1
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Janas T, Sapoń K, Janas T. Selection of bifunctional RNAs with specificity for arginine and lipid membranes. FEBS Lett 2024; 598:1061-1079. [PMID: 38649155 DOI: 10.1002/1873-3468.14880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/23/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
The molecular mechanisms of selective RNA loading into exosomes and other extracellular vesicles are not yet completely understood. In order to show that a pool of RNA sequences binds both the amino acid arginine and lipid membranes, we constructed a bifunctional RNA 10Arg aptamer specific for arginine and lipid vesicles. The preference of RNA 10Arg for lipid rafts was visualized and confirmed using FRET microscopy in neuroblastoma cells. The selection-amplification (SELEX) method using a doped (with the other three nucleotides) pool of RNA 10Arg sequences yielded several RNA 10Arg(D) sequences, and the affinities of these RNAs both to arginine and liposomes are improved in comparison to pre-doped RNA. Generation of these bispecific aptamers supports the hypothesis that an RNA molecule can bind both to RNA-binding proteins (RBPs) through arginine within the RBP-binding site and to membrane lipid rafts, thus facilitating RNA loading into exosomes and other extracellular vesicles.
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Affiliation(s)
- Teresa Janas
- Institute of Biology, University of Opole, Poland
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2
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Huster D, Maiti S, Herrmann A. Phospholipid Membranes as Chemically and Functionally Tunable Materials. Adv Mater 2024:e2312898. [PMID: 38456771 DOI: 10.1002/adma.202312898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/12/2024] [Indexed: 03/09/2024]
Abstract
The sheet-like lipid bilayer is the fundamental structural component of all cell membranes. Its building blocks are phospholipids and cholesterol. Their amphiphilic structure spontaneously leads to the formation of a bilayer in aqueous environment. Lipids are not just structural elements. Individual lipid species, the lipid membrane structure, and lipid dynamics influence and regulate membrane protein function. An exciting field is emerging where the membrane-associated material properties of different bilayer systems are used in designing innovative solutions for widespread applications across various fields, such as the food industry, cosmetics, nano- and biomedicine, drug storage and delivery, biotechnology, nano- and biosensors, and computing. Here, the authors summarize what is known about how lipids determine the properties and functions of biological membranes and how this has been or can be translated into innovative applications. Based on recent progress in the understanding of membrane structure, dynamics, and physical properties, a perspective is provided on how membrane-controlled regulation of protein functions can extend current applications and even offer new applications.
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Affiliation(s)
- Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, D-04107, Leipzig, Germany
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, 400 005, India
| | - Andreas Herrmann
- Freie Universität Berlin, Department Chemistry and Biochemistry, SupraFAB, Altensteinstr. 23a, D-14195, Berlin, Germany
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3
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Shang W, Lichtenberg E, Mlesnita AM, Wilde A, Koch HG. The contribution of mRNA targeting to spatial protein localization in bacteria. FEBS J 2024. [PMID: 38226707 DOI: 10.1111/febs.17054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and must be inserted into or translocated across the cytoplasmic membrane. This requires efficient targeting systems that recognize N-terminal signal sequences in client proteins and deliver them to protein transport complexes in the membrane. While the importance of these protein transport machineries for the spatial organization of the bacterial cell is well documented in multiple studies, the contribution of mRNA targeting and localized translation to protein transport is only beginning to emerge. mRNAs can exhibit diverse subcellular localizations in the bacterial cell and can accumulate at sites where new protein is required. This is frequently observed for mRNAs encoding membrane proteins, but the physiological importance of membrane enrichment of mRNAs and the consequences it has for the insertion of the encoded protein have not been explored in detail. Here, we briefly highlight some basic concepts of signal sequence-based protein targeting and describe in more detail strategies that enable the monitoring of mRNA localization in bacterial cells and potential mechanisms that route mRNAs to particular positions within the cell. Finally, we summarize some recent developments that demonstrate that mRNA targeting and localized translation can sustain membrane protein insertion under stress conditions when the protein-targeting machinery is compromised. Thus, mRNA targeting likely acts as a back-up strategy and complements the canonical signal sequence-based protein targeting.
