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Cao G, Li HB, Yin Z, Flavell RA. Recent advances in dynamic m6A RNA modification. Open Biol 2016; 6:160003. [PMID: 27249342 PMCID: PMC4852458 DOI: 10.1098/rsob.160003] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/18/2016] [Indexed: 12/19/2022] Open
Abstract
The identification of m6A demethylases and high-throughput sequencing analysis of methylated transcriptome corroborated m6A RNA epigenetic modification as a dynamic regulation process, and reignited its investigation in the past few years. Many basic concepts of cytogenetics have been revolutionized by the growing understanding of the fundamental role of m6A in RNA splicing, degradation and translation. In this review, we summarize typical features of methylated transcriptome in mammals, and highlight the ‘writers’, ‘erasers’ and ‘readers’ of m6A RNA modification. Moreover, we emphasize recent advances of biological functions of m6A and conceive the possible roles of m6A in the regulation of immune response and related diseases.
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Affiliation(s)
- Guangchao Cao
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Hua-Bing Li
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Zhinan Yin
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China The First Affiliated Hospital, Biomedical Translational Research Institute, Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, People's Republic of China
| | - Richard A Flavell
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT 06520, USA Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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Meyer KD, Jaffrey SR. The dynamic epitranscriptome: N6-methyladenosine and gene expression control. Nat Rev Mol Cell Biol 2014; 15:313-26. [PMID: 24713629 DOI: 10.1038/nrm3785] [Citation(s) in RCA: 767] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
N(6)-methyladenosine (m(6)A) is a modified base that has long been known to be present in non-coding RNAs, ribosomal RNA, polyadenylated RNA and at least one mammalian mRNA. However, our understanding of the prevalence of this modification has been fundamentally redefined by transcriptome-wide m(6)A mapping studies, which have shown that m(6)A is present in a large subset of the transcriptome in specific regions of mRNA. This suggests that mRNA may undergo post-transcriptional methylation to regulate its fate and function, which is analogous to methyl modifications in DNA. Thus, the pattern of methylation constitutes an mRNA 'epitranscriptome'. The identification of adenosine methyltransferases ('writers'), m(6)A demethylating enzymes ('erasers') and m(6)A-binding proteins ('readers') is helping to define cellular pathways for the post-transcriptional regulation of mRNAs.
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Affiliation(s)
- Kate D Meyer
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York City, New York 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York City, New York 10065, USA
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Chang JH, Tong L. Mitochondrial poly(A) polymerase and polyadenylation. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1819:992-7. [PMID: 22172994 PMCID: PMC3307840 DOI: 10.1016/j.bbagrm.2011.10.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 10/25/2011] [Accepted: 10/27/2011] [Indexed: 01/22/2023]
Abstract
Polyadenylation of mitochondrial RNAs in higher eukaryotic organisms have diverse effects on their function and metabolism. Polyadenylation completes the UAA stop codon of a majority of mitochondrial mRNAs in mammals, regulates the translation of the mRNAs, and has diverse effects on their stability. In contrast, polyadenylation of most mitochondrial mRNAs in plants leads to their degradation, consistent with the bacterial origin of this organelle. PAPD1 (mtPAP, TUTase1), a noncanonical poly(A) polymerase (ncