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Organelle Genetics in Plants 2.0
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Organelle Genetics in Plants 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 18778

Special Issue Editors

Prof. Dr. Víctor Quesada

E-Mail Website
Guest Editor
Instituto de Bioingeniería, Universidad Miguel Hernandez de Elche, 3202 Elche, Spain
Interests: genetics; plant development; abiotic stress; arabidopsis; chloroplast biogenesis; mTERF; organelle gene expression
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Pedro Robles

E-Mail Website
Guest Editor
Instituto de Bioingeniería, Universidad Miguel Hernandez de Elche, 3202 Elche, Spain
Interests: plant genetics; leaf and fruit development; Arabidopsis; organelles and development, mTERF, chlororibosome; organelles stress sensors
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Most of the DNA of eukaryotes is located in the nucleus. However, chloroplasts in photosynthetic organisms and mitochondria in a vast majority of eukaryotes also contain part of the genetic material of a eukaryotic cell. The organisation and inheritance patterns of this organellar DNA are quite different from those of nuclear DNA.

The presence of DNA in chloroplasts and mitochondria reveals their evolutionary origin. Considerable phylogenetic evidence supports the hypothesis that both organelles come from ancestral free-living prokaryotes that established an endosymbiotic relationship with a primitive eukaryotic cell. Most genes of ancestral prokaryotes were transferred to the nucleus of the host cell throughout evolution. Consequently, present-day chloroplast and mitochondrial genomes contain only a few dozen genes, required for ATP synthesis, photosynthesis, and gene expression. Nevertheless, chloroplasts and mitochondria harbour several thousand proteins, of which the vast majority are encoded by the nucleus and are, hence, synthesised in the cytoplasm and subsequently transported to their target organelle. As a result, the expression of nuclear and organelle genomes must be very precisely coordinated.

This Special Issue encourages the publication of both experimental and review papers principally from a molecular genetics and/or mutational perspective, covering a wide range of topics in chloroplast and plant mitochondria research: replication and dynamics of nucleoids, transcriptional and posttranscriptional regulation of gene expression in organelles, organelle translation, protein import into organelles, retrograde and anterograde signalling pathways, organelle biogenesis and plant development, organelle genome sequencing and databases, organelle evolution, and technical advances in organelle biotechnology. Other related topics are also welcome.

Prof. Dr. Victor Manuel Quesada-Pérez
Prof. Dr. Pedro Robles
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • Chloroplast and mitochondria biogenesis
  • Evolution of organelles
  • Organelle nucleoids
  • Posttranscriptional regulation in organelles
  • Protein import into mitochondria and chloroplasts
  • Sequencing of organelle genomes
  • Retrograde and anterograde signalling pathways
  • Technical advances in organelle biotechnology
  • Transcriptional regulation in organelles
  • Translation in organelles

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Published Papers (7 papers)

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Editorial

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4 pages, 213 KiB  
Editorial
Organelle Genetics in Plants 2.0
by Pedro Robles and Víctor Quesada
Int. J. Mol. Sci. 2023, 24(15), 12128; https://doi.org/10.3390/ijms241512128 - 28 Jul 2023
Viewed by 821
Abstract
Most of the DNA of eukaryotes is located in the nucleus [...] Full article
(This article belongs to the Special Issue Organelle Genetics in Plants 2.0)