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Affiliation(s)
- Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | | | - Andreea Mihaela Mlesnita
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
| | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
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4
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Rome S, Tacconi S. High-fat diets: You are what you eat….your extracellular vesicles too! J Extracell Vesicles 2024; 13:e12382. [PMID: 38151475 PMCID: PMC10752826 DOI: 10.1002/jev2.12382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/13/2023] [Accepted: 11/10/2023] [Indexed: 12/29/2023] Open
Abstract
Recent works indicate that the lipid composition of extracellular vesicles (EVs) can modify their biological functions and their incorporation into recipient cells. In particular high-fat diets affect EV biogenesis, EV lipid composition, EV targeting and consequently the cross-talk between tissues. This review connects different research topics to show that a vicious circle is established during the development of high-fat diet-induced obesity, connecting the alteration of lipid metabolism, the composition of extracellular vesicles and the spread of deleterious lipids between tissues, which participates in NAFLD/NASH and diabetes development. According to the studies described in this review, it is urgent to take an interest in this question as the modulation of EV lipid composition could be an important factor to take into account during the therapeutic management of patients suffering from metabolic syndrome and related pathologies such as obesity and diabetes. Furthermore, as lipid modification of EVs is a strategy currently being tested to enable better integration into their target tissue or cell, it is important to consider the impact of these lipid modifications on the homeostasis of these targets.
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Affiliation(s)
- Sophie Rome
- CarMeN Laboratory, INSERM 1060‐INRAE 1397, Department of Human Nutrition, Lyon Sud HospitalUniversity of LyonLyonFrance
| | - Stefano Tacconi
- CarMeN Laboratory, INSERM 1060‐INRAE 1397, Department of Human Nutrition, Lyon Sud HospitalUniversity of LyonLyonFrance
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5
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Toparlak Ö, Sebastianelli L, Egas Ortuno V, Karki M, Xing Y, Szostak JW, Krishnamurthy R, Mansy SS. Cyclophospholipids Enable a Protocellular Life Cycle. ACS Nano 2023; 17:23772-23783. [PMID: 38038709 PMCID: PMC10722605 DOI: 10.1021/acsnano.3c07706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
There is currently no plausible path for the emergence of a self-replicating protocell, because prevalent formulations of model protocells are built with fatty acid vesicles that cannot withstand the concentrations of Mg2+ needed for the function and replication of nucleic acids. Although prebiotic chelates increase the survivability of fatty acid vesicles, the resulting model protocells are incapable of growth and division. Here, we show that protocells made of mixtures of cyclophospholipids and fatty acids can grow and divide in the presence of Mg2+-citrate. Importantly, these protocells retain encapsulated nucleic acids during growth and division, can acquire nucleotides from their surroundings, and are compatible with the nonenzymatic extension of an RNA oligonucleotide, chemistry needed for the replication of a primitive genome. Our work shows that prebiotically plausible mixtures of lipids form protocells that are active under the conditions necessary for the emergence of Darwinian evolution.
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Affiliation(s)
- Ö.
