morley et al, 2019 ; Brieba, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

“…However, these replication or recombination/repair proteins, which participate in genome stability maintenance mechanisms in mitochondria and chloroplast, are encoded by either of these organellar genomes ( Morley et al, 2019 ; Brieba, 2019 ). Analyses of the replication and repair machinery in mitochondria and chloroplast have revealed that the protein components involved in replication and repair machinery are mainly encoded by the nuclear genome and then subsequently targeted to the respective organelle ( Saki and Prakash, 2017 ; Ahmad and Nielsen, 2020 ; Duan et al, 2020 ). Except for about 13 mitochondrial genome encoded proteins, more than 1500 proteins in the overall mitochondrial proteome are encoded by various nuclear genes and are targeted to mitochondria for maintenance of mitochondrial genome stability ( Chacinska et al, 2009 ; Van Houten et al, 2016 ; Saki and Prakash, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

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An Insight Into the Mechanism of Plant Organelle Genome Maintenance and Implications of Organelle Genome in Crop Improvement: An Update

Mahapatra

Banerjee

et al. 2021

Front. Cell Dev. Biol.

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Besides the nuclear genome, plants possess two small extra chromosomal genomes in mitochondria and chloroplast, respectively, which contribute a small fraction of the organelles’ proteome. Both mitochondrial and chloroplast DNA have originated endosymbiotically and most of their prokaryotic genes were either lost or transferred to the nuclear genome through endosymbiotic gene transfer during the course of evolution. Due to their immobile nature, plant nuclear and organellar genomes face continuous threat from diverse exogenous agents as well as some reactive by-products or intermediates released from various endogenous metabolic pathways. These factors eventually affect the overall plant growth and development and finally productivity. The detailed mechanism of DNA damage response and repair following accumulation of various forms of DNA lesions, including single and double-strand breaks (SSBs and DSBs) have been well documented for the nuclear genome and now it has been extended to the organelles also. Recently, it has been shown that both mitochondria and chloroplast possess a counterpart of most of the nuclear DNA damage repair pathways and share remarkable similarities with different damage repair proteins present in the nucleus. Among various repair pathways, homologous recombination (HR) is crucial for the repair as well as the evolution of organellar genomes. Along with the repair pathways, various other factors, such as the MSH1 and WHIRLY family proteins, WHY1, WHY2, and WHY3 are also known to be involved in maintaining low mutation rates and structural integrity of mitochondrial and chloroplast genome. SOG1, the central regulator in DNA damage response in plants, has also been found to mediate endoreduplication and cell-cycle progression through chloroplast to nucleus retrograde signaling in response to chloroplast genome instability. Various proteins associated with the maintenance of genome stability are targeted to both nuclear and organellar compartments, establishing communication between organelles as well as organelles and nucleus. Therefore, understanding the mechanism of DNA damage repair and inter compartmental crosstalk mechanism in various sub-cellular organelles following induction of DNA damage and identification of key components of such signaling cascades may eventually be translated into strategies for crop improvement under abiotic and genotoxic stress conditions. This review mainly highlights the current understanding as well as the importance of different aspects of organelle genome maintenance mechanisms in higher plants.

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The relative copy number of mitochondrial and chloroplast DNA in young and mature leaves of different grape varieties

Vodolazhsky,

Kryukov

2023

BIO Web of Conferences

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The copy number of DNA matrices of subcellular organelles (plants) can serve as an indicator of the intensity of photosynthesis and oxidative phosphorylation processes. We assessed the relative copy numbers (RCN) of mitochondrial and chloroplast DNA in young and mature leaves of three grape varieties: ‘Traminer Pink’, ‘Chardonnay’, and ‘Syrah’, grown under field conditions. Leaf samples (5–10 mg) were randomly selected from each group of plants for subsequent total DNA extraction. The qRTPCR reaction was performed using LightCycler 480 SYBR Green I Master Mix (LifeScience, Roche) and a LightCycler 96 Automatic Analyzer (Roche Life Science). The relative copy numbers of the NAD1 gene (mitochondrial DNA) and rps16 gene (chloroplast DNA) were determined using the GAPDH gene (chromosomal DNA) as a reference. Quantitative assessment was conducted using the 2--Ct и 2---Ct algorithms. It has been established that the relative copy number (RCN) values of chloroplast and mitochondrial DNA vary and depend on the grape variety and leaf maturity. RCN of chloroplast and mitochondrial DNA is significantly higher in mature grape leaves of all studied varieties, indicating a higher intensity of photosynthesis and oxidative phosphorylation in mature grape leaves compared to young leaves. When assessing the MacroErgic Balance (MEB) indicator, it can be concluded that from 2 to 4% of the energy obtained in chloroplasts through photosynthetic processes is used for the production of macroergic compounds in the mitochondria of various grape varieties in both young and mature leaves. The experimental scheme we have developed can be successfully used as a testing system to assess the potential yield of various grape varieties.

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Plant Organelle DNA Maintenance

Cited by 4 publications

References 8 publications

Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales

Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales

An Insight Into the Mechanism of Plant Organelle Genome Maintenance and Implications of Organelle Genome in Crop Improvement: An Update

The relative copy number of mitochondrial and chloroplast DNA in young and mature leaves of different grape varieties

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