1
|
Hegde RS, Keenan RJ. A unifying model for membrane protein biogenesis. Nat Struct Mol Biol 2024; 31:1009-1017. [PMID: 38811793 PMCID: PMC7616256 DOI: 10.1038/s41594-024-01296-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 05/31/2024]
Abstract
α-Helical integral membrane proteins comprise approximately 25% of the proteome in all organisms. The membrane proteome is highly diverse, varying in the number, topology, spacing and properties of transmembrane domains. This diversity imposes different constraints on the insertion of different regions of a membrane protein into the lipid bilayer. Here, we present a cohesive framework to explain membrane protein biogenesis, in which different parts of a nascent substrate are triaged between Oxa1 and SecY family members for insertion. In this model, Oxa1 family proteins insert transmembrane domains flanked by short translocated segments, whereas the SecY channel is required for insertion of transmembrane domains flanked by long translocated segments. Our unifying model rationalizes evolutionary, genetic, biochemical and structural data across organisms and provides a foundation for future mechanistic studies of membrane protein biogenesis.
Collapse
Affiliation(s)
- Ramanujan S Hegde
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Robert J Keenan
- Gordon Center for Integrative Science, The University of Chicago, Chicago, IL, USA.
| |
Collapse
|
2
|
Schmid LM, Manavski N, Chi W, Meurer J. Chloroplast Ribosome Biogenesis Factors. PLANT & CELL PHYSIOLOGY 2024; 65:516-536. [PMID: 37498958 DOI: 10.1093/pcp/pcad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
The formation of chloroplasts can be traced back to an ancient event in which a eukaryotic host cell containing mitochondria ingested a cyanobacterium. Since then, chloroplasts have retained many characteristics of their bacterial ancestor, including their transcription and translation machinery. In this review, recent research on the maturation of rRNA and ribosome assembly in chloroplasts is explored, along with their crucial role in plant survival and their implications for plant acclimation to changing environments. A comparison is made between the ribosome composition and auxiliary factors of ancient and modern chloroplasts, providing insights into the evolution of ribosome assembly factors. Although the chloroplast contains ancient proteins with conserved functions in ribosome assembly, newly evolved factors have also emerged to help plants acclimate to changes in their environment and internal signals. Overall, this review offers a comprehensive analysis of the molecular mechanisms underlying chloroplast ribosome assembly and highlights the importance of this process in plant survival, acclimation and adaptation.
Collapse
Affiliation(s)
- Lisa-Marie Schmid
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| | - Nikolay Manavski
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| |
Collapse
|
3
|
Sandoval-Ibáñez O, Rolo D, Ghandour R, Hertle AP, Armarego-Marriott T, Sampathkumar A, Zoschke R, Bock R. De-etiolation-induced protein 1 (DEIP1) mediates assembly of the cytochrome b 6f complex in Arabidopsis. Nat Commun 2022; 13:4045. [PMID: 35831297 PMCID: PMC9279372 DOI: 10.1038/s41467-022-31758-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/01/2022] [Indexed: 11/26/2022] Open
Abstract
The conversion of light energy to chemical energy by photosynthesis requires the concerted action of large protein complexes in the thylakoid membrane. Recent work has provided fundamental insights into the three-dimensional structure of these complexes, but how they are assembled from hundreds of parts remains poorly understood. Particularly little is known about the biogenesis of the cytochrome b6f complex (Cytb6f), the redox-coupling complex that interconnects the two photosystems. Here we report the identification of a factor that guides the assembly of Cytb6f in thylakoids of chloroplasts. The protein, DE-ETIOLATION-INDUCED PROTEIN 1 (DEIP1), resides in the thylakoid membrane and is essential for photoautotrophic growth. Knock-out mutants show a specific loss of Cytb6f, and are defective in complex assembly. We demonstrate that DEIP1 interacts with the two cytochrome subunits of the complex, PetA and PetB, and mediates the assembly of intermediates in Cytb6f biogenesis. The identification of DEIP1 provides an entry point into the study of the assembly pathway of a crucial complex in photosynthetic electron transfer. The Cytb6f complex is a multi-subunit enzyme that couples the two photosystems during the light reactions of photosynthesis. Here the authors show that the thylakoid-localized DEIP1 protein interacts with the PetA and PetB subunits, and is essential for Cytb6f complex assembly in Arabidopsis.
Collapse
Affiliation(s)
- Omar Sandoval-Ibáñez
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - David Rolo
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rabea Ghandour
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alexander P Hertle
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Tegan Armarego-Marriott
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| |
Collapse
|
4
|
Ackermann B, Dünschede B, Pietzenuk B, Justesen BH, Krämer U, Hofmann E, Günther Pomorski T, Schünemann D. Chloroplast Ribosomes Interact With the Insertase Alb3 in the Thylakoid Membrane. FRONTIERS IN PLANT SCIENCE 2021; 12:781857. [PMID: 35003166 PMCID: PMC8733628 DOI: 10.3389/fpls.2021.781857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
Members of the Oxa1/YidC/Alb3 protein family are involved in the insertion, folding, and assembly of membrane proteins in mitochondria, bacteria, and chloroplasts. The thylakoid membrane protein Alb3 mediates the chloroplast signal recognition particle (cpSRP)-dependent posttranslational insertion of nuclear-encoded light harvesting chlorophyll a/b-binding proteins and participates in the biogenesis of plastid-encoded subunits of the photosynthetic complexes. These subunits are cotranslationally inserted into the thylakoid membrane, yet very little is known about the molecular mechanisms underlying docking of the ribosome-nascent chain complexes to the chloroplast SecY/Alb3 insertion machinery. Here, we show that nanodisc-embedded Alb3 interacts with ribosomes, while the homolog Alb4, also located in the thylakoid membrane, shows no ribosome binding. Alb3 contacts the ribosome with its C-terminal region and at least one additional binding site within its hydrophobic core region. Within the C-terminal region, two conserved motifs (motifs III and IV) are cooperatively required to enable the ribosome contact. Furthermore, our data suggest that the negatively charged C-terminus of the ribosomal subunit uL4c is involved in Alb3 binding. Phylogenetic analyses of uL4 demonstrate that this region newly evolved in the green lineage during the transition from aquatic to terrestrial life.
Collapse
Affiliation(s)
- Bernd Ackermann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Björn Pietzenuk
- Department of Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Bo Højen Justesen
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Ute Krämer
- Department of Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| |
Collapse
|
5
|
Baucom DR, Furr M, Govind Kumar V, Okoto P, Losey JL, Henry RL, Moradi M, Kumar TKS, Heyes CD. Transient local secondary structure in the intrinsically disordered C-term of the Albino3 insertase. Biophys J 2021; 120:4992-5004. [PMID: 34662559 PMCID: PMC8633824 DOI: 10.1016/j.bpj.2021.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/16/2021] [Accepted: 10/13/2021] [Indexed: 11/26/2022] Open
Abstract
Albino3 (Alb3) is an integral membrane protein fundamental to the targeting and insertion of light-harvesting complex (LHC) proteins into the thylakoid membrane. Alb3 contains a stroma-exposed C-terminus (Alb3-Cterm) that is responsible for binding the LHC-loaded transit complex before LHC membrane insertion. Alb3-Cterm has been reported to be intrinsically disordered, but precise mechanistic details underlying how it recognizes and binds to the transit complex are lacking, and the functional roles of its four different motifs have been debated. Using a novel combination of experimental and computational techniques such as single-molecule fluorescence resonance energy transfer, circular dichroism with deconvolution analysis, site-directed mutagenesis, trypsin digestion assays, and all-atom molecular dynamics simulations in conjunction with enhanced sampling techniques, we show that Alb3-Cterm contains transient secondary structure in motifs I and II. The excellent agreement between the experimental and computational data provides a quantitatively consistent picture and allows us to identify a heterogeneous structural ensemble that highlights the local and transient nature of the secondary structure. This structural ensemble was used to predict both the inter-residue distance distributions of single molecules and the apparent unfolding free energy of the transient secondary structure, which were both in excellent agreement with those determined experimentally. We hypothesize that this transient local secondary structure may play an important role in the recognition of Alb3-Cterm for the LHC-loaded transit complex, and these results should provide a framework to better understand protein targeting by the Alb3-Oxa1-YidC family of insertases.