Duhan Toparlak
- Department
of Cellular, Computational and Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo, Trentino, Italy
| | - Lorenzo Sebastianelli
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton Alberta T6G 2G2, Canada
| | - Veronica Egas Ortuno
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Megha Karki
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yanfeng Xing
- Department
of Biochemistry and Molecular Biology, University
of Chicago, Chicago, Illinois 60637, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Ramanarayanan Krishnamurthy
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sheref S. Mansy
- Department
of Cellular, Computational and Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo, Trentino, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton Alberta T6G 2G2, Canada
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6
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Wang Y, Pan Z, Mou M, Xia W, Zhang H, Zhang H, Liu J, Zheng L, Luo Y, Zheng H, Yu X, Lian X, Zeng Z, Li Z, Zhang B, Zheng M, Li H, Hou T, Zhu F. A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder. Nucleic Acids Res 2023; 51:e110. [PMID: 37889083 PMCID: PMC10682500 DOI: 10.1093/nar/gkad929] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/01/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
RNAs play essential roles in diverse physiological and pathological processes by interacting with other molecules (RNA/protein/compound), and various computational methods are available for identifying these interactions. However, the encoding features provided by existing methods are limited and the existing tools does not offer an effective way to integrate the interacting partners. In this study, a task-specific encoding algorithm for RNAs and RNA-associated interactions was therefore developed. This new algorithm was unique in (a) realizing comprehensive RNA feature encoding by introducing a great many of novel features and (b) enabling task-specific integration of interacting partners using convolutional autoencoder-directed feature embedding. Compared with existing methods/tools, this novel algorithm demonstrated superior performances in diverse benchmark testing studies. This algorithm together with its source code could be readily accessed by all user at: https://idrblab.org/corain/ and https://github.com/idrblab/corain/.
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Affiliation(s)
- Yunxia Wang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Ziqi Pan
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Weiqi Xia
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Hanyu Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Jin Liu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Lingyan Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Hanqi Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Xinyuan Yu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Xichen Lian
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Zhenyu Zeng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Bing Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Mingyue Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Honglin Li
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
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7
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Hatzianestis IH, Mountourakis F, Stavridou S, Moschou PN. Plant condensates: no longer membrane-less? Trends Plant Sci 2023; 28:1101-1112. [PMID: 37183142 DOI: 10.1016/j.tplants.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/16/2023]
Abstract
Cellular condensation is a reinvigorated area of study in biology, with scientific discussions focusing mainly on the forces that drive condensate formation, properties, and functions. Usually, condensates are called 'membrane-less' to highlight the absence of a surrounding membrane and the lack of associated contacts. In this opinion article we take a different direction, focusing on condensates that may be interfacing with membranes and their possible functions. We also highlight changes in condensate material properties brought about by condensate-membrane interactions, proposing how condensates-membrane interfaces could potentially affect interorganellar communication, development, and growth, but also adaptation in an evolutionary context. We would thus like to stimulate research in this area, which is much less understood in plants compared with the animal field.
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Affiliation(s)
- Ioannis H Hatzianestis
- Department of Biology, University of Crete, Heraklion, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
| | - Fanourios Mountourakis
- Department of Biology, University of Crete, Heraklion, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
| | | | - Panagiotis N Moschou
- Department of Biology, University of Crete, Heraklion, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece; Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
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8
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Szatkowska R, Furmanek E, Kierzek AM, Ludwig C, Adamczyk M. Mitochondrial Metabolism in the Spotlight: Maintaining Balanced RNAP III Activity Ensures Cellular Homeostasis. Int J Mol Sci 2023; 24:14763. [PMID: 37834211 PMCID: PMC10572830 DOI: 10.3390/ijms241914763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
RNA polymerase III (RNAP III) holoenzyme activity and the processing of its products have been linked to several metabolic dysfunctions in lower and higher eukaryotes. Alterations in the activity of RNAP III-driven synthesis of non-coding RNA cause extensive changes in glucose metabolism. Increased RNAP III activity in the S. cerevisiae maf1Δ strain is lethal when grown on a non-fermentable carbon source. This lethal phenotype is suppressed by reducing tRNA synthesis. Neither the cause of the lack of growth nor the underlying molecular mechanism have been deciphered, and this area has been awaiting scientific explanation for a decade. Our previous proteomics data suggested mitochondrial dysfunction in the strain. Using model mutant strains maf1Δ (with increased tRNA abundance) and rpc128-1007 (with reduced tRNA abundance), we collected data showing major changes in the TCA cycle metabolism of the mutants that explain the phenotypic observations. Based on 13C flux data and analysis of TCA enzyme activities, the present study identifies the flux constraints in the mitochondrial metabolic network. The lack of growth is associated with a decrease in TCA cycle activity and downregulation of the flux towards glutamate, aspartate and phosphoenolpyruvate (PEP), the metabolic intermediate feeding the gluconeogenic pathway. rpc128-1007, the strain that is unable to increase tRNA synthesis due to a mutation in the C128 subunit, has increased TCA cycle activity under non-fermentable conditions. To summarize, cells with non-optimal activity of RNAP III undergo substantial adaptation to a new metabolic state, which makes them vulnerable under specific growth conditions. Our results strongly suggest that balanced, non-coding RNA synthesis that is coupled to glucose signaling is a fundamental requirement to sustain a cell's intracellular homeostasis and flexibility under changing growth conditions. The presented results provide insight into the possible role of RNAP III in the mitochondrial metabolism of other cell types.
