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Chloroplast Development and Function

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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 (31 December 2020) | Viewed by 36537

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Dr. Koichi Kobayashi

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Faculty of Liberal Arts and Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Japan
Interests: plant; chloroplast; thylakoid; photosynthesis; membrane lipids; chlorophyll
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Special Issue Information

Dear Colleagues,

Chloroplasts, the photosynthetic organelles in plant and algal cells, are the prototypical members of the plastids. Reflecting their endosymbiotic origin from a cyanobacterial ancestor, plastids retain their own genome, carrying ~120–135 genes, which include genes encoding core photosynthetic proteins and those for genetic machinery. Most of the proteins functioning in chloroplasts are encoded in the nucleus and are transported to chloroplasts after translation in the cytosol. Therefore, coordinated regulation of nuclear genes and plastid genes is essential for the development and function of chloroplasts. Photosynthetic activity in chloroplasts determines the productivity of plants, but with a potential risk of photooxidative damage to photosynthetic cells, so the functionality of chloroplasts is strictly regulated according to growth conditions and developmental stages. Moreover, chloroplasts are involved in diverse metabolic activities such as the biosynthesis of amino acids, lipids, tetrapyrroles, and hormones, and thus studies of chloroplast development and function include a broad spectrum of cellular and organellar processes.

This Special Issue seeks research and review articles with a focus on chloroplast development and function in plants and algae, but also will cover a wide range of topics related to molecular biology, physiology, biochemistry, and the genetics of chloroplasts.

Dr. Koichi Kobayashi
Guest Editor

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Keywords

Alga;
Chlorophyll;
Cyanobacterium;
Endosymbiosis;
Photosynthesis;
Plant;
Plastid;
Thylakoid membrane.

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Published Papers (10 papers)

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19 pages, 4763 KiB

Open AccessArticle

Plastid Anionic Lipids Are Essential for the Development of Both Photosynthetic and Non-Photosynthetic Organs in Arabidopsis thaliana

by Akiko Yoshihara, Noriko Nagata, Hajime Wada and Koichi Kobayashi

Int. J. Mol. Sci. 2021, 22(9), 4860; https://doi.org/10.3390/ijms22094860 - 4 May 2021

Cited by 10 | Viewed by 3317

Abstract

The lipid bilayer matrix of the thylakoid membrane of cyanobacteria and chloroplasts of plants and algae is mainly composed of uncharged galactolipids, but also contains anionic lipids sulfoquinovosyldiacylglycerol (SQDG) and phosphatidylglycerol (PG) as major constituents. The necessity of PG for photosynthesis is evident in all photosynthetic organisms examined to date, whereas the requirement of SQDG varies with species. In plants, although PG and SQDG are also found in non-photosynthetic plastids, their importance for the growth and functions of non-photosynthetic organs remains unclear. In addition, plants synthesize another anionic lipid glucuronosyldiacylglycerol (GlcADG) during phosphorus starvation, but its role in plant cells is not elucidated yet. To understand the functional relationships among PG, SQDG, and GlcADG, we characterized several Arabidopsis thaliana mutants defective in biosynthesis of these lipids. The mutants completely lacking both PG and SQDG biosynthesis in plastids showed developmental defects of roots, hypocotyls, and embryos in addition to leaves, which suggests that these lipids are pleiotropically required for the development of both photosynthetic and non-photosynthetic organs. Furthermore, our analysis revealed that SQDG, but not GlcADG, is essential for complementing the role of PG, particularly in photosynthesis under PG-deficient conditions such as phosphorus starvation. Full article

(This article belongs to the Special Issue Chloroplast Development and Function)

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16 pages, 47637 KiB

Open AccessArticle

The Photosystem II Assembly Factor Ycf48 from the Cyanobacterium Synechocystis sp. PCC 6803 Is Lipidated Using an Atypical Lipobox Sequence

by Jana Knoppová, Jianfeng Yu, Jan Janouškovec, Petr Halada, Peter J. Nixon, Julian P. Whitelegge and Josef Komenda

Int. J. Mol. Sci. 2021, 22(7), 3733; https://doi.org/10.3390/ijms22073733 - 2 Apr 2021