Collapse
Affiliation(s)
- Dustin R Baucom
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Mercede Furr
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Vivek Govind Kumar
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Patience Okoto
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - James L Losey
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Ralph L Henry
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas.
| | | | - Colin D Heyes
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas.
| |
Collapse
|
6
|
Srinivasan K, Banerjee A, Baid P, Dhur A, Sengupta J. Ribosome-membrane crosstalk: Co-translational targeting pathways of proteins across membranes in prokaryotes and eukaryotes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:163-198. [PMID: 35034718 DOI: 10.1016/bs.apcsb.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ribosomes are the molecular machine of living cells designed for decoding mRNA-encoded genetic information into protein. Being sophisticated machinery, both in design and function, the ribosome not only carries out protein synthesis, but also coordinates several other ribosome-associated cellular processes. One such process is the translocation of proteins across or into the membrane depending on their secretory or membrane-associated nature. These proteins comprise a large portion of a cell's proteome and act as key factors for cellular survival as well as several crucial functional pathways. Protein transport to extra- and intra-cytosolic compartments (across the eukaryotic endoplasmic reticulum (ER) or across the prokaryotic plasma membrane) or insertion into membranes majorly occurs through an evolutionarily conserved protein-conducting channel called translocon (eukaryotic Sec61 or prokaryotic SecYEG channels). Targeting proteins to the membrane-bound translocon may occur via post-translational or co-translational modes and it is often mediated by recognition of an N-terminal signal sequence in the newly synthesizes polypeptide chain. Co-translational translocation is coupled to protein synthesis where the ribosome-nascent chain complex (RNC) itself is targeted to the translocon. Here, in the light of recent advances in structural and functional studies, we discuss our current understanding of the mechanistic models of co-translational translocation, coordinated by the actively translating ribosomes, in prokaryotes and eukaryotes.
Collapse
Affiliation(s)
- Krishnamoorthi Srinivasan
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aneek Banerjee
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priya Baid
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Ankit Dhur
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jayati Sengupta
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
| |
Collapse
|
7
|
Wojcik S, Kriechbaumer V. Go your own way: membrane-targeting sequences. PLANT PHYSIOLOGY 2021; 185:608-618. [PMID: 33822216 PMCID: PMC8133554 DOI: 10.1093/plphys/kiaa058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/19/2020] [Indexed: 05/05/2023]
Abstract
Membrane-targeting sequences, connected targeting mechanisms, and co-factors orchestrate primary targeting of proteins to membranes.
Collapse
Affiliation(s)
- Stefan Wojcik
- Plant Cell Biology, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Verena Kriechbaumer
- Plant Cell Biology, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Author for communication: (V.K.)
| |
Collapse
|
8
|
Hristou A, Gerlach I, Stolle DS, Neumann J, Bischoff A, Dünschede B, Nowaczyk MM, Zoschke R, Schünemann D. Ribosome-Associated Chloroplast SRP54 Enables Efficient Cotranslational Membrane Insertion of Key Photosynthetic Proteins. THE PLANT CELL 2019; 31:2734-2750. [PMID: 31444312 PMCID: PMC6881123 DOI: 10.1105/tpc.19.00169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/12/2019] [Accepted: 08/22/2019] [Indexed: 05/20/2023]
Abstract
Key proteins of the photosynthetic complexes are encoded in the chloroplast genome and cotranslationally inserted into the thylakoid membrane. However, the molecular details of this process are largely unknown. Here, we demonstrate by ribosome profiling that the conserved chloroplast signal recognition particle subunit (cpSRP54) is required for efficient cotranslational targeting of several central photosynthetic proteins, such as the PSII PsbA (D1) subunit, in Arabidopsis (Arabidopsis thaliana). High-resolution analysis of membrane-associated and soluble ribosome footprints revealed that the SRP-dependent membrane targeting of PsbA is already initiated at an early translation step before exposure of the nascent chain from the ribosome. In contrast to cytosolic SRP, which contacts the ribosome close to the peptide tunnel exit site, analysis of the cpSRP54/ribosome binding interface revealed a direct interaction of cpSRP54 and the ribosomal subunit uL4, which is not located at the tunnel exit site but forms a part of the internal peptide tunnel wall by a loop domain. The plastid-specific C-terminal tail region of cpSRP54 plays a crucial role in uL4 binding. Our data indicate a novel mechanism of SRP-dependent membrane protein transport with the cpSRP54/uL4 interaction as a central element in early initiation of cotranslational membrane targeting.