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Affiliation(s)
- Roza Szatkowska
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
| | - Emil Furmanek
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
| | - Andrzej M. Kierzek
- Certara UK Limited, Sheffield S1 2BJ, UK;
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, UK;
| | - Malgorzata Adamczyk
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
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9
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Solaguren-Beascoa M, Gámez-Valero A, Escaramís G, Herrero-Lorenzo M, Ortiz AM, Minguet C, Gonzalo R, Bravo MI, Costa M, Martí E. Phospho-RNA-Seq Highlights Specific Small RNA Profiles in Plasma Extracellular Vesicles. Int J Mol Sci 2023; 24:11653. [PMID: 37511412 PMCID: PMC10380198 DOI: 10.3390/ijms241411653] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/04/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Small RNAs (sRNAs) are bioactive molecules that can be detected in biofluids, reflecting physiological and pathological states. In plasma, sRNAs are found within extracellular vesicles (EVs) and in extravesicular compartments, offering potential sources of highly sensitive biomarkers. Deep sequencing strategies to profile sRNAs favor the detection of microRNAs (miRNAs), the best-known class of sRNAs. Phospho-RNA-seq, through the enzymatic treatment of sRNAs with T4 polynucleotide kinase (T4-PNK), has been recently developed to increase the detection of thousands of previously inaccessible RNAs. In this study, we investigated the value of phospho-RNA-seq on both the EVs and extravesicular plasma subfractions. Phospho-RNA-seq increased the proportion of sRNAs used for alignment and highlighted the diversity of the sRNA transcriptome. Unsupervised clustering analysis using sRNA counts matrices correctly classified the EVs and extravesicular samples only in the T4-PNK treated samples, indicating that phospho-RNA-seq stresses the features of sRNAs in each plasma subfraction. Furthermore, T4-PNK treatment emphasized specific miRNA variants differing in the 5'-end (5'-isomiRs) and certain types of tRNA fragments in each plasma fraction. Phospho-RNA-seq increased the number of tissue-specific messenger RNA (mRNA) fragments in the EVs compared with the extravesicular fraction, suggesting that phospho-RNA-seq favors the discovery of tissue-specific sRNAs in EVs. Overall, the present data emphasizes the value of phospho-RNA-seq in uncovering RNA-based biomarkers in EVs.
