1
|
Uszczynska-Ratajczak B, Sugunan S, Kwiatkowska M, Migdal M, Carbonell-Sala S, Sokol A, Winata CL, Chacinska A. Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish. Life Sci Alliance 2022; 6:6/1/e202201514. [PMID: 36283702 PMCID: PMC9595208 DOI: 10.26508/lsa.202201514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/08/2022] Open
Abstract
Most mitochondrial proteins are encoded by nuclear genes, synthetized in the cytosol and targeted into the organelle. To characterize the spatial organization of mitochondrial gene products in zebrafish (Danio rerio), we sequenced RNA from different cellular fractions. Our results confirmed the presence of nuclear-encoded mRNAs in the mitochondrial fraction, which in unperturbed conditions, are mainly transcripts encoding large proteins with specific properties, like transmembrane domains. To further explore the principles of mitochondrial protein compartmentalization in zebrafish, we quantified the transcriptomic changes for each subcellular fraction triggered by the chchd4a -/- mutation, causing the disorders in the mitochondrial protein import. Our results indicate that the proteostatic stress further restricts the population of transcripts on the mitochondrial surface, allowing only the largest and the most evolutionary conserved proteins to be synthetized there. We also show that many nuclear-encoded mitochondrial transcripts translated by the cytosolic ribosomes stay resistant to the global translation shutdown. Thus, vertebrates, in contrast to yeast, are not likely to use localized translation to facilitate synthesis of mitochondrial proteins under proteostatic stress conditions.
Collapse
Affiliation(s)
- Barbara Uszczynska-Ratajczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland .,Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Sreedevi Sugunan
- ReMedy International Research Agenda Unit, University of Warsaw, Warsaw, Poland,International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Monika Kwiatkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland,Centre of New Technologies, University of Warsaw, Warsaw, Poland,International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Maciej Migdal
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Silvia Carbonell-Sala
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anna Sokol
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany,Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Cecilia L Winata
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Agnieszka Chacinska
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
2
|
Li Z, Liu R, Liu Y, Zhao M, Luan J, Wang Y, Shang W, Song X, Sun Y, Han F. H55 N variation in citrate synthase leads to decrement in the enzyme activity and transport rate to mitochondria in HEI-OC1 cells. Biochem Biophys Res Commun 2022; 612:134-140. [PMID: 35525197 DOI: 10.1016/j.bbrc.2022.04.104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 04/22/2022] [Indexed: 11/16/2022]
Abstract
A/J mouse is a typical animal model of age-related deafness. Previous studies have shown that the mice suffer from progressive hearing loss and degeneration of cochlear cells, and a variation of H55 N in citrate synthase (CS) causes about 40% the hearing loss. CS is a key enzyme in the tricarboxylic acid cycle, which is transported from cytoplasm to mitochondria after synthesis, sorted by the mitochondrial targeting sequence (MTS). To explore the mechanism of CS (H55 N) variation in affecting its function, HEI-OC1 cells were infected with lentivirus particles to express CS-Flag or CS(H55 N)-Flag. The results showed that H55 N variation in CS, as purified by co-immunoprecipitation, decreased the enzyme activity by about 50%. Confocal microscope co-localization indicated that the CS (H55 N) variation led to a decrement in its mitochondrial content. Western blot also showed the amount of CS(H55 N)-Flag was more than that of CS(WT)-Flag in the cytosol. The results suggest H55 N variation in CS lead to decrement of its enzyme activity and targeting transport to mitochondria. We therefore conclude that decrement in CS activity and mitochondrial delivery contributes to the degeneration of cochlear cells and thus the hearing loss in A/J mice.
