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Organelle Genetics in Plants

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

Deadline for manuscript submissions: closed (30 June 2020) | Viewed by 51952

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Prof. Dr. Víctor Quesada

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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

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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

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Dear Colleagues,

Most of the DNA of eukaryotes is located in the nucleus. However, the 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 to that 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 the 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 has to 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.

Assoc. Prof. Dr. Víctor Quesada Pérez
Assoc. Prof. Dr. Pedro Robles
Guest Editors

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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.

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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

Published Papers (12 papers)

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Editorial

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5 pages, 218 KiB

Open AccessEditorial

Organelle Genetics in Plants

by Pedro Robles and Víctor Quesada

Int. J. Mol. Sci. 2021, 22(4), 2104; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22042104 - 20 Feb 2021

Cited by 9 | Viewed by 2234

Abstract

Eleven published articles (4 reviews, 7 research papers) are collected in the Special Issue entitled “Organelle Genetics in Plants.” This selection of papers covers a wide range of topics related to chloroplasts and plant mitochondria research: (i) organellar gene expression (OGE) and, more specifically, chloroplast RNA editing in soybean, mitochondria RNA editing, and intron splicing in soybean during nodulation, as well as the study of the roles of transcriptional and posttranscriptional regulation of OGE in plant adaptation to environmental stress; (ii) analysis of the nuclear integrants of mitochondrial DNA (NUMTs) or plastid DNA (NUPTs); (iii) sequencing and characterization of mitochondrial and chloroplast genomes; (iv) recent advances in plastid genome engineering. Here we summarize the main findings of these works, which represent the latest research on the genetics, genomics, and biotechnology of chloroplasts and mitochondria. Full article

(This article belongs to the Special Issue Organelle Genetics in Plants)

Research

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16 pages, 1936 KiB

Open AccessArticle

Differential RNA Editing and Intron Splicing in Soybean Mitochondria during Nodulation

by Yuzhe Sun, Min Xie, Zhou Xu, Koon Chuen Chan, Jia Yi Zhong, Kejing Fan, Johanna Wong-Bajracharya, Hon-Ming Lam and Boon Leong Lim

Int. J. Mol. Sci. 2020, 21(24), 9378; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21249378 - 09 Dec 2020

Cited by 2 | Viewed by 2417

Abstract

Nitrogen fixation in soybean consumes a tremendous amount of energy, leading to substantial differences in energy metabolism and mitochondrial activities between nodules and uninoculated roots. While C-to-U RNA editing and intron splicing of mitochondrial transcripts are common in plant species, their roles in relation to nodule functions are still elusive. In this study, we performed RNA-seq to compare transcript profiles and RNA editing of mitochondrial genes in soybean nodules and roots. A total of 631 RNA editing sites were identified on mitochondrial transcripts, with 12% or 74 sites differentially edited among the transcripts isolated from nodules, stripped roots, and uninoculated roots. Eight out of these 74 differentially edited sites are located on the matR transcript, of which the degrees of RNA editing were the highest in the nodule sample. The degree of mitochondrial intron splicing was also examined. The splicing efficiencies of several introns in nodules and stripped roots were higher than in uninoculated roots. These include nad1 introns 2/3/4, nad4 intron 3, nad5 introns 2/3, cox2 intron 1, and ccmFc intron 1. A greater splicing efficiency of nad4 intron 1, a higher NAD4 protein abundance, and a reduction in supercomplex I + III₂ were also observed in nodules, although the causal relationship between these observations requires further investigation. Full article

(This article belongs to the Special Issue Organelle Genetics in Plants)

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15 pages, 2621 KiB

Open AccessArticle

Mutation of YL Results in a Yellow Leaf with Chloroplast RNA Editing Defect in Soybean

by Xiaowei Zhu, Yi Pan, Zhi Liu, Yucheng Liu, Deyi Zhong, Zongbiao Duan, Zhixi Tian, Baoge Zhu and Guoan Zhou

Int. J. Mol. Sci. 2020, 21(12), 4275; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21124275 - 16 Jun 2020