Cited by 8 | Viewed by 3340

Abstract

Photochemical energy conversion during oxygenic photosynthesis is performed by membrane-embedded chlorophyll-binding protein complexes. The biogenesis and maintenance of these complexes requires auxiliary protein factors that optimize the assembly process and protect nascent complexes from photodamage. In cyanobacteria, several lipoproteins contribute to the biogenesis and function of the photosystem II (PSII) complex. They include CyanoP, CyanoQ, and Psb27, which are all attached to the lumenal side of PSII complexes. Here, we show that the lumenal Ycf48 assembly factor found in the cyanobacterium Synechocystis sp. PCC 6803 is also a lipoprotein. Detailed mass spectrometric analysis of the isolated protein supported by site-directed mutagenesis experiments indicates lipidation of the N-terminal C29 residue of Ycf48 and removal of three amino acids from the C-terminus. The lipobox sequence in Ycf48 contains a cysteine residue at the −3 position compared to Leu/Val/Ile residues found in the canonical lipobox sequence. The atypical Ycf48 lipobox sequence is present in most cyanobacteria but is absent in eukaryotes. A possible role for lipoproteins in the coordinated assembly of cyanobacterial PSII is discussed. Full article

(This article belongs to the Special Issue Chloroplast Development and Function)

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23 pages, 3188 KiB

Open AccessArticle

ZnJ6 Is a Thylakoid Membrane DnaJ-Like Chaperone with Oxidizing Activity in Chlamydomonas reinhardtii

by Richa Amiya and Michal Shapira

Int. J. Mol. Sci. 2021, 22(3), 1136; https://doi.org/10.3390/ijms22031136 - 24 Jan 2021

Cited by 5 | Viewed by 2998

Abstract

Assembly of photosynthetic complexes is sensitive to changing light intensities, drought and pathogens, each of which induces a redox imbalance that requires the assistance of specific chaperones to maintain protein structure. Here we report a thylakoid membrane-associated DnaJ-like protein, ZnJ6 (Cre06.g251716.t1.2), in Chlamydomonas reinhardtii. The protein has four CXXCX(G)X(G) motifs that form two zinc fingers (ZFs). Site-directed mutagenesis (Cys > Ser) eliminates the ability to bind zinc. An intact ZF is required for ZnJ6 stability at elevated temperatures. Chaperone assays with recombinant ZnJ6 indicate that it has holding and oxidative activities. ZnJ6 is unable to reduce the disulfide bonds of insulin but prevents its aggregation in a reducing environment. It also assists in the reactivation of reduced denatured RNaseA, possibly by its oxidizing activity. ZnJ6 pull-down assays revealed interactions with oxidoreductases, photosynthetic proteins and proteases. In vivo experiments with a C. reinhardtii insertional mutant (∆ZnJ6) indicate enhanced tolerance to oxidative stress but increased sensitivity to heat and reducing conditions. Moreover, ∆ZnJ6 has reduced photosynthetic efficiency shown by the Chlorophyll fluorescence transient. Taken together, we identify a role for this thylakoid-associated DnaJ-like oxidizing chaperone that assists in the prevention of protein misfolding and aggregation, thus contributing to stress endurance, redox maintenance and photosynthetic balance. Full article

(This article belongs to the Special Issue Chloroplast Development and Function)

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22 pages, 10821 KiB

Open AccessArticle

Plastid Genomes of the Early Vascular Plant Genus Selaginella Have Unusual Direct Repeat Structures and Drastically Reduced Gene Numbers

by Hyeonah Shim, Hyeon Ju Lee, Junki Lee, Hyun-Oh Lee, Jong-Hwa Kim, Tae-Jin Yang and Nam-Soo Kim

Int. J. Mol. Sci. 2021, 22(2), 641; https://doi.org/10.3390/ijms22020641 - 11 Jan 2021

Cited by 11 | Viewed by 3532

Abstract

The early vascular plants in the genus Selaginella, which is the sole genus of the Selaginellaceae family, have an important place in evolutionary history, along with ferns, as such plants are valuable resources for deciphering plant evolution. In this study, we sequenced and assembled the plastid genome (plastome) sequences of two Selaginella tamariscina individuals, as well as Selaginella stauntoniana and Selaginella involvens. Unlike the inverted repeat (IR) structures typically found in plant plastomes, Selaginella species had direct repeat (DR) structures, which were confirmed by Oxford Nanopore long-read sequence assembly. Comparative analyses of 19 lycophytes, including two Huperzia and one Isoetes species, revealed unique phylogenetic relationships between Selaginella species and related lycophytes, reflected by structural rearrangements involving two rounds of large inversions that resulted in dynamic changes between IR and DR blocks in the plastome sequence. Furthermore, we present other uncommon characteristics, including a small genome size, drastic reductions in gene and intron numbers, a high GC content, and extensive RNA editing. Although the 16 Selaginella species examined may not fully represent the genus, our findings suggest that Selaginella plastomes have undergone unique evolutionary events yielding genomic features unparalleled in other lycophytes, ferns, or seed plants. Full article