Collapse
Affiliation(s)
- Zhen Li
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China; Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China
| | - Rongrong Liu
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China; Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China
| | - Yingying Liu
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China
| | - Mengmeng Zhao
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China; Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China
| | - Jun Luan
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China
| | - Yan Wang
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China
| | - Wenjing Shang
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China
| | - Xicheng Song
- Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China
| | - Yan Sun
- Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China.
| | - Fengchan Han
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China.
| |
Collapse
|
3
|
The Mitochondrial Genome in Aging and Disease and the Future of Mitochondrial Therapeutics. Biomedicines 2022; 10:biomedicines10020490. [PMID: 35203698 PMCID: PMC8962324 DOI: 10.3390/biomedicines10020490] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/10/2022] [Accepted: 02/16/2022] [Indexed: 11/29/2022] Open
Abstract
Mitochondria are intracellular organelles that utilize nutrients to generate energy in the form of ATP by oxidative phosphorylation. Mitochondrial DNA (mtDNA) in humans is a 16,569 base pair double-stranded circular DNA that encodes for 13 vital proteins of the electron transport chain. Our understanding of the mitochondrial genome’s transcription, translation, and maintenance is still emerging, and human pathologies caused by mtDNA dysfunction are widely observed. Additionally, a correlation between declining mitochondrial DNA quality and copy number with organelle dysfunction in aging is well-documented in the literature. Despite tremendous advancements in nuclear gene-editing technologies and their value in translational avenues, our ability to edit mitochondrial DNA is still limited. In this review, we discuss the current therapeutic landscape in addressing the various pathologies that result from mtDNA mutations. We further evaluate existing gene therapy efforts, particularly allotopic expression and its potential to become an indispensable tool for restoring mitochondrial health in disease and aging.
Collapse
|
4
|
Avendaño-Monsalve MC, Ponce-Rojas JC, Funes S. From cytosol to mitochondria: the beginning of a protein journey. Biol Chem 2020; 401:645-661. [DOI: 10.1515/hsz-2020-0110] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/24/2020] [Indexed: 01/18/2023]
Abstract
AbstractMitochondrial protein import is one of the key processes during mitochondrial biogenesis that involves a series of events necessary for recognition and delivery of nucleus-encoded/cytosol-synthesized mitochondrial proteins into the organelle. The past research efforts have mainly unraveled how membrane translocases ensure the correct protein sorting within the different mitochondrial subcompartments. However, early steps of recognition and delivery remain relatively uncharacterized. In this review, we discuss our current understanding about the signals on mitochondrial proteins, as well as in the mRNAs encoding them, which with the help of cytosolic chaperones and membrane receptors support protein targeting to the organelle in order to avoid improper localization. In addition, we discuss recent findings that illustrate how mistargeting of mitochondrial proteins triggers stress responses, aiming to restore cellular homeostasis.
Collapse
Affiliation(s)
- Maria Clara Avendaño-Monsalve
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n Ciudad Universitaria Coyoacán, México, Cd.Mx. 04510, Mexico
| | - José Carlos Ponce-Rojas
- Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Soledad Funes
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n Ciudad Universitaria Coyoacán, México, Cd.Mx. 04510, Mexico
| |
Collapse
|
5
|
Chaudhuri A, Das S, Das B. Localization elements and zip codes in the intracellular transport and localization of messenger RNAs in Saccharomyces cerevisiae. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1591. [PMID: 32101377 DOI: 10.1002/wrna.1591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
Intracellular trafficking and localization of mRNAs provide a mechanism of regulation of expression of genes with excellent spatial control. mRNA localization followed by localized translation appears to be a mechanism of targeted protein sorting to a specific cell-compartment, which is linked to the establishment of cell polarity, cell asymmetry, embryonic axis determination, and neuronal plasticity in metazoans. However, the complexity of the mechanism and the components of mRNA localization in higher organisms prompted the use of the unicellular organism Saccharomyces cerevisiae as a simplified model organism to study this vital process. Current knowledge indicates that a variety of mRNAs are asymmetrically and selectively localized to the tip of the bud of the daughter cells, to the vicinity of endoplasmic reticulum, mitochondria, and nucleus in this organism, which are connected to diverse cellular processes. Interestingly, specific cis-acting RNA localization elements (LEs) or RNA zip codes play a crucial role in the localization and trafficking of these localized mRNAs by providing critical binding sites for the specific RNA-binding proteins (RBPs). In this review, we present a comprehensive account of mRNA localization in S. cerevisiae, various types of localization elements influencing the mRNA localization, and the RBPs, which bind to these LEs to implement a number of vital physiological processes. Finally, we emphasize the significance of this process by highlighting their connection to several neuropathological disorders and cancers. This article is categorized under: RNA Export and Localization > RNA Localization.