Cited by 11 | Viewed by 3212

Abstract

RNA editing plays a key role in organelle gene expression. Little is known about how RNA editing factors influence soybean plant development. Here, we report the isolation and characterization of a soybean yl (yellow leaf) mutant. The yl plants showed decreased chlorophyll accumulation, lower PS II activity, an impaired net photosynthesis rate, and an altered chloroplast ultrastructure. Fine mapping of YL uncovered a point mutation in Glyma.20G187000, which encodes a chloroplast-localized protein homologous to Arabidopsis thaliana (Arabidopsis) ORRM1. YL is mainly expressed in trifoliate leaves, and its deficiency affects the editing of multiple chloroplast RNA sites, leading to inferior photosynthesis in soybean. Taken together, these results demonstrate the importance of the soybean YL protein in chloroplast RNA editing and photosynthesis. Full article

(This article belongs to the Special Issue Organelle Genetics in Plants)

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20 pages, 2917 KiB

Open AccessArticle

Characterization and Analysis of the Mitochondrial Genome of Common Bean (Phaseolus vulgaris) by Comparative Genomic Approaches

by Changwei Bi, Na Lu, Yiqing Xu, Chunpeng He and Zuhong Lu

Int. J. Mol. Sci. 2020, 21(11), 3778; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21113778 - 27 May 2020

Cited by 41 | Viewed by 3160

Abstract

The common bean (Phaseolus vulgaris) is a major source of protein and essential nutrients for humans. To explore the genetic diversity and phylogenetic relationships of P. vulgaris, its complete mitochondrial genome (mitogenome) was sequenced and assembled. The mitogenome is 395,516 bp in length, including 31 unique protein-coding genes (PCGs), 15 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Among the 31 PCGs, four genes (mttB, nad1, nad4L, and rps10) use ACG as initiation codons, which are altered to standard initiation codons by RNA editing. In addition, the termination codon CGA in the ccmF_C gene is converted to UGA. Selective pressure analysis indicates that the ccmB, ccmF_C, rps1, rps10, and rps14 genes were under evolutionary positive selection. The proportions of five amino acids (Phe, Leu, Pro, Arg, and Ser) in the whole amino acid profile of the proteins in each mitogenome can be used to distinguish angiosperms from gymnosperms. Phylogenetic analyses show that P. vulgaris is evolutionarily closer to the Glycininae than other leguminous plants. The results of the present study not only provide an important opportunity to conduct further genomic breeding studies in the common bean, they also provide valuable information for future evolutionary and molecular studies of leguminous plants. Full article

(This article belongs to the Special Issue Organelle Genetics in Plants)

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17 pages, 7504 KiB

Open AccessArticle

Comparative Mitogenome Analysis of the Genus Trifolium Reveals Independent Gene Fission of ccmFn and Intracellular Gene Transfers in Fabaceae

by In-Su Choi, Tracey A. Ruhlman and Robert K. Jansen

Int. J. Mol. Sci. 2020, 21(6), 1959; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21061959 - 13 Mar 2020

Cited by 15 | Viewed by 3232

Abstract

The genus Trifolium is the largest of the tribe Trifolieae in the subfamily Papilionoideae (Fabaceae). The paucity of mitochondrial genome (mitogenome) sequences has hindered comparative analyses among the three genomic compartments of the plant cell (nucleus, mitochondrion and plastid). We assembled four mitogenomes from the two subgenera (Chronosemium and Trifolium) of the genus. The four Trifolium mitogenomes were compact (294,911–348,724 bp in length) and contained limited repetitive (6.6–8.6%) DNA. Comparison of organelle repeat content highlighted the distinct evolutionary trajectory of plastid genomes in a subset of Trifolium species. Intracellular gene transfer (IGT) was analyzed among the three genomic compartments revealing functional transfer of mitochondrial rps1 to nuclear genome along with other IGT events. Phylogenetic analysis based on mitochondrial and nuclear rps1 sequences revealed that the functional transfer in Trifolieae was independent from the event that occurred in robinioid clade that includes genus Lotus. A novel, independent fission event of ccmFn in Trifolium was identified, caused by a 59 bp deletion. Fissions of this gene reported previously in land plants were reassessed and compared with Trifolium. Full article