(This article belongs to the Special Issue Chloroplast Development and Function)

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16 pages, 1959 KiB

Open AccessArticle

SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species

by Lidia Skuza, Ewa Filip, Izabela Szućko and Jan Bocianowski

Int. J. Mol. Sci. 2020, 21(24), 9421; https://doi.org/10.3390/ijms21249421 - 10 Dec 2020

Cited by 1 | Viewed by 2391

Abstract

Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species. Full article

(This article belongs to the Special Issue Chloroplast Development and Function)

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9 pages, 1740 KiB

Open AccessArticle

Long-Chain Saturated Fatty Acids, Palmitic and Stearic Acids, Enhance the Repair of Photosystem II

by Haruhiko Jimbo, Kensuke Takagi, Takashi Hirashima, Yoshitaka Nishiyama and Hajime Wada

Int. J. Mol. Sci. 2020, 21(20), 7509; https://doi.org/10.3390/ijms21207509 - 12 Oct 2020

Cited by 14 | Viewed by 3469

Abstract

Free fatty acids (FFA) generated in cyanobacterial cells can be utilized for the biodiesel that is required for our sustainable future. The combination of FFA and strong light induces severe photoinhibition of photosystem II (PSII), which suppresses the production of FFA in cyanobacterial cells. In the present study, we examined the effects of exogenously added FFA on the photoinhibition of PSII in Synechocystis sp. PCC 6803. The addition of lauric acid (12:0) to cells accelerated the photoinhibition of PSII by inhibiting the repair of PSII and the de novo synthesis of D1. α-Linolenic acid (18:3) affected both the repair of and photodamage to PSII. Surprisingly, palmitic (16:0) and stearic acids (18:0) enhanced the repair of PSII by accelerating the de novo synthesis of D1 with the mitigation of the photoinhibition of PSII. Our results show chemical potential of FFA in the regulation of PSII without genetic manipulation. Full article

(This article belongs to the Special Issue Chloroplast Development and Function)

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14 pages, 2067 KiB

Open AccessArticle

The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation

by Benjamin Lenzen, Thilo Rühle, Marie-Kristin Lehniger, Ayako Okuzaki, Mathias Labs, Jose M. Muino, Uwe Ohler, Dario Leister and Christian Schmitz-Linneweber

Int. J. Mol. Sci. 2020, 21(16), 5633; https://doi.org/10.3390/ijms21165633 - 6 Aug 2020

Cited by 8 | Viewed by 3176

Abstract

Chloroplast RNA processing requires a large number of nuclear-encoded RNA binding proteins (RBPs) that are imported post-translationally into the organelle. Most of these RBPs are highly specific for one or few target RNAs. By contrast, members of the chloroplast ribonucleoprotein family (cpRNPs) have a wider RNA target range. We here present a quantitative analysis of RNA targets of the cpRNP CP31A using digestion-optimized RNA co-immunoprecipitation with deep sequencing (DO-RIP-seq). This identifies the mRNAs coding for subunits of the chloroplast NAD(P)H dehydrogenase (NDH) complex as main targets for CP31A. We demonstrate using whole-genome gene expression analysis and targeted RNA gel blot hybridization that the ndh mRNAs are all down-regulated in cp31a mutants. This diminishes the activity of the NDH complex. Our findings demonstrate how a chloroplast RNA binding protein can combine functionally related RNAs into one post-transcriptional operon. Full article

(This article belongs to the Special Issue Chloroplast Development and Function)

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19 pages, 4299 KiB

Open AccessArticle

OsCpn60β1 is Essential for Chloroplast Development in Rice (Oryza sativa L.)