Collapse
Affiliation(s)
- Anusha Chaudhuri
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Subhadeep Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| |
Collapse
|
6
|
Ryder PV, Lerit DA. RNA localization regulates diverse and dynamic cellular processes. Traffic 2018; 19:496-502. [PMID: 29653028 DOI: 10.1111/tra.12571] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/05/2018] [Accepted: 04/05/2018] [Indexed: 02/06/2023]
Abstract
At the nexus of specialized cellular responses are localized enrichments of protein activity. The localization of messenger RNA (mRNA) coupled with translational control often plays a crucial role in the generation of protein concentrations at defined subcellular domains. Although mRNA localization is classically associated with large specialized cells, such as neurons and embryos, RNA localization is a highly conserved paradigm of post-transcriptional regulation observed in diverse cellular contexts. Functions of localized mRNAs extend far beyond the well-studied examples of neuronal polarization and developmental patterning. Since the initial discovery of the intracellular localization of cytoskeletal mRNAs within migrating cells, hundreds of mRNAs are now known to be enriched at specific organelles where they contribute to cell function. In this short review, we discuss basic principles regulating RNA localization and consider the contribution of localized mRNA to several essential cellular behaviors. We consider RNA localization as a mechanism with widespread implications for cellular function.
Collapse
Affiliation(s)
- Pearl V Ryder
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia
| | - Dorothy A Lerit
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia
| |
Collapse
|
7
|
Abstract
Cells are highly organized entities that rely on intricate addressing mechanisms to sort their constituent molecules to precise subcellular locations. These processes are crucial for cells to maintain their proper organization and carry out specialized functions in the body, consequently genetic perturbations that clog up these addressing systems can contribute to disease aetiology. The trafficking of RNA molecules represents an important layer in the control of cellular organization, a process that is both highly prevalent and for which features of the regulatory machineries have been deeply conserved evolutionarily. RNA localization is commonly driven by trans-regulatory factors, including RNA binding proteins at the core, which recognize specific cis-acting zipcode elements within the RNA transcripts. Here, we first review the functions and biological benefits of intracellular RNA trafficking, from the perspective of both coding and non-coding RNAs. Next, we discuss the molecular mechanisms that modulate this localization, emphasizing the diverse features of the cis- and trans-regulators involved, while also highlighting emerging technologies and resources that will prove instrumental in deciphering RNA targeting pathways. We then discuss recent findings that reveal how co-transcriptional regulatory mechanisms operating in the nucleus can dictate the downstream cytoplasmic localization of RNAs. Finally, we survey the growing number of human diseases in which RNA trafficking pathways are impacted, including spinal muscular atrophy, Alzheimer's disease, fragile X syndrome and myotonic dystrophy. Such examples highlight the need to further dissect RNA localization mechanisms, which could ultimately pave the way for the development of RNA-oriented diagnostic and therapeutic strategies. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
Collapse
Affiliation(s)
- Ashley Chin
- Institut de recherches cliniques de Montréal (IRCM), 110 Avenue des Pins Ouest, Montreal, Quebec, Canada; Division of Experimental Medicine, McGill University, 1001 Decarie Boulevard, Montreal, Quebec, Canada
| | - Eric Lécuyer
- Institut de recherches cliniques de Montréal (IRCM), 110 Avenue des Pins Ouest, Montreal, Quebec, Canada; Division of Experimental Medicine, McGill University, 1001 Decarie Boulevard, Montreal, Quebec, Canada; Department of Biochemistry and Molecular Medicine, University of Montreal, 2900 Boulevard Edouard-Montpetit, Montreal, Quebec, Canada.
| |
Collapse
|
8
|
Abstract
The localization of mRNAs to specific subcellular sites is widespread, allowing cells to spatially restrict and regulate protein production, and playing important roles in development and cellular physiology. This process has been studied in mechanistic detail for several RNAs. However, the generality or specificity of RNA localization systems and mechanisms that impact the many thousands of localized mRNAs has been difficult to assess. In this review, we discuss the current state of the field in determining which RNAs localize, which RNA sequences mediate localization, the protein factors involved, and the biological implications of localization. For each question, we examine prominent systems and techniques that are used to study individual messages, highlight recent genome-wide studies of RNA localization, and discuss the potential for adapting other high-throughput approaches to the study of localization.