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Affiliation(s)
- Maria Solaguren-Beascoa
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
| | - Ana Gámez-Valero
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Ministerio de Ciencia Innovación y Universidades, 28029 Madrid, Spain
| | - Georgia Escaramís
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Ministerio de Ciencia Innovación y Universidades, 28029 Madrid, Spain
| | - Marina Herrero-Lorenzo
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
| | - Ana M Ortiz
- Grifols Scientific Innovation Office, 08022 Barcelona, Spain
| | - Carla Minguet
- Grifols Scientific Innovation Office, 08022 Barcelona, Spain
| | - Ricardo Gonzalo
- Grifols Scientific Innovation Office, 08022 Barcelona, Spain
| | | | | | - Eulàlia Martí
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Ministerio de Ciencia Innovación y Universidades, 28029 Madrid, Spain
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10
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Han L, Huang D, Wu S, Liu S, Wang C, Sheng Y, Lu X, Broxmeyer HE, Wan J, Yang L. Lipid droplet-associated lncRNA LIPTER preserves cardiac lipid metabolism. Nat Cell Biol 2023; 25:1033-1046. [PMID: 37264180 PMCID: PMC10344779 DOI: 10.1038/s41556-023-01162-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/03/2023] [Indexed: 06/03/2023]
Abstract
Lipid droplets (LDs) are cellular organelles critical for lipid homeostasis, with intramyocyte LD accumulation implicated in metabolic disorder-associated heart diseases. Here we identify a human long non-coding RNA, Lipid-Droplet Transporter (LIPTER), essential for LD transport in human cardiomyocytes. LIPTER binds phosphatidic acid and phosphatidylinositol 4-phosphate on LD surface membranes and the MYH10 protein, connecting LDs to the MYH10-ACTIN cytoskeleton and facilitating LD transport. LIPTER and MYH10 deficiencies impair LD trafficking, mitochondrial function and survival of human induced pluripotent stem cell-derived cardiomyocytes. Conditional Myh10 deletion in mouse cardiomyocytes leads to LD accumulation, reduced fatty acid oxidation and compromised cardiac function. We identify NKX2.5 as the primary regulator of cardiomyocyte-specific LIPTER transcription. Notably, LIPTER transgenic expression mitigates cardiac lipotoxicity, preserves cardiac function and alleviates cardiomyopathies in high-fat-diet-fed and Leprdb/db mice. Our findings unveil a molecular connector role of LIPTER in intramyocyte LD transport, crucial for lipid metabolism of the human heart, and hold significant clinical implications for treating metabolic syndrome-associated heart diseases.
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Affiliation(s)
- Lei Han
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dayang Huang
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shiyong Wu
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Cheng Wang
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yi Sheng
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiongbin Lu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hal E Broxmeyer
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lei Yang
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.
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11
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Salibi E, Peter B, Schwille P, Mutschler H. Periodic temperature changes drive the proliferation of self-replicating RNAs in vesicle populations. Nat Commun 2023; 14:1222. [PMID: 36869058 PMCID: PMC9984477 DOI: 10.1038/s41467-023-36940-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Growth and division of biological cells are based on the complex orchestration of spatiotemporally controlled reactions driven by highly evolved proteins. In contrast, it remains unknown how their primordial predecessors could achieve a stable inheritance of cytosolic components before the advent of translation. An attractive scenario assumes that periodic changes of environmental conditions acted as pacemakers for the proliferation of early protocells. Using catalytic RNA (ribozymes) as models for primitive biocatalytic molecules, we demonstrate that the repeated freezing and thawing of aqueous solutions enables the assembly of active ribozymes from inactive precursors encapsulated in separate lipid vesicle populations. Furthermore, we show that encapsulated ribozyme replicators can overcome freezing-induced content loss and successive dilution by freeze-thaw driven propagation in feedstock vesicles. Thus, cyclic freezing and melting of aqueous solvents - a plausible physicochemical driver likely present on early Earth - provides a simple scenario that uncouples compartment growth and division from RNA self-replication, while maintaining the propagation of these replicators inside new vesicle populations.
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Affiliation(s)
- Elia Salibi
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Benedikt Peter
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
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12
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Sarmah P, Shang W, Origi A, Licheva M, Kraft C, Ulbrich M, Lichtenberg E, Wilde A, Koch HG. mRNA targeting eliminates the need for the signal recognition particle during membrane protein insertion in bacteria. Cell Rep 2023; 42:112140. [PMID: 36842086 PMCID: PMC10066597 DOI: 10.1016/j.celrep.2023.112140] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 01/10/2023] [Accepted: 02/02/2023] [Indexed: 02/26/2023] Open
Abstract
Signal-sequence-dependent protein targeting is essential for the spatiotemporal organization of eukaryotic and prokaryotic cells and is facilitated by dedicated protein targeting factors such as the signal recognition particle (SRP). However, targeting signals are not exclusively contained within proteins but can also be present within mRNAs. By in vivo and in vitro assays, we show that mRNA targeting is controlled by the nucleotide content and by secondary structures within mRNAs. mRNA binding to bacterial membranes occurs independently of soluble targeting factors but is dependent on the SecYEG translocon and YidC. Importantly, membrane insertion of proteins translated from membrane-bound mRNAs occurs independently of the SRP pathway, while the latter is strictly required for proteins translated from cytosolic mRNAs. In summary, our data indicate that mRNA targeting acts in parallel to the canonical SRP-dependent protein targeting and serves as an alternative strategy for safeguarding membrane protein insertion when the SRP pathway is compromised.
