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Molecular Biology of Chloroplast: Structure, Function and Development—2nd Edition
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Molecular Biology of Chloroplast: Structure, Function and Development—2nd Edition

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

Deadline for manuscript submissions: 30 October 2025 | Viewed by 7713

Special Issue Editors

Dr. Xiaomin Liu

E-Mail Website
Guest Editor
Plant Science, Beijing Forestry University, Beijing 100083, China
Interests: chloroplast; plant stem cell; cytoskeleton
Special Issues, Collections and Topics in MDPI journals
Dr. Li'na Yin

E-Mail Website
Guest Editor
College of Soil and Water Conservation Science and Engineering (Institute of Soil and Water Conservation), Northwest A&F University, Yangling 712100, China
Interests: plant physiology and molecular biology; abiotic stresses; photosynthesis; chloroplast membrane lipid; galactolipid; antioxidant
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Chloroplasts are essential organelles specific to plants. The structure, function, development and propagation of chloroplasts are important for the growth and development of plants and their interactions with the environment. Chloroplasts are the main site of photosynthesis. They also participate in the synthesis of amino acids, fatty acids, pigments and hormones. Chloroplast division maintains the stability of chloroplast numbers in cells, ensuring the normal running of various physiological processes in chloroplasts. Chloroplasts are reported to have avoidance movement in response to intense light. In recent years, chloroplast movement has also been reported to be involved in plant immunity. Stromules, structures that emanate from chloroplasts, function in plant development and defense. Exploring the diverse roles of chloroplasts in plants will help to improve the yield of crops and enhance the stress tolerance of plants. However, there are still many unknowns worth discovering, for example, how chloroplasts respond to environmental signals and why do different types of cells have different numbers of chloroplasts. This Special Issue of Plants will highlight the structure, function, development and propagation of chloroplasts in plants.

Dr. Xiaomin Liu
Dr. Li'na Yin
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. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • chloroplasts
  • thylakoid
  • structure and function
  • division and development

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Related Special Issue

Published Papers (5 papers)