Collapse
Affiliation(s)
- J Matthew Taliaferro
- a Department of Biology; Massachusetts Institute of Technology ; Cambridge , MA USA
| | | | | |
Collapse
|
9
|
Abstract
The mitochondrion is arguably the most complex organelle in the budding yeast cell cytoplasm. It is essential for viability as well as respiratory growth. Its innermost aqueous compartment, the matrix, is bounded by the highly structured inner membrane, which in turn is bounded by the intermembrane space and the outer membrane. Approximately 1000 proteins are present in these organelles, of which eight major constituents are coded and synthesized in the matrix. The import of mitochondrial proteins synthesized in the cytoplasm, and their direction to the correct soluble compartments, correct membranes, and correct membrane surfaces/topologies, involves multiple pathways and macromolecular machines. The targeting of some, but not all, cytoplasmically synthesized mitochondrial proteins begins with translation of messenger RNAs localized to the organelle. Most proteins then pass through the translocase of the outer membrane to the intermembrane space, where divergent pathways sort them to the outer membrane, inner membrane, and matrix or trap them in the intermembrane space. Roughly 25% of mitochondrial proteins participate in maintenance or expression of the organellar genome at the inner surface of the inner membrane, providing 7 membrane proteins whose synthesis nucleates the assembly of three respiratory complexes.
Collapse
|
10
|
Weis BL, Schleiff E, Zerges W. Protein targeting to subcellular organelles via MRNA localization. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:260-73. [PMID: 23457718 DOI: 10.1016/j.bbamcr.2012.04.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cells have complex membranous organelles for the compartmentalization and the regulation of most intracellular processes. Organelle biogenesis and maintenance requires newly synthesized proteins, each of which needs to go from the ribosome translating its mRNA to the correct membrane for insertion or transclocation to an a organellar subcompartment. Decades of research have revealed how proteins are targeted to the correct organelle and translocated across one or more organelle membranes ro the compartment where they function. The paradigm examples involve interactions between a peptide sequence in the protein, localization factors, and various membrane embedded translocation machineries. Membrane translocation is either cotranslational or posttranslational depending on the protein and target organelle. Meanwhile research in embryos, neurons and yeast revealed an alternative targeting mechanism in which the mRNA is localized and only then translated to synthesize the protein in the correct location. In these cases, the targeting information is coded by the cis-acting sequences in the mRNA ("Zipcodes") that interact with localization factors and, in many cases, are transported by the molecular motors on the cytoskeletal filaments. Recently, evidence has been found for this "mRNA based" mechanism in organelle protein targeting to endoplasmic reticulum, mitochondria, and the photosynthetic membranes within chloroplasts. Here we review known and potential roles of mRNA localization in protein targeting to and within organelles. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
Collapse
Affiliation(s)
- Benjamin L Weis
- Goether University, Cluster of Excellence Macromolecular Complexes, Institute for Molecular Biosciences, Max-von-Laue Str. 9, D-60438 Frankfort, Germany
| | | | | |
Collapse
|
11
|
Gadir N, Haim-Vilmovsky L, Kraut-Cohen J, Gerst JE. Localization of mRNAs coding for mitochondrial proteins in the yeast Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2011; 17:1551-65. [PMID: 21705432 PMCID: PMC3153978 DOI: 10.1261/rna.2621111] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Targeted mRNA localization is a likely determinant of localized protein synthesis. To investigate whether mRNAs encoding mitochondrial proteins (mMPs) localize to mitochondria and, thus, might confer localized protein synthesis and import, we visualized endogenously expressed mMPs in vivo for the first time. We determined the localization of 24 yeast mMPs encoding proteins of the mitochondrial matrix, outer and inner membrane, and intermembrane space and found that many mMPs colocalize with mitochondria in vivo. This supports earlier cell fractionation and microarray-based studies that proposed mMP association with the mitochondrial fraction. Interestingly, a number of mMPs showed a dependency on the mitochondrial Puf3 RNA-binding protein, as well as nonessential proteins of the translocase of the outer membrane (TOM) complex import machinery, for normal colocalization with mitochondria. We examined the specific determinants of ATP2 and OXA1 mRNA localization and found a mutual dependency on the 3' UTR, Puf3, Tom7, and Tom70, but not Tom20, for localization. Tom6 may facilitate the localization of specific mRNAs as OXA1, but not ATP2, mRNA was mislocalized in tom6Δ cells. Interestingly, a substantial fraction of OXA1 and ATP2 RNA granules colocalized with the endoplasmic reticulum (ER) and a deletion in MDM10, which mediates mitochondria-ER tethering, resulted in a significant loss of OXA1 mRNA localization with ER. Finally, neither ATP2 nor OXA1 mRNA targeting was affected by a block in translation initiation, indicating that translation may not be essential for mRNA anchoring. Thus, endogenously expressed mRNAs are targeted to the mitochondria in vivo, and multiple factors contribute to mMP localization.