Research

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15 pages, 3165 KiB  
Article
Comparative Mitogenomic Analysis Reveals Gene and Intron Dynamics in Rubiaceae and Intra-Specific Diversification in Damnacanthus indicus
by Eun-Kyeong Han, Won-Bum Cho, Ichiro Tamaki, In-Su Choi and Jung-Hyun Lee
Int. J. Mol. Sci. 2021, 22(13), 7237; https://doi.org/10.3390/ijms22137237 - 5 Jul 2021
Cited by 7 | Viewed by 2997
Abstract
The dynamic evolution of mitochondrial gene and intron content has been reported across the angiosperms. However, a reference mitochondrial genome (mitogenome) is not available in Rubiaceae. The phylogenetic utility of mitogenome data at a species level is rarely assessed. Here, we assembled mitogenomes [...] Read more.
The dynamic evolution of mitochondrial gene and intron content has been reported across the angiosperms. However, a reference mitochondrial genome (mitogenome) is not available in Rubiaceae. The phylogenetic utility of mitogenome data at a species level is rarely assessed. Here, we assembled mitogenomes of six Damnacanthus indicus (Rubiaceae, Rubioideae) representing two varieties (var. indicus and var. microphyllus). The gene and intron content of D. indicus was compared with mitogenomes from representative angiosperm species and mitochondrial contigs from the other Rubiaceae species. Mitogenome structural rearrangement and sequence divergence in D. indicus were analyzed in six individuals. The size of the mitogenome in D. indicus varied from 417,661 to 419,435 bp. Comparing the number of intact mitochondrial protein-coding genes in other Gentianales taxa (38), D. indicus included 32 genes representing several losses. The intron analysis revealed a shift from cis to trans splicing of a nad1 intron (nad1i728) in D. indicus and it is a shared character with the other four Rubioideae taxa. Two distinct mitogenome structures (type A and B) were identified. Two-step direct repeat-mediated recombination was proposed to explain structural changes between type A and B mitogenomes. The five individuals from two varieties in D. indicus diverged well in the whole mitogenome-level comparison with one exception. Collectively, our study elucidated the mitogenome evolution in Rubiaceae along with D. indicus and showed the reliable phylogenetic utility of the whole mitogenome data at a species-level evolution. Full article
(This article belongs to the Special Issue Organelle Genetics in Plants 2.0)
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20 pages, 5572 KiB  
Article
Structural Mutations in the Organellar Genomes of Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara Show Dynamic Gene Transfer
by Hyoung Tae Kim and Jung Sung Kim
Int. J. Mol. Sci. 2021, 22(7), 3770; https://doi.org/10.3390/ijms22073770 - 5 Apr 2021
Cited by 3 | Viewed by 2243
Abstract
Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara is a broad-leaved valerian endemic to Ulleung Island, a noted hot spot of endemism in Korea. However, despite its widespread pharmacological use, this plant remains comparatively understudied. Plant cells generally contain two types of organellar [...] Read more.
Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara is a broad-leaved valerian endemic to Ulleung Island, a noted hot spot of endemism in Korea. However, despite its widespread pharmacological use, this plant remains comparatively understudied. Plant cells generally contain two types of organellar genomes (the plastome and the mitogenome) that have undergone independent evolution, which accordingly can provide valuable information for elucidating the phylogenetic relationships and evolutionary histories of terrestrial plants. Moreover, the extensive mega-data available for plant genomes, particularly those of plastomes, can enable researchers to gain an in-depth understanding of the transfer of genes between different types of genomes. In this study, we analyzed two organellar genomes (the 155,179 bp plastome and the 1,187,459 bp mitogenome) of V. sambucifolia f. dageletiana and detected extensive changes throughout the plastome sequence, including rapid structural mutations associated with inverted repeat (IR) contraction and genetic variation. We also described features characterizing the first reported mitogenome sequence obtained for a plant in the order Dipsacales and confirmed frequent gene transfer in this mitogenome. We identified eight non-plastome-originated regions (NPRs) distributed within the plastome of this endemic plant, for six of which there were no corresponding sequences in the current nucleotide sequence databases. Indeed, one of these unidentified NPRs unexpectedly showed certain similarities to sequences from bony fish. Although this is ostensibly difficult to explain, we suggest that this surprising association may conceivably reflect the occurrence of gene transfer from a bony fish to the plastome of an ancestor of V. sambucifolia f. dageletiana mediated by either fungi or bacteria. Full article
(This article belongs to the Special Issue Organelle Genetics in Plants 2.0)
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17 pages, 29282 KiB  
Article
A PPR Protein ACM1 Is Involved in Chloroplast Gene Expression and Early Plastid Development in Arabidopsis
by Xinwei Wang, Yaqi An, Ye Li and Jianwei Xiao
Int. J. Mol. Sci. 2021, 22(5), 2512; https://doi.org/10.3390/ijms22052512 - 3 Mar 2021
Cited by 9 | Viewed by 2824
Abstract
Chloroplasts cannot develop normally without the coordinated action of various proteins and signaling connections between the nucleus and the chloroplast genome. Many questions regarding these processes remain unanswered. Here, we report a novel P-type pentatricopeptide repeat (PPR) factor, named Albino Cotyledon Mutant1 (ACM1), [...] Read more.
Chloroplasts cannot develop normally without the coordinated action of various proteins and signaling connections between the nucleus and the chloroplast genome. Many questions regarding these processes remain unanswered. Here, we report a novel P-type pentatricopeptide repeat (PPR) factor, named Albino Cotyledon Mutant1 (ACM1), which is encoded by a nuclear gene and involved in chloroplast development. Knock-down of ACM1 transgenic plants displayed albino cotyledons but normal true leaves, while knock-out of the ACM1 gene in seedlings was lethal. Fluorescent protein analysis showed that ACM1 was specifically localized within chloroplasts. PEP-dependent plastid transcript levels and splicing efficiency of several group II introns were seriously affected in cotyledons in the RNAi line. Furthermore, denaturing gel electrophoresis and Western blot experiments showed that the accumulation of chloroplast ribosomes was probably damaged. Collectively, our results indicate ACM1 is indispensable in early chloroplast development in Arabidopsis cotyledons. Full article
(This article belongs to the Special Issue Organelle Genetics in Plants 2.0)
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19 pages, 3391 KiB  
Article
Clade-Specific Plastid Inheritance Patterns Including Frequent Biparental Inheritance in Passiflora Interspecific Crosses
by Bikash Shrestha, Lawrence E. Gilbert, Tracey A. Ruhlman and Robert K. Jansen
Int. J. Mol. Sci. 2021, 22(5), 2278; https://doi.org/10.3390/ijms22052278 - 25 Feb 2021
Cited by 11 | Viewed by 2375
Abstract
Plastid inheritance in angiosperms is presumed to be largely maternal, with the potential to inherit plastids biparentally estimated for about 20% of species. In Passiflora, maternal, paternal and biparental inheritance has been reported; however, these studies were limited in the number of [...] Read more.
Plastid inheritance in angiosperms is presumed to be largely maternal, with the potential to inherit plastids biparentally estimated for about 20% of species. In Passiflora, maternal, paternal and biparental inheritance has been reported; however, these studies were limited in the number of crosses and progeny examined. To improve the understanding of plastid transmission in Passiflora, the progeny of 45 interspecific crosses were analyzed in the three subgenera: Passiflora, Decaloba and Astrophea. Plastid types were assessed following restriction digestion of PCR amplified plastid DNA in hybrid embryos, cotyledons and leaves at different developmental stages. Clade-specific patterns of inheritance were detected such that hybrid progeny from subgenera Passiflora and Astrophea predominantly inherited paternal plastids with occasional incidences of maternal inheritance, whereas subgenus Decaloba showed predominantly maternal and biparental inheritance. Biparental plastid inheritance was also detected in some hybrids from subgenus Passiflora. Heteroplasmy due to biparental inheritance was restricted to hybrid cotyledons and first leaves with a single parental plastid type detectable in mature plants. This indicates that in Passiflora, plastid retention at later stages of plant development may not reflect the plastid inheritance patterns in embryos. Passiflora exhibits diverse patterns of plastid inheritance, providing an excellent system to investigate underlying mechanisms in angiosperms. Full article
(This article belongs to the Special Issue Organelle Genetics in Plants 2.0)
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Review

