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Plant Communications Sep 2023Chloroplasts evolved from an ancient cyanobacterial endosymbiont more than 1.5 billion years ago. During subsequent coevolution with the nuclear genome, the chloroplast... (Review)
Review
Chloroplasts evolved from an ancient cyanobacterial endosymbiont more than 1.5 billion years ago. During subsequent coevolution with the nuclear genome, the chloroplast genome has remained independent, albeit strongly reduced, with its own transcriptional machinery and distinct features, such as chloroplast-specific innovations in gene expression and complicated post-transcriptional processing. Light activates the expression of chloroplast genes via mechanisms that optimize photosynthesis, minimize photodamage, and prioritize energy investments. Over the past few years, studies have moved from describing phases of chloroplast gene expression to exploring the underlying mechanisms. In this review, we focus on recent advances and emerging principles that govern chloroplast gene expression in land plants. We discuss engineering of pentatricopeptide repeat proteins and its biotechnological effects on chloroplast RNA research; new techniques for characterizing the molecular mechanisms of chloroplast gene expression; and important aspects of chloroplast gene expression for improving crop yield and stress tolerance. We also discuss biological and mechanistic questions that remain to be answered in the future.
Topics: Genes, Chloroplast; Chloroplasts; Photosynthesis
PubMed: 37147800
DOI: 10.1016/j.xplc.2023.100611 -
The EMBO Journal Jul 2023Chloroplasts are plant organelles responsible for photosynthesis and environmental sensing. Most chloroplast proteins are imported from the cytosol through the...
Chloroplasts are plant organelles responsible for photosynthesis and environmental sensing. Most chloroplast proteins are imported from the cytosol through the translocon at the outer envelope membrane of chloroplasts (TOC). Previous work has shown that TOC components are regulated by the ubiquitin-proteasome system (UPS) to control the chloroplast proteome, which is crucial for the organelle's function and plant development. Here, we demonstrate that the TOC apparatus is also subject to K63-linked polyubiquitination and regulation by selective autophagy, potentially promoting plant stress tolerance. We identify NBR1 as a selective autophagy adaptor targeting TOC components, and mediating their relocation into vacuoles for autophagic degradation. Such selective autophagy is shown to control TOC protein levels and chloroplast protein import and to influence photosynthetic activity as well as tolerance to UV-B irradiation and heat stress in Arabidopsis plants. These findings uncover the vital role of selective autophagy in the proteolytic regulation of specific chloroplast proteins, and how dynamic control of chloroplast protein import is critically important for plants to cope with challenging environments.
Topics: Chloroplasts; Plants; Organelles; Protein Transport; Chloroplast Proteins; Arabidopsis; Autophagy; Plant Proteins; Arabidopsis Proteins; Carrier Proteins
PubMed: 37248861
DOI: 10.15252/embj.2022112534 -
Cell Aug 2023Chloroplasts are eukaryotic photosynthetic organelles that drive the global carbon cycle. Despite their importance, our understanding of their protein composition,...
Chloroplasts are eukaryotic photosynthetic organelles that drive the global carbon cycle. Despite their importance, our understanding of their protein composition, function, and spatial organization remains limited. Here, we determined the localizations of 1,034 candidate chloroplast proteins using fluorescent protein tagging in the model alga Chlamydomonas reinhardtii. The localizations provide insights into the functions of poorly characterized proteins; identify novel components of nucleoids, plastoglobules, and the pyrenoid; and reveal widespread protein targeting to multiple compartments. We discovered and further characterized cellular organizational features, including eleven chloroplast punctate structures, cytosolic crescent structures, and unexpected spatial distributions of enzymes within the chloroplast. We also used machine learning to predict the localizations of other nuclear-encoded Chlamydomonas proteins. The strains and localization atlas developed here will serve as a resource to accelerate studies of chloroplast architecture and functions.
Topics: Biosynthetic Pathways; Chlamydomonas reinhardtii; Chloroplast Proteins; Chloroplasts; Photosynthesis
PubMed: 37437571
DOI: 10.1016/j.cell.2023.06.008 -
Protoplasma Jan 2024
Topics: Plastids
PubMed: 38102506
DOI: 10.1007/s00709-023-01913-y -
Nature Communications Nov 2023Microbial eukaryotes are important components of marine ecosystems, and the Marine Alveolates (MALVs) are consistently both abundant and diverse in global environmental...