(This article belongs to the Special Issue Organelle Genetics in Plants)

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19 pages, 3776 KiB

Open AccessArticle

Intraspecific Variation within the Utricularia amethystina Species Morphotypes Based on Chloroplast Genomes

by Saura R. Silva, Daniel G. Pinheiro, Helen A. Penha, Bartosz J. Płachno, Todd P. Michael, Elliott J. Meer, Vitor F. O. Miranda and Alessandro M. Varani

Int. J. Mol. Sci. 2019, 20(24), 6130; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20246130 - 05 Dec 2019

Cited by 21 | Viewed by 4399

Abstract

Utricularia amethystina Salzm. ex A.St.-Hil. & Girard (Lentibulariaceae) is a highly polymorphic carnivorous plant taxonomically rearranged many times throughout history. Herein, the complete chloroplast genomes (cpDNA) of three U. amethystina morphotypes: purple-, white-, and yellow-flowered, were sequenced, compared, and putative markers for systematic, populations, and evolutionary studies were uncovered. In addition, RNA-Seq and RNA-editing analysis were employed for functional cpDNA evaluation. The cpDNA of three U. amethystina morphotypes exhibits typical quadripartite structure. Fine-grained sequence comparison revealed a high degree of intraspecific genetic variability in all morphotypes, including an exclusive inversion in the psbM and petN genes in U. amethystina yellow. Phylogenetic analyses indicate that U. amethystina morphotypes are monophyletic. Furthermore, in contrast to the terrestrial Utricularia reniformis cpDNA, the U. amethystina morphotypes retain all the plastid NAD(P)H-dehydrogenase (ndh) complex genes. This observation supports the hypothesis that the ndhs in terrestrial Utricularia were independently lost and regained, also suggesting that different habitats (aquatic and terrestrial) are not related to the absence of Utricularia ndhs gene repertoire as previously assumed. Moreover, RNA-Seq analyses recovered similar patterns, including nonsynonymous RNA-editing sites (e.g., rps14 and petB). Collectively, our results bring new insights into the chloroplast genome architecture and evolution of the photosynthesis machinery in the Lentibulariaceae. Full article

(This article belongs to the Special Issue Organelle Genetics in Plants)

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14 pages, 5908 KiB

Open AccessArticle

Gene Losses and Variations in Chloroplast Genome of Parasitic Plant Macrosolen and Phylogenetic Relationships within Santalales

by Liping Nie, Yingxian Cui, Liwei Wu, Jianguo Zhou, Zhichao Xu, Yonghua Li, Xiwen Li, Yu Wang and Hui Yao

Int. J. Mol. Sci. 2019, 20(22), 5812; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20225812 - 19 Nov 2019

Cited by 15 | Viewed by 3662

Abstract

Macrosolen plants are parasitic shrubs, several of which are important medicinal plants, that are used as folk medicine in some provinces of China. However, reports on Macrosolen are limited. In this study, the complete chloroplast genome sequences of Macrosolen cochinchinensis, Macrosolen tricolor and Macrosolen bibracteolatus are reported. The chloroplast genomes were sequenced by Illumina HiSeq X. The length of the chloroplast genomes ranged from 129,570 bp (M. cochinchinensis) to 126,621 bp (M. tricolor), with a total of 113 genes, including 35 tRNA, eight rRNA, 68 protein-coding genes, and two pseudogenes (ycf1 and rpl2). The simple sequence repeats are mainly comprised of A/T mononucleotide repeats. Comparative genome analyses of the three species detected the most divergent regions in the non-coding spacers. Phylogenetic analyses using maximum parsimony and maximum likelihood strongly supported the idea that Loranthaceae and Viscaceae are monophyletic clades. The data obtained in this study are beneficial for further investigations of Macrosolen in respect to evolution and molecular identification. Full article

(This article belongs to the Special Issue Organelle Genetics in Plants)

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14 pages, 5011 KiB

Open AccessArticle

Characterization of the Chloroplast Genome of Trentepohlia odorata (Trentepohliales, Chlorophyta), and Discussion of its Taxonomy

by Huan Zhu, Yuxin Hu, Feng Liu, Zhengyu Hu and Guoxiang Liu

Int. J. Mol. Sci. 2019, 20(7), 1774; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20071774 - 10 Apr 2019