Collapse
Affiliation(s)
- Athina Hristou
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Ines Gerlach
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Dominique S Stolle
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Jennifer Neumann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Annika Bischoff
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Marc M Nowaczyk
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| |
Collapse
|
9
|
Zoschke R, Bock R. Chloroplast Translation: Structural and Functional Organization, Operational Control, and Regulation. THE PLANT CELL 2018; 30:745-770. [PMID: 29610211 PMCID: PMC5969280 DOI: 10.1105/tpc.18.00016] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/26/2018] [Accepted: 04/01/2018] [Indexed: 05/20/2023]
Abstract
Chloroplast translation is essential for cellular viability and plant development. Its positioning at the intersection of organellar RNA and protein metabolism makes it a unique point for the regulation of gene expression in response to internal and external cues. Recently obtained high-resolution structures of plastid ribosomes, the development of approaches allowing genome-wide analyses of chloroplast translation (i.e., ribosome profiling), and the discovery of RNA binding proteins involved in the control of translational activity have greatly increased our understanding of the chloroplast translation process and its regulation. In this review, we provide an overview of the current knowledge of the chloroplast translation machinery, its structure, organization, and function. In addition, we summarize the techniques that are currently available to study chloroplast translation and describe how translational activity is controlled and which cis-elements and trans-factors are involved. Finally, we discuss how translational control contributes to the regulation of chloroplast gene expression in response to developmental, environmental, and physiological cues. We also illustrate the commonalities and the differences between the chloroplast and bacterial translation machineries and the mechanisms of protein biosynthesis in these two prokaryotic systems.
Collapse
Affiliation(s)
- Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| |
Collapse
|
10
|
Króliczewski J, Bartoszewski R, Króliczewska B. Chloroplast PetD protein: evidence for SRP/Alb3-dependent insertion into the thylakoid membrane. BMC PLANT BIOLOGY 2017; 17:213. [PMID: 29162052 PMCID: PMC5697057 DOI: 10.1186/s12870-017-1176-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 11/13/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND In thylakoid membrane, each monomer of the dimeric complex of cytochrome b 6 f is comprised of eight subunits that are both nucleus- and plastid-encoded. Proper cytochrome b 6 f complex integration into the thylakoid membrane requires numerous regulatory factors for coordinated transport, insertion and assembly of the subunits. Although, the chloroplast-encoded cytochrome b 6 f subunit IV (PetD) consists of three transmembrane helices, the signal and the mechanism of protein integration into the thylakoid membrane have not been identified. RESULTS Here, we demonstrate that the native PetD subunit cannot incorporate into the thylakoid membranes spontaneously, but that proper integration occurs through the post-translational signal recognition particle (SRP) pathway. Furthermore, we show that PetD insertion into thylakoid membrane involves the coordinated action of cpFTSY, cpSRP54 and ALB3 insertase. CONCLUSIONS PetD subunit integration into the thylakoid membrane is a post-translational and an SRP-dependent process that requires the formation of the cpSRP-cpFtsY-ALB3-PetD complex. This data provides a new insight into the molecular mechanisms by which membrane proteins integration into the thylakoid membrane is accomplished and is not limited to PetD.