Microbial eukaryotes are important components of marine ecosystems, and the Marine Alveolates (MALVs) are consistently both abundant and diverse in global environmental sequencing surveys. MALVs are dinoflagellates that are thought to be parasites of other protists and animals, but the lack of data beyond ribosomal RNA gene sequences from all but a few described species means much of their biology and evolution remain unknown. Using single-cell transcriptomes from several MALVs and their free-living relatives, we show that MALVs evolved independently from two distinct, free-living ancestors and that their parasitism evolved in parallel. Phylogenomics shows one subgroup (MALV-II and -IV, or Syndiniales) is related to a novel lineage of free-living, eukaryovorous predators, the eleftherids, while the other (MALV-I, or Ichthyodinida) is related to the free-living predator Oxyrrhis and retains proteins targeted to a non-photosynthetic plastid. Reconstructing the evolution of photosynthesis, plastids, and parasitism in early-diverging dinoflagellates shows a number of parallels with the evolution of their apicomplexan sisters. In both groups, similar forms of parasitism evolved multiple times and photosynthesis was lost many times. By contrast, complete loss of the plastid organelle is infrequent and, when this does happen, leaves no residual genes.
Topics: Animals; Parasites; Ecosystem; Phylogeny; Plastids; Photosynthesis; Dinoflagellida
PubMed: 37923716
DOI: 10.1038/s41467-023-42807-0 -
Plant & Cell Physiology May 2024RNA-binding proteins play integral roles in the regulation of essential processes in cells and as such are attractive targets for engineering to manipulate gene... (Review)
Review
RNA-binding proteins play integral roles in the regulation of essential processes in cells and as such are attractive targets for engineering to manipulate gene expression at the RNA level. Expression of transcripts in chloroplasts and mitochondria is heavily regulated by pentatricopeptide repeat (PPR) proteins. The diverse roles of PPR proteins and their naturally modular architecture make them ideal candidates for engineering. Synthetic PPR proteins are showing great potential to become valuable tools for controlling the expression of plastid and mitochondrial transcripts. In this review, by 'synthetic', we mean both rationally modified natural PPR proteins and completely novel proteins designed using the principles learned from their natural counterparts. We focus on the many different applications of synthetic PPR proteins, covering both their use in basic research to learn more about protein-RNA interactions and their use to achieve specific outcomes in RNA processing and the control of gene expression. We describe the challenges associated with the design, construction and deployment of synthetic PPR proteins and provide perspectives on how they might be assembled and used in future biotechnology applications.
Topics: RNA-Binding Proteins; Chloroplasts; Plant Proteins; Mitochondria; Gene Expression Regulation, Plant
PubMed: 38035801
DOI: 10.1093/pcp/pcad150 -
Biochemical Society Transactions Dec 2023Plant organelles predominantly rely on the actin cytoskeleton and the myosin motors for long-distance trafficking, while using microtubules and the kinesin motors mostly...
Plant organelles predominantly rely on the actin cytoskeleton and the myosin motors for long-distance trafficking, while using microtubules and the kinesin motors mostly for short-range movement. The distribution and motility of organelles in the plant cell are fundamentally important to robust plant growth and defense. Chloroplasts, mitochondria, and peroxisomes are essential organelles in plants that function independently and coordinately during energy metabolism and other key metabolic processes. In response to developmental and environmental stimuli, these energy organelles modulate their metabolism, morphology, abundance, distribution and motility in the cell to meet the need of the plant. Consistent with their metabolic links in processes like photorespiration and fatty acid mobilization is the frequently observed inter-organellar physical interaction, sometimes through organelle membranous protrusions. The development of various organelle-specific fluorescent protein tags has allowed the simultaneous visualization of organelle movement in living plant cells by confocal microscopy. These energy organelles display an array of morphology and movement patterns and redistribute within the cell in response to changes such as varying light conditions, temperature fluctuations, ROS-inducible treatments, and during pollen tube development and immune response, independently or in association with one another. Although there are more reports on the mechanism of chloroplast movement than that of peroxisomes and mitochondria, our knowledge of how and why these three energy organelles move and distribute in the plant cell is still scarce at the functional and mechanistic level. It is critical to identify factors that control organelle motility coupled with plant growth, development, and stress response.