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Research

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16 pages, 3163 KB  
Article
Chloroplast Hibernation-Promoting Factor PSRP1 Prevents Ribosome Degradation Under Darkness Independently of 100S Dimer Formation
by Kenta Tanaka, Yusuke Yoshizawa, Takashi Oda and Yasuhiko Sekine
Plants 2025, 14(20), 3155; https://doi.org/10.3390/plants14203155 - 13 Oct 2025
Viewed by 387
Abstract
Ribosome hibernation is a conserved translational stress response in bacteria, regulated by the hibernation-promoting factor (HPF). Plastid-specific ribosomal protein 1 (PSRP1) is the chloroplast ortholog of bacterial HPF. Although bacterial HPFs have been extensively characterized, both structurally and mechanistically, the physiological roles and [...] Read more.
Ribosome hibernation is a conserved translational stress response in bacteria, regulated by the hibernation-promoting factor (HPF). Plastid-specific ribosomal protein 1 (PSRP1) is the chloroplast ortholog of bacterial HPF. Although bacterial HPFs have been extensively characterized, both structurally and mechanistically, the physiological roles and mechanisms of PSRP1 in plant chloroplasts remain unclear. Here, we aimed to clarify the role of PSRP1 in chloroplast ribosome hibernation by examining its function under dark-stress conditions in the moss Physcomitrium patens. The PSRP1 knockout mutant exhibited moderate but statistically significant growth defects under both long- and short-day conditions compared to those of the wild-type plants. Moreover, the mutant displayed pronounced growth delay when co-cultured with wild-type plants, indicating a competitive disadvantage. Under dark conditions, wild-type plants exhibit increased PSRP1 protein accumulation, whereas the knockout mutant displayed reduction in chloroplast rRNA content. Notably, although PSRP1 is capable of inducing 100S dimers, we detected no chloroplast 100S dimers either in vivo or in vitro, suggesting a chloroplast-specific ribosome protection mechanism distinct from that of bacteria. These findings reveal PSRP1-mediated chloroplast ribosome protection and could provide new insights into plant stress tolerance. Full article
(This article belongs to the Special Issue Molecular Biology of Chloroplast: Structure, Function and Development—2nd Edition)
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21 pages, 6745 KB  
Article
Characterization and Role of AP2/EREBP Genes with Decreasing Expression During Leaf Development in 84K Poplar
by Sanjiao Wang, Nan Liu, Jingna Si, Sihan Zhang and Xiaomin Liu
Plants 2025, 14(18), 2842; https://doi.org/10.3390/plants14182842 - 11 Sep 2025
Viewed by 475
Abstract
The 84K poplar (Populus alba × Populus glandulosa) is a fast-growing hybrid poplar that was introduced from South Korea by the Chinese Academy of Forestry in 1984. To gain deeper insight into the regulatory mechanisms of leaf development in 84K poplar, [...] Read more.
The 84K poplar (Populus alba × Populus glandulosa) is a fast-growing hybrid poplar that was introduced from South Korea by the Chinese Academy of Forestry in 1984. To gain deeper insight into the regulatory mechanisms of leaf development in 84K poplar, we performed bulk RNA sequencing and found that numerous members of the AP2/EREBP family exhibited expression changes, suggesting their crucial roles in leaf development. The AP2/EREBP transcription factor family is one of the largest and most conserved gene families in plants. These genes play a crucial role in plant growth, development, and stress responses. In this study, we identified and analyzed 400 AP2/EREBP genes through transcriptome analysis, excluding genes with missing values (NAs) or FPKM < 1, and selected 76 genes based on their expression patterns at different stages of leaf development. The 76 genes were classified into three subfamilies based on phylogenetic analysis and structural domain characteristics: the RAV subfamily, the ERF subfamily, and the AP2 subfamily. Each subfamily shares similar gene structures and motifs while also exhibiting distinct differences. Segmental duplication events may have contributed to the evolution of this gene family. Most of the promoter cis-acting elements are related to light responses, with fewer elements associated with palisade tissues and hormones. Eight genes, selected for their gradually decreasing expression during leaf development, were validated through RT-PCR experiments. Among them, five genes—Pop_G10G022861, Pop_A01G003858, Pop_A01G081120, Pop_A01G074798, and Pop_A07G010900—exhibited a decreasing trend in expression across the three stages of leaf development. Subcellular localization analysis indicated that Pop_A01G003858 and Pop_G11G077730, two randomly selected genes from the eight AP2/EREBP members validated by RT-PCR, are localized in the nucleus. In conclusion, these findings provide valuable insights into the evolutionary relationships of the 73 AP2/EREBP family members in 84K poplar leaves and lay a foundation for future studies on leaf development. Full article
(This article belongs to the Special Issue Molecular Biology of Chloroplast: Structure, Function and Development—2nd Edition)
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22 pages, 6635 KB  
Article
A PPR Protein RFCD1 Affects Chloroplast Gene Expression and Chloroplast Development in Arabidopsis
by Tianming Tan, Shengnan Xu, Jiyun Liu, Min Ouyang and Jing Zhang
Plants 2025, 14(6), 921; https://doi.org/10.3390/plants14060921 - 15 Mar 2025
Viewed by 1380
Abstract
Chloroplast development is a highly complex process, involving many regulatory mechanisms that remain poorly understood. This study reports a novel PPR protein, RFCD1 (Regulation Factor of Chloroplast Development 1). Fluorescence localization analysis reveals that the N-terminal 60 amino acids of RFCD1 fused with [...] Read more.
Chloroplast development is a highly complex process, involving many regulatory mechanisms that remain poorly understood. This study reports a novel PPR protein, RFCD1 (Regulation Factor of Chloroplast Development 1). Fluorescence localization analysis reveals that the N-terminal 60 amino acids of RFCD1 fused with GFP protein specifically direct the protein to the chloroplast. The knockout mutant of RFCD1 is embryo-lethal. RFCD1 RNA interference (RNAi) transgenic lines display chlorosis phenotypes and abnormal chloroplast development. Quantitative real-time PCR (qRT-PCR) showed that the expression levels of the plastid-encoded RNA polymerase (PEP) genes were significantly decreased in the RNAi lines. Furthermore, RNA blotting results and RNA-seq data showed that the processing of plastid rRNA was also affected in the RNAi lines. Taken together, these results indicate that RFCD1 might be involved in chloroplast gene expression and rRNA processing, which is essential for chloroplast development in Arabidopsis. Full article
(This article belongs to the Special Issue Molecular Biology of Chloroplast: Structure, Function and Development—2nd Edition)
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15 pages, 7536 KB  
Article
RAS, a Pentatricopeptide Repeat Protein, Interacts with OsTRX z to Regulate Chloroplast Gene Transcription and RNA Processing
by Zhennan Qiu, Shiyong Wen, Peinan Sun, Dongdong Chen, Chunmiao Wang, Xiliang Song, Liying Xiao, Peiliang Zhang, Dongying Zhao, Cuiping Wen, Peiyan Guan, Xuechu Du, Yinghui Sun, Chenshan Xu and Jian Song
Plants 2025, 14(2), 247; https://doi.org/10.3390/plants14020247 - 16 Jan 2025
Viewed by 1303
Abstract
Thioredoxin z (TRX z) plays a significant role in chloroplast development by regulating the transcription of chloroplast genes. In this study, we identified a pentatricopeptide repeat (PPR) protein, rice albino seedling-lethal (RAS), that interacts with OsTRX z. This interaction was initially discovered by [...] Read more.
Thioredoxin z (TRX z) plays a significant role in chloroplast development by regulating the transcription of chloroplast genes. In this study, we identified a pentatricopeptide repeat (PPR) protein, rice albino seedling-lethal (RAS), that interacts with OsTRX z. This interaction was initially discovered by using a yeast two-hybrid (Y2H) screening technique and was further validated through Y2H and bimolecular fluorescence complementation (BiFC) experiments. RAS contains 16 PPR motifs and features a small MutS-related (SMR) domain at its C-terminus. CRISPR/Cas9-generated ras mutants exhibited an albino seedling-lethal phenotype characterized by abnormal chloroplast structures and a significantly reduced chlorophyll content. RAS localizes to the chloroplast and is predominantly expressed in young leaves. Mutations in RAS affect RNA editing at the rpl2, rps14, and ndhA sites, as well as RNA splicing at the rpl2, atpF, and ndhA transcripts within the chloroplast. Furthermore, the expression levels of genes associated with chloroplast formation are altered in the ras mutant. Both OsTRX z and RAS were found to interact with chloroplast signal recognition particle (cpSRP) proteins, indicating that their proper localization within the chloroplast may be dependent on the SRP pathway. Collectively, our findings highlight the critical role of RAS in chloroplast development, as it is involved in RNA processing and the regulation of chloroplast gene expression. Full article
(This article belongs to the Special Issue Molecular Biology of Chloroplast: Structure, Function and Development—2nd Edition)
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Review