Cited by 8 | Viewed by 4442

Abstract

Trentepohliales is an aerial order of Chlorophyta with approximately 80 species distributed mainly in tropical and subtropical regions. The taxonomy of this genus is quite difficult and presents a challenge for many phycologists. Although plentiful molecular data is available, most of the sequences are not identified at the species level. In the present study, we described a new specimen with detailed morphological data and identified it as Trentepohlia odorata. A phylogenetic analysis showed T. odorata as a novel lineage in Trentepohliales. T. odorata has the closest relationship with T. annulata, which is expected since sporangia of both species are without stalk cell and with dorsal pore. Species with such morphological characteristics may represent deep lineages in Trentepohliales. Although an increasing number of chloroplast genomes of Ulvophyceae have been reported in recent years, the whole plastome of Trentepohliales has not yet been reported. Thus, the chloroplast genome of Trentepohlia odorata was reported in the present study. The whole plastome was 399,372 bp in length, with 63 predicted protein-coding genes, 31 tRNAs, and 3 rRNAs. Additionally, we annotated 95 free-standing open reading frames, of which seven were annotated with plastid origins, 16 with eukaryotic genome origins, and 33 with bacterial genome origins. Four rpo genes (rpoA, rpoB, rpoC1, and rpoC2) were annotated within ORF clusters. These four genes were fragmented into several (partial) ORFs by in-frame stop codons. Additionally, we detected a frame shift mutation in the rpoB gene. The phylogenetic analysis supported that Trentepohliales clustered with Dasycladales and nested into the BDT clade (Bryopsidales, Dasycladales and Trentepohliales). Our results present the first whole chloroplast genome of a species of Trentepohliales and provided new data for understanding the evolution of the chloroplast genome in Ulvophyceae. Full article

(This article belongs to the Special Issue Organelle Genetics in Plants)

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Review

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16 pages, 748 KiB

Open AccessReview

The Role of Chloroplast Gene Expression in Plant Responses to Environmental Stress

by Yi Zhang, Aihong Zhang, Xiuming Li and Congming Lu

Int. J. Mol. Sci. 2020, 21(17), 6082; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21176082 - 24 Aug 2020

Cited by 43 | Viewed by 6287

Abstract

Chloroplasts are plant organelles that carry out photosynthesis, produce various metabolites, and sense changes in the external environment. Given their endosymbiotic origin, chloroplasts have retained independent genomes and gene-expression machinery. Most genes from the prokaryotic ancestors of chloroplasts were transferred into the nucleus over the course of evolution. However, the importance of chloroplast gene expression in environmental stress responses have recently become more apparent. Here, we discuss the emerging roles of the distinct chloroplast gene expression processes in plant responses to environmental stresses. For example, the transcription and translation of psbA play an important role in high-light stress responses. A better understanding of the connection between chloroplast gene expression and environmental stress responses is crucial for breeding stress-tolerant crops better able to cope with the rapidly changing environment. Full article

(This article belongs to the Special Issue Organelle Genetics in Plants)

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21 pages, 403 KiB

Open AccessReview

Plastid Transformation: How Does it Work? Can it Be Applied to Crops? What Can it Offer?

by Yihe Yu, Po-Cheng Yu, Wan-Jung Chang, Keke Yu and Choun-Sea Lin

Int. J. Mol. Sci. 2020, 21(14), 4854; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21144854 - 09 Jul 2020