Topics: Organelles; Actin Cytoskeleton; Peroxisomes; Chloroplasts; Mitochondria; Microtubules
PubMed: 37975429
DOI: 10.1042/BST20221093 -
The Plant Cell Sep 2023The pyrenoid is a phase-separated organelle that enhances photosynthetic carbon assimilation in most eukaryotic algae and the land plant hornwort lineage. Pyrenoids...
The pyrenoid is a phase-separated organelle that enhances photosynthetic carbon assimilation in most eukaryotic algae and the land plant hornwort lineage. Pyrenoids mediate approximately one-third of global CO2 fixation, and engineering a pyrenoid into C3 crops is predicted to boost CO2 uptake and increase yields. Pyrenoids enhance the activity of the CO2-fixing enzyme Rubisco by supplying it with concentrated CO2. All pyrenoids have a dense matrix of Rubisco associated with photosynthetic thylakoid membranes that are thought to supply concentrated CO2. Many pyrenoids are also surrounded by polysaccharide structures that may slow CO2 leakage. Phylogenetic analysis and pyrenoid morphological diversity support a convergent evolutionary origin for pyrenoids. Most of the molecular understanding of pyrenoids comes from the model green alga Chlamydomonas (Chlamydomonas reinhardtii). The Chlamydomonas pyrenoid exhibits multiple liquid-like behaviors, including internal mixing, division by fission, and dissolution and condensation in response to environmental cues and during the cell cycle. Pyrenoid assembly and function are induced by CO2 availability and light, and although transcriptional regulators have been identified, posttranslational regulation remains to be characterized. Here, we summarize the current knowledge of pyrenoid function, structure, components, and dynamic regulation in Chlamydomonas and extrapolate to pyrenoids in other species.
Topics: Carbon Dioxide; Eukaryota; Ribulose-Bisphosphate Carboxylase; Phylogeny; Plastids; Chlamydomonas
PubMed: 37279536
DOI: 10.1093/plcell/koad157 -
Biology Jul 2023The metabarcoding methods for studying the diversity of freshwater microalgae and routine biomonitoring are actively used in modern research. A lot of experience has... (Review)
Review
The metabarcoding methods for studying the diversity of freshwater microalgae and routine biomonitoring are actively used in modern research. A lot of experience has been accumulated already, and many methodological questions have been solved (such as the influence of the methods and time of sample conservation, DNA extraction and bioinformatical processing). The reproducibility of the method has been tested and confirmed. However, one of the main problems-choosing a genetic marker for the study-still lacks a clear answer. We analyzed 70 publications and found out that studies on eukaryotic freshwater microalgae use 12 markers (different nuclear regions 18S and ITS and plastids L, 23S and 16S). Each marker has its peculiarities; they amplify differently and have various levels of efficiency (variability) in different groups of algae. The V4 and V9 18S and L regions are used most often. We concentrated especially on the studies that compare the results of using different markers and microscopy. We summarize the data on the primers for each region and on how the choice of a marker affects the taxonomic composition of a community.
PubMed: 37508467
DOI: 10.3390/biology12071038 -
Cell Feb 2024Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex...
Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex composed of plastid-encoded subunits similar to bacterial RNA polymerases (RNAPs) stably bound to a set of nuclear-encoded PEP-associated proteins (PAPs). PAPs are essential to PEP activity and chloroplast biogenesis, but their roles are poorly defined. Here, we present cryoelectron microscopy (cryo-EM) structures of native 21-subunit PEP and a PEP transcription elongation complex from white mustard (Sinapis alba). We identify that PAPs encase the core polymerase, forming extensive interactions that likely promote complex assembly and stability. During elongation, PAPs interact with DNA downstream of the transcription bubble and with the nascent mRNA. The models reveal details of the superoxide dismutase, lysine methyltransferase, thioredoxin, and amino acid ligase enzymes that are subunits of PEP. Collectively, these data provide a foundation for the mechanistic understanding of chloroplast transcription and its role in plant growth and adaptation.
Topics: Arabidopsis Proteins; Chloroplasts; Cryoelectron Microscopy; DNA-Directed RNA Polymerases; Gene Expression Regulation, Plant; Plant Proteins; Plastids; Transcription, Genetic
PubMed: 38428394
DOI: 10.1016/j.cell.2024.01.036