Collapse
Affiliation(s)
- Jarosław Króliczewski
- Faculty of Biotechnology, University of Wrocław, Fryderyka Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Rafał Bartoszewski
- Department of Biology and Pharmaceutical Botany Medical University of Gdańsk, Hallera 107, 80-416 Gdansk, Poland
| | - Bożena Króliczewska
- Department of Animal Physiology and Biostructure, Faculty of Veterinary Medicine Wroclaw University of Environmental and Life Sciences, C.K Norwida 31, 50-375 Wrocław, Poland
| |
Collapse
|
11
|
Covarrubias AA, Cuevas-Velazquez CL, Romero-Pérez PS, Rendón-Luna DF, Chater CCC. Structural disorder in plant proteins: where plasticity meets sessility. Cell Mol Life Sci 2017; 74:3119-3147. [PMID: 28643166 PMCID: PMC11107788 DOI: 10.1007/s00018-017-2557-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 01/08/2023]
Abstract
Plants are sessile organisms. This intriguing nature provokes the question of how they survive despite the continual perturbations caused by their constantly changing environment. The large amount of knowledge accumulated to date demonstrates the fascinating dynamic and plastic mechanisms, which underpin the diverse strategies selected in plants in response to the fluctuating environment. This phenotypic plasticity requires an efficient integration of external cues to their growth and developmental programs that can only be achieved through the dynamic and interactive coordination of various signaling networks. Given the versatility of intrinsic structural disorder within proteins, this feature appears as one of the leading characters of such complex functional circuits, critical for plant adaptation and survival in their wild habitats. In this review, we present information of those intrinsically disordered proteins (IDPs) from plants for which their high level of predicted structural disorder has been correlated with a particular function, or where there is experimental evidence linking this structural feature with its protein function. Using examples of plant IDPs involved in the control of cell cycle, metabolism, hormonal signaling and regulation of gene expression, development and responses to stress, we demonstrate the critical importance of IDPs throughout the life of the plant.
Collapse
Affiliation(s)
- Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico.
| | - Cesar L Cuevas-Velazquez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - Paulette S Romero-Pérez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - David F Rendón-Luna
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - Caspar C C Chater
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| |
Collapse
|
12
|
Wang Z, Liu W, Fan G, Zhai X, Zhao Z, Dong Y, Deng M, Cao Y. Quantitative proteome-level analysis of paulownia witches' broom disease with methyl methane sulfonate assistance reveals diverse metabolic changes during the infection and recovery processes. PeerJ 2017; 5:e3495. [PMID: 28690927 PMCID: PMC5497676 DOI: 10.7717/peerj.3495] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/02/2017] [Indexed: 12/17/2022] Open
Abstract
Paulownia witches' broom (PaWB) disease caused by phytoplasma is a fatal disease that leads to considerable economic losses. Although there are a few reports describing studies of PaWB pathogenesis, the molecular mechanisms underlying phytoplasma pathogenicity in Paulownia trees remain uncharacterized. In this study, after building a transcriptome database containing 67,177 sequences, we used isobaric tags for relative and absolute quantification (iTRAQ) to quantify and analyze the proteome-level changes among healthy P. fortunei (PF), PaWB-infected P. fortunei (PFI), and PaWB-infected P. fortunei treated with 20 mg L-1 or 60 mg L-1 methyl methane sulfonate (MMS) (PFI-20 and PFI-60, respectively). A total of 2,358 proteins were identified. We investigated the proteins profiles in PF vs. PFI (infected process) and PFI-20 vs. PFI-60 (recovered process), and further found that many of the MMS-response proteins mapped to "photosynthesis" and "ribosome" pathways. Based on our comparison scheme, 36 PaWB-related proteins were revealed. Among them, 32 proteins were classified into three functional groups: (1) carbohydrate and energy metabolism, (2) protein synthesis and degradation, and (3) stress resistance. We then investigated the PaWB-related proteins involved in the infected and recovered processes, and discovered that carbohydrate and energy metabolism was inhibited, and protein synthesis and degradation decreased, as the plant responded to PaWB. Our observations may be useful for characterizing the proteome-level changes that occur at different stages of PaWB disease. The data generated in this study may serve as a valuable resource for elucidating the pathogenesis of PaWB disease during phytoplasma infection and recovery stages.
Collapse
Affiliation(s)
- Zhe Wang
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, China
| | - Wenshan Liu
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, China.,College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Guoqiang Fan
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, China.,College of Forestry, Henan Agricultural University, Zhengzhou, China
| | | | - Zhenli Zhao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, China.,College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yanpeng Dong
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, China.,College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Minjie Deng
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, China.,College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yabing Cao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, China
| |
Collapse
|