by Qingfei Wu, Cheng Zhang, Yue Chen, Kaiyue Zhou, Yihua Zhan and Dean Jiang

Int. J. Mol. Sci. 2020, 21(11), 4023; https://doi.org/10.3390/ijms21114023 - 4 Jun 2020

Cited by 8 | Viewed by 3548

Abstract

The chaperonin 60 (Cpn60) protein is of great importance to plants due to its involvement in modulating the folding of numerous chloroplast protein polypeptides. In chloroplasts, Cpn60 is differentiated into two subunit types—Cpn60α and Cpn60β and the rice genome encodes three α and three β plastid chaperonin subunits. However, the functions of Cpn60 family members in rice were poorly understood. In order to investigate the molecular mechanism of OsCpn60β1, we attempted to disrupt the OsCpn60β1 gene by CRISPR/Cas9-mediated targeted mutagenesis in this study. We succeeded in the production of homozygous OsCpn60β1 knockout rice plants. The OsCpn60β1 mutant displayed a striking albino leaf phenotype and was seedling lethal. Electron microscopy observation demonstrated that chloroplasts were severely disrupted in the OsCpn60β1 mutant. In addition, OsCpn60β1 was located in the chloroplast and OsCpn60β1 is constitutively expressed in various tissues particularly in the green tissues. The label-free qualitative proteomics showed that photosynthesis-related pathways and ribosomal pathways were significantly inhibited in OsCpn60β1 mutants. These results indicate that OsCpn60β1 is essential for chloroplast development in rice. Full article

(This article belongs to the Special Issue Chloroplast Development and Function)

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18 pages, 6712 KiB

Open AccessArticle

Comparative Analyses of Five Complete Chloroplast Genomes from the Genus Pterocarpus (Fabacaeae)

by Zhou Hong, Zhiqiang Wu, Kunkun Zhao, Zengjiang Yang, Ningnan Zhang, Junyu Guo, Luke R. Tembrock and Daping Xu

Int. J. Mol. Sci. 2020, 21(11), 3758; https://doi.org/10.3390/ijms21113758 - 26 May 2020

Cited by 57 | Viewed by 4938

Abstract

Pterocarpus is a genus of trees mainly distributed in tropical Asia, Africa, and South America. Some species of Pterocarpus are rosewood tree species, having important economic value for timber, and for some species, medicinal value as well. Up to now, information about this genus with regard to the genomic characteristics of the chloroplasts has been limited. Based on a combination of next-generation sequencing (Illumina Hiseq) and long-read sequencing (PacBio), the whole chloroplast genomes (cp genomes) of five species (rosewoods) in Pterocarpus (Pterocarpus macrocarpus, P. santalinus, P. indicus, P. pedatus, P. marsupium) have been assembled. The cp genomes of five species in Pterocarpus have similar structural characteristics, gene content, and sequence to other flowering plants. The cp genomes have a typical four-part structure, containing 110 unique genes (77 protein coding genes, 4 rRNAs, 29 tRNAs). Through comparative genomic analysis, abundant simple sequence repeat (SSR)loci (333–349) were detected in Pterocarpus, among which A /T single nucleotide repeats accounted for the highest proportion (72.8–76.4%). In the five cp genomes of Pterocarpus, eight hypervariable regions, including trnH-GUG_psbA, trnS-UGA_psbC, accD-psaI, ndhI-exon2_ndhI-exon1, ndhG_ndhi-exon2, rpoC2-exon2, ccsA, and trnfM-CAU, are proposed for use as DNA barcode regions. In the comparison of gene selection pressures (P. santalinus as the reference genome), purifying selection was inferred as the primary mode of selection in maintaining important biological functions. Phylogenetic analysis shows that Pterocarpus is a monophyletic group. The species P. tinctorius is resolved as early diverging in the genus. Pterocarpus was resolved as sister to the genus Tipuana. Full article

(This article belongs to the Special Issue Chloroplast Development and Function)

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Review

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16 pages, 784 KiB

Open AccessReview

Horizontal Gene Transfer Involving Chloroplasts

by Ewa Filip and Lidia Skuza

Int. J. Mol. Sci. 2021, 22(9), 4484; https://doi.org/10.3390/ijms22094484 - 25 Apr 2021

Cited by 23 | Viewed by 4496

Abstract

Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments. Full article

(This article belongs to the Special Issue Chloroplast Development and Function)

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