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13 pages, 804 KiB  
Review
Contribution of Massive Mitochondrial Fusion and Subsequent Fission in the Plant Life Cycle to the Integrity of the Mitochondrion and Its Genome
by Ray J. Rose
Int. J. Mol. Sci. 2021, 22(11), 5429; https://doi.org/10.3390/ijms22115429 - 21 May 2021
Cited by 16 | Viewed by 3387
Abstract
Plant mitochondria have large genomes to house a small number of key genes. Most mitochondria do not contain a whole genome. Despite these latter characteristics, the mitochondrial genome is faithfully maternally inherited. To maintain the mitochondrial genes—so important for energy production—the fusion and [...] Read more.
Plant mitochondria have large genomes to house a small number of key genes. Most mitochondria do not contain a whole genome. Despite these latter characteristics, the mitochondrial genome is faithfully maternally inherited. To maintain the mitochondrial genes—so important for energy production—the fusion and fission of mitochondria are critical. Fission in plants is better understood than fusion, with the dynamin-related proteins (DRP 3A and 3B) driving the constriction of the mitochondrion. How the endoplasmic reticulum and the cytoskeleton are linked to the fission process is not yet fully understood. The fusion mechanism is less well understood, as obvious orthologues are not present. However, there is a recently described gene, MIRO2, that appears to have a significant role, as does the ER and cytoskeleton. Massive mitochondrial fusion (MMF or hyperfusion) plays a significant role in plants. MMF occurs at critical times of the life cycle, prior to flowering, in the enlarging zygote and at germination, mixing the cells’ mitochondrial population—the so-called “discontinuous whole”. MMF in particular aids genome repair, the conservation of critical genes and possibly gives an energy boost to important stages of the life cycle. MMF is also important in plant regeneration, an important component of plant biotechnology. Full article
(This article belongs to the Special Issue Organelle Genetics in Plants 2.0)
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Other

10 pages, 1302 KiB  
Perspective
A Structural Perspective on the RNA Editing of Plant Respiratory Complexes
by Maria Maldonado, Kaitlyn Madison Abe and James Anthony Letts
Int. J. Mol. Sci. 2022, 23(2), 684; https://doi.org/10.3390/ijms23020684 - 8 Jan 2022
Cited by 10 | Viewed by 2546
Abstract
The last steps of respiration, a core energy-harvesting process, are carried out by a chain of multi-subunit complexes in the inner mitochondrial membrane. Several essential subunits of the respiratory complexes are RNA-edited in plants, frequently leading to changes in the encoded amino acids. [...] Read more.
The last steps of respiration, a core energy-harvesting process, are carried out by a chain of multi-subunit complexes in the inner mitochondrial membrane. Several essential subunits of the respiratory complexes are RNA-edited in plants, frequently leading to changes in the encoded amino acids. While the impact of RNA editing is clear at the sequence and phenotypic levels, the underlying biochemical explanations for these effects have remained obscure. Here, we used the structures of plant respiratory complex I, complex III2 and complex IV to analyze the impact of the amino acid changes of RNA editing in terms of their location and biochemical features. Through specific examples, we demonstrate how the structural information can explain the phenotypes of RNA-editing mutants. This work shows how the structural perspective can bridge the gap between sequence and phenotype and provides a framework for the continued analysis of RNA-editing mutants in plant mitochondria and, by extension, in chloroplasts. Full article
(This article belongs to the Special Issue Organelle Genetics in Plants 2.0)
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