Collapse
Affiliation(s)
- Noga Gadir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Liora Haim-Vilmovsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Judith Kraut-Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jeffrey E. Gerst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
- Corresponding author.E-mail
| |
Collapse
|
12
|
Gilligan PC, Kumari P, Lim S, Cheong A, Chang A, Sampath K. Conservation defines functional motifs in the squint/nodal-related 1 RNA dorsal localization element. Nucleic Acids Res 2010; 39:3340-9. [PMID: 21149265 PMCID: PMC3082914 DOI: 10.1093/nar/gkq1185] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
RNA localization is emerging as a general principle of sub-cellular protein localization and cellular organization. However, the sequence and structural requirements in many RNA localization elements remain poorly understood. Whereas transcription factor-binding sites in DNA can be recognized as short degenerate motifs, and consensus binding sites readily inferred, protein-binding sites in RNA often contain structural features, and can be difficult to infer. We previously showed that zebrafish squint/nodal-related 1 (sqt/ndr1) RNA localizes to the future dorsal side of the embryo. Interestingly, mammalian nodal RNA can also localize to dorsal when injected into zebrafish embryos, suggesting that the sequence motif(s) may be conserved, even though the fish and mammal UTRs cannot be aligned. To define potential sequence and structural features, we obtained ndr1 3′-UTR sequences from approximately 50 fishes that are closely, or distantly, related to zebrafish, for high-resolution phylogenetic footprinting. We identify conserved sequence and structural motifs within the zebrafish/carp family and catfish. We find that two novel motifs, a single-stranded AGCAC motif and a small stem-loop, are required for efficient sqt RNA localization. These findings show that comparative sequencing in the zebrafish/carp family is an efficient approach for identifying weak consensus binding sites for RNA regulatory proteins.
Collapse
Affiliation(s)
- Patrick C Gilligan
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
| | | | | | | | | | | |
Collapse
|
13
|
Ding D, Dave KR, Bhattacharya SK. On Message Ribonucleic Acids Targeting to Mitochondria. BIOCHEMISTRY INSIGHTS 2009. [DOI: 10.4137/bci.s3745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Mitochondria are subcellular organelles that provide energy for a variety of basic cellular processes in eukaryotic cells. Mitochondria maintain their own genomes and many of their endosymbiont genes are encoded by nuclear genomes. The crosstalk between the mitochondrial and nuclear genomes ensures mitochondrial biogenesis, dynamics and maintenance. Mitochondrial proteins are partly encoded by nucleus and synthesized in the cytosol and partly in the mitochondria coded by mitochondrial genome. The efficiency of transport systems that transport nuclear encoded gene products such as proteins and mRNAs to the mitochondrial vicinity to allow for their translation and/or import are recently receiving wide attention. There is currently no concrete evidence that nuclear encoded mRNA is transported into the mitochondria, however, they can be transported onto the mitochondrial surface and translated at the surface of mitochondria utilizing cytosolic machinery. In this review we present an overview of the recent advances in the mRNA transport, with emphasis on the transport of nuclear-encoded mitochondrial protein mRNA into the mitochondria.
Collapse
Affiliation(s)
- Di Ding
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, USA
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA
| | - Kunjan R. Dave
- Department of Neurology, University of Miami, Miami, FL, USA
| | - Sanjoy K. Bhattacharya
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, USA
- Department of Neurology, University of Miami, Miami, FL, USA
| |
Collapse
|
14
|
Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|