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Affiliation(s)
- Pinku Sarmah
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Andrea Origi
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University Freiburg, 79104 Freiburg, Germany
| | - Maximilian Ulbrich
- Internal Medicine IV, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | | | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.
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13
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Dézé O, Laffleur B, Cogné M. Roles of G4-DNA and G4-RNA in Class Switch Recombination and Additional Regulations in B-Lymphocytes. Molecules 2023; 28. [PMID: 36770824 DOI: 10.3390/molecules28031159] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Mature B cells notably diversify immunoglobulin (Ig) production through class switch recombination (CSR), allowing the junction of distant "switch" (S) regions. CSR is initiated by activation-induced deaminase (AID), which targets cytosines adequately exposed within single-stranded DNA of transcribed targeted S regions, with a specific affinity for WRCY motifs. In mammals, G-rich sequences are additionally present in S regions, forming canonical G-quadruplexes (G4s) DNA structures, which favor CSR. Small molecules interacting with G4-DNA (G4 ligands), proved able to regulate CSR in B lymphocytes, either positively (such as for nucleoside diphosphate kinase isoforms) or negatively (such as for RHPS4). G4-DNA is also implicated in the control of transcription, and due to their impact on both CSR and transcriptional regulation, G4-rich sequences likely play a role in the natural history of B cell malignancies. Since G4-DNA stands at multiple locations in the genome, notably within oncogene promoters, it remains to be clarified how it can more specifically promote legitimate CSR in physiology, rather than pathogenic translocation. The specific regulatory role of G4 structures in transcribed DNA and/or in corresponding transcripts and recombination hereby appears as a major issue for understanding immune responses and lymphomagenesis.
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14
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Boyd MA, Thavarajah W, Lucks JB, Kamat NP. Robust and tunable performance of a cell-free biosensor encapsulated in lipid vesicles. Sci Adv 2023; 9:eadd6605. [PMID: 36598992 PMCID: PMC9812392 DOI: 10.1126/sciadv.add6605] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/23/2022] [Indexed: 05/21/2023]
Abstract
Cell-free systems have enabled the development of genetically encoded biosensors to detect a range of environmental and biological targets. Encapsulation of these systems in synthetic membranes to form artificial cells can reintroduce features of the cellular membrane, including molecular containment and selective permeability, to modulate cell-free sensing capabilities. Here, we demonstrate robust and tunable performance of a transcriptionally regulated, cell-free riboswitch encapsulated in lipid membranes, allowing the detection of fluoride, an environmentally important molecule. Sensor response can be tuned by varying membrane composition, and encapsulation protects from sensor degradation, facilitating detection in real-world samples. These sensors can detect fluoride using two types of genetically encoded outputs, enabling detection of fluoride at the Environmental Protection Agency maximum contaminant level of 0.2 millimolars. This work demonstrates the capacity of bilayer membranes to confer tunable permeability to encapsulated, genetically encoded sensors and establishes the feasibility of artificial cell platforms to detect environmentally relevant small molecules.
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Affiliation(s)
- Margrethe A. Boyd
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Walter Thavarajah
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Julius B. Lucks
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Corresponding author. (N.P.K.); (J.B.L.)
| | - Neha P. Kamat
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Corresponding author. (N.P.K.); (J.B.L.)