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35 pages, 6825 KB  
Review
Chloroplast Functionality at the Interface of Growth, Defense, and Genetic Innovation: A Multi-Omics and Technological Perspective
by Chunhua Zhang, Wenting Li, Yahan Wu, Shengli Li, Bao Hua and Haizhou Sun
Plants 2025, 14(6), 978; https://doi.org/10.3390/plants14060978 - 20 Mar 2025
Cited by 3 | Viewed by 3346
Abstract
Chloroplasts are important in plant growth, development, and defense mechanisms, making them central to addressing global agricultural challenges. This review explores the multi-faceted contributions of chloroplasts, including photosynthesis, hormone biosynthesis, and stress signaling, which orchestrate the trade-off between growth and defense. Advancements in [...] Read more.
Chloroplasts are important in plant growth, development, and defense mechanisms, making them central to addressing global agricultural challenges. This review explores the multi-faceted contributions of chloroplasts, including photosynthesis, hormone biosynthesis, and stress signaling, which orchestrate the trade-off between growth and defense. Advancements in chloroplast genomics, transcription, translation, and proteomics have deepened our understanding of their regulatory functions and interactions with nuclear-encoded proteins. Case studies have demonstrated the potential of chloroplast-targeted strategies, such as the expression of elongation factor EF-2 for heat tolerance and flavodiiron proteins for drought resilience, to enhance crop productivity and stress adaptation. Future research directions should focus on the need for integrating omics data with nanotechnology and synthetic biology to develop sustainable and resilient agricultural systems. This review uniquely integrates recent advancements in chloroplast genomics, transcriptional regulation, and synthetic biology to present a holistic perspective on optimizing plant growth and stress tolerance. We emphasize the role of chloroplast-driven trade-off in balancing growth and immunity, leveraging omics technologies and emerging biotechnological innovations. This comprehensive approach offers new insights into sustainable agricultural practices, making it a significant contribution to the field. Full article
(This article belongs to the Special Issue Molecular Biology of Chloroplast: Structure, Function and Development—2nd Edition)
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