Cited by 41 | Viewed by 7025

Abstract

In recent years, plant genetic engineering has advanced agriculture in terms of crop improvement, stress and disease resistance, and pharmaceutical biosynthesis. Cells from land plants and algae contain three organelles that harbor DNA: the nucleus, plastid, and mitochondria. Although the most common approach for many plant species is the introduction of foreign DNA into the nucleus (nuclear transformation) via Agrobacterium- or biolistics-mediated delivery of transgenes, plastid transformation offers an alternative means for plant transformation. Since there are many copies of the chloroplast genome in each cell, higher levels of protein accumulation can often be achieved from transgenes inserted in the chloroplast genome compared to the nuclear genome. Chloroplasts are therefore becoming attractive hosts for the introduction of new agronomic traits, as well as for the biosynthesis of high-value pharmaceuticals, biomaterials and industrial enzymes. This review provides a comprehensive historical and biological perspective on plastid transformation, with a focus on current and emerging approaches such as the use of single-walled carbon nanotubes (SWNTs) as DNA delivery vehicles, overexpressing morphogenic regulators to enhance regeneration ability, applying genome editing techniques to accelerate double-stranded break formation, and reconsidering protoplasts as a viable material for plastid genome engineering, even in transformation-recalcitrant species. Full article

(This article belongs to the Special Issue Organelle Genetics in Plants)

15 pages, 913 KiB

Open AccessReview

Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants

by Guo-Jun Zhang, Ran Dong, Li-Na Lan, Shu-Fen Li, Wu-Jun Gao and Hong-Xing Niu

Int. J. Mol. Sci. 2020, 21(3), 707; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21030707 - 21 Jan 2020

Cited by 29 | Viewed by 4972

Abstract

The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of plastid DNA (NUPTs). This frequently occurring DNA transfer is ongoing and has important evolutionary implications. In this review, based on previous studies and the analysis of NUMT/NUPT insertions of more than 200 sequenced plant genomes, we analyzed and summarized the general features of NUMTs/NUPTs and highlighted the genetic consequence of organellar DNA insertions. The statistics of organellar DNA integrants among various plant genomes revealed that organellar DNA-derived sequence content is positively correlated with the nuclear genome size. After integration, the nuclear organellar DNA could undergo different fates, including elimination, mutation, rearrangement, fragmentation, and proliferation. The integrated organellar DNAs play important roles in increasing genetic diversity, promoting gene and genome evolution, and are involved in sex chromosome evolution in dioecious plants. The integrating mechanisms, involving non-homologous end joining at double-strand breaks were also discussed. Full article

(This article belongs to the Special Issue Organelle Genetics in Plants)

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16 pages, 1154 KiB

Open AccessReview

Transcriptional and Post-transcriptional Regulation of Organellar Gene Expression (OGE) and Its Roles in Plant Salt Tolerance

by Pedro Robles and Víctor Quesada

Int. J. Mol. Sci. 2019, 20(5), 1056; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20051056 - 28 Feb 2019

Cited by 26 | Viewed by 5760

Abstract

Given their endosymbiotic origin, chloroplasts and mitochondria genomes harbor only between 100 and 200 genes that encode the proteins involved in organellar gene expression (OGE), photosynthesis, and the electron transport chain. However, as the activity of these organelles also needs a few thousand proteins encoded by the nuclear genome, a close coordination of the gene expression between the nucleus and organelles must exist. In line with this, OGE regulation is crucial for plant growth and development, and is achieved mainly through post-transcriptional mechanisms performed by nuclear genes. In this way, the nucleus controls the activity of organelles and these, in turn, transmit information about their functional state to the nucleus by modulating nuclear expression according to the organelles’ physiological requirements. This adjusts organelle function to plant physiological, developmental, or growth demands. Therefore, OGE must appropriately respond to both the endogenous signals and exogenous environmental cues that can jeopardize plant survival. As sessile organisms, plants have to respond to adverse conditions to acclimate and adapt to them. Salinity is a major abiotic stress that negatively affects plant development and growth, disrupts chloroplast and mitochondria function, and leads to reduced yields. Information on the effects that the disturbance of the OGE function has on plant tolerance to salinity is still quite fragmented. Nonetheless, many plant mutants which display altered responses to salinity have been characterized in recent years, and interestingly, several are affected in nuclear genes encoding organelle-localized proteins that regulate the expression of organelle genes. These results strongly support a link between OGE and plant salt tolerance, likely through retrograde signaling. Our review analyzes recent findings on the OGE functions required by plants to respond and tolerate salinity, and highlights the fundamental role that chloroplast and mitochondrion homeostasis plays in plant adaptation to salt stress. Full article

(This article belongs to the Special Issue Organelle Genetics in Plants)

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