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15
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Tekin E, Salditt A, Schwintek P, Wunnava S, Langlais J, Saenz J, Tang D, Schwille P, Mast C, Braun D. Prebiotic Foam Environments to Oligomerize and Accumulate RNA. Chembiochem 2022; 23:e202200423. [PMID: 36354762 PMCID: PMC10100173 DOI: 10.1002/cbic.202200423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/24/2022] [Indexed: 11/12/2022]
Abstract
When water interacts with porous rocks, its wetting and surface tension properties create air bubbles in large number. To probe their relevance as a setting for the emergence of life, we microfluidically created foams that were stabilized with lipids. A persistent non-equilibrium setting was provided by a thermal gradient. The foam's large surface area triggers capillary flows and wet-dry reactions that accumulate, aggregate and oligomerize RNA, offering a compelling habitat for RNA-based early life as it offers both wet and dry conditions in direct neighborhood. Lipids were screened to stabilize the foams. The prebiotically more probable myristic acid stabilized foams over many hours. The capillary flow created by the evaporation at the water-air interface provided an attractive force for molecule localization and selection for molecule size. For example, self-binding oligonucleotide sequences accumulated and formed micrometer-sized aggregates which were shuttled between gas bubbles. The wet-dry cycles at the foam bubble interfaces triggered a non-enzymatic RNA oligomerization from 2',3'-cyclic CMP and GMP which despite the small dry reaction volume was superior to the corresponding dry reaction. The found characteristics make heated foams an interesting, localized setting for early molecular evolution.
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Affiliation(s)
- Emre Tekin
- Systems BiophysicsCenter for Nano-Science and Origins Cluster Initiative Department of PhysicsLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MünchenGermany
| | - Annalena Salditt
- Systems BiophysicsCenter for Nano-Science and Origins Cluster Initiative Department of PhysicsLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MünchenGermany
| | - Philipp Schwintek
- Systems BiophysicsCenter for Nano-Science and Origins Cluster Initiative Department of PhysicsLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MünchenGermany
| | - Sreekar Wunnava
- Systems BiophysicsCenter for Nano-Science and Origins Cluster Initiative Department of PhysicsLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MünchenGermany
| | - Juliette Langlais
- Systems BiophysicsCenter for Nano-Science and Origins Cluster Initiative Department of PhysicsLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MünchenGermany
| | - James Saenz
- Center for Molecular BioengineeringTechnische Universität DresdenHelmholtzstrasse 1001069DresdenGermany
| | - Dora Tang
- Dynamic Protocellular SystemsMax-Planck Institute for Molecular Cell Biology and GeneticsPfotenhauerstrasse 10801307DresdenGermany
| | - Petra Schwille
- Cellular and Molecular BiophysicsMax-Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Christof Mast
- Systems BiophysicsCenter for Nano-Science and Origins Cluster Initiative Department of PhysicsLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MünchenGermany
| | - Dieter Braun
- Systems BiophysicsCenter for Nano-Science and Origins Cluster Initiative Department of PhysicsLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MünchenGermany
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16
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An K, Kurek D, Mahadeo M, Zhang Y, Thewalt JL, Cullis PR, Kulkarni JA. On the Influence of Nucleic Acid Backbone Modifications on Lipid Nanoparticle Morphology. Langmuir 2022; 38:14036-14043. [PMID: 36367350 DOI: 10.1021/acs.langmuir.2c01492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nucleic acid therapeutics represent a major advance toward treating diseases at their root cause. However, nucleic acids are prone to degradation by serum endonucleases, clearance through the immune system, and rapid degradation in complex medium. To overcome these barriers, nucleic acids frequently include chemical modifications to improve stability or decrease immune responses. Lipid nanoparticles (LNPs) have enabled a dramatic reduction in the dose required to achieve a therapeutic effect by protecting these nucleic acids and improving their intracellular delivery. It has been assumed thus far that nonspecific ionic interactions drive LNP formation and chemical modifications to the nucleic acid backbone to confer improved stability do not impact LNP delivery in any way. Here, we demonstrate that these chemical modifications do impact LNP morphology substantially, and phosphorothioate modifications produce stronger interactions with ionizable amino lipids, resulting in enhanced entrapment. This work represents a major first step toward greater understanding of the interaction between the lipid components and nucleic acids within an LNP.
