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Yi S, Guo X, Lou W, Mao S, Luan G, Lu X. Structure, Regulation, and Significance of Cyanobacterial and Chloroplast Adenosine Triphosphate Synthase in the Adaptability of Oxygenic Photosynthetic Organisms. Microorganisms 2024; 12:940. [PMID: 38792770 PMCID: PMC11124002 DOI: 10.3390/microorganisms12050940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
In cyanobacteria and chloroplasts (in algae and plants), ATP synthase plays a pivotal role as a photosynthetic membrane complex responsible for producing ATP from adenosine diphosphate and inorganic phosphate, utilizing a proton motive force gradient induced by photosynthesis. These two ATP synthases exhibit similarities in gene organization, amino acid sequences of subunits, structure, and functional mechanisms, suggesting that cyanobacterial ATP synthase is probably the evolutionary precursor to chloroplast ATP synthase. In this review, we explore the precise synthesis and assembly of ATP synthase subunits to address the uneven stoichiometry within the complex during transcription, translation, and assembly processes. We also compare the regulatory strategies governing ATP synthase activity to meet varying energy demands in cyanobacteria and chloroplasts amid fluctuating natural environments. Furthermore, we delve into the role of ATP synthase in stress tolerance and photosynthetic carbon fixation efficiency in oxygenic photosynthetic organisms (OPsOs), along with the current researches on modifying ATP synthase to enhance carbon fixation efficiency under stress conditions. This review aims to offer theoretical insights and serve as a reference for understanding the functional mechanisms of ATP synthase, sparking innovative ideas for enhancing photosynthetic carbon fixation efficiency by utilizing ATP synthase as an effective module in OPsOs.
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Affiliation(s)
- Siyan Yi
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China;
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha 410004, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (X.G.); (G.L.); (X.L.)
| | - Xin Guo
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (X.G.); (G.L.); (X.L.)
- College of Live Science, Henan University, Kaifeng 450001, China
| | - Wenjing Lou
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (X.G.); (G.L.); (X.L.)
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Shaoming Mao
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China;
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha 410004, China
| | - Guodong Luan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (X.G.); (G.L.); (X.L.)
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (X.G.); (G.L.); (X.L.)
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
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Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
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Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res 2007; 35:4809-19. [PMID: 17621584 PMCID: PMC1950547 DOI: 10.1093/nar/gkm487] [Citation(s) in RCA: 231] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We applied a computational pipeline based on comparative genomics to bacteria, and identified 22 novel candidate RNA motifs. We predicted six to be riboswitches, which are mRNA elements that regulate gene expression on binding a specific metabolite. In separate studies, we confirmed that two of these are novel riboswitches. Three other riboswitch candidates are upstream of either a putative transporter gene in the order Lactobacillales, citric acid cycle genes in Burkholderiales or molybdenum cofactor biosynthesis genes in several phyla. The remaining riboswitch candidate, the widespread Genes for the Environment, for Membranes and for Motility (GEMM) motif, is associated with genes important for natural competence in Vibrio cholerae and the use of metal ions as electron acceptors in Geobacter sulfurreducens. Among the other motifs, one has a genetic distribution similar to a previously published candidate riboswitch, ykkC/yxkD, but has a different structure. We identified possible non-coding RNAs in five phyla, and several additional cis-regulatory RNAs, including one in ε-proteobacteria (upstream of purD, involved in purine biosynthesis), and one in Cyanobacteria (within an ATP synthase operon). These candidate RNAs add to the growing list of RNA motifs involved in multiple cellular processes, and suggest that many additional RNAs remain to be discovered.
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Affiliation(s)
- Zasha Weinberg
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
- *To whom correspondence should be addressed.(203) 432-6554(203) 432-6161
| | - Jeffrey E. Barrick
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Zizhen Yao
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Adam Roth
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Jane N. Kim
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Jeremy Gore
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Joy Xin Wang
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Elaine R. Lee
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Kirsten F. Block
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Narasimhan Sudarsan
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Shane Neph
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Martin Tompa
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Walter L. Ruzzo
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
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