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Affiliation(s)
- Kevin An
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British ColumbiaV6T 1Z3, Canada
- NanoVation Therapeutics, 2405 Wesbrook Mall, Vancouver, British ColumbiaV6T 1Z3, Canada
| | - Daniel Kurek
- NanoVation Therapeutics, 2405 Wesbrook Mall, Vancouver, British ColumbiaV6T 1Z3, Canada
| | - Mark Mahadeo
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, British ColumbiaV5A 1S6, Canada
| | - Yao Zhang
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British ColumbiaV6T 1Z3, Canada
| | - Jenifer L Thewalt
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, British ColumbiaV5A 1S6, Canada
| | - Pieter R Cullis
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British ColumbiaV6T 1Z3, Canada
- NanoVation Therapeutics, 2405 Wesbrook Mall, Vancouver, British ColumbiaV6T 1Z3, Canada
- NanoMedicines Innovation Network, VancouverV6T 1Z3, Canada
| | - Jayesh A Kulkarni
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British ColumbiaV6T 1Z3, Canada
- NanoVation Therapeutics, 2405 Wesbrook Mall, Vancouver, British ColumbiaV6T 1Z3, Canada
- NanoMedicines Innovation Network, VancouverV6T 1Z3, Canada
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17
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Luthey-Schulten Z, Thornburg ZR, Gilbert BR. Integrating cellular and molecular structures and dynamics into whole-cell models. Curr Opin Struct Biol 2022; 75:102392. [PMID: 35623188 DOI: 10.1016/j.sbi.2022.102392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/03/2022]
Abstract
A complete description of the state of the cell requires knowledge of its size, shape, components, intracellular reactions, and interactions with its environment-all of these as a function of time and cell growth. Adding to this list is the need for theoretical models and simulations that integrate and help to interpret this daunting amount of experimental data. It seems like an overwhelming list of requirements, but progress is being made on many fronts. In this review, we discuss the current challenges and problems in obtaining sufficient information about each aspect of a dynamical whole-cell model (DWCM) for simple and well-studied bacterial systems.
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Affiliation(s)
- Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA; Center for the Physics of the Living Cell, University of Illinois at Urbana-Champaign, USA.
| | - Zane R Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, USA
| | - Benjamin R Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, USA
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18
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Wang X, Han X, Powell CA. Lipids and genes: Regulatory roles of lipids in RNA expression. Clin Transl Med 2022; 12:e863. [PMID: 35588460 PMCID: PMC9119606 DOI: 10.1002/ctm2.863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 11/11/2022] Open
Abstract
Nuclear lipid metabolism and metabolites play important roles in regulation of lipid-lipid, lipid-gene, lipid-chromatin, lipid-membrane and lipid-protein interactions to maintain the nuclear microenvironment, three-dimensional chromatin architecture, gene expression and transcription and biological function. This Editorial highlights the value of lipid-gene interaction in the identification and development of biomarkers and targets and emphasizes the significance of inter-regulation between lipids and genes in innovation and application of precise therapies for patients. Regulatory functions of nuclear lipid dynamics and biophysics modify transcriptomic expression, and modification (lipotranscriptome) can be a new approach for discovery and development of disease-specific diagnoses and therapies, although there are several challenges to be overcome. Better understanding of how lipid-based changes of nuclear functions and transcriptomic profiles modify clinical phenomes will provide new insights to understand molecular mechanisms of diseases and to develop spatiotemporal molecular medicine diagnostics and therapeutics.
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Affiliation(s)
- Xiangdong Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, China.,Shanghai Institute of Clinical Bioinformatics, Shanghai, China.,Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China
| | - Xianlin Han
- Department of Medicine - Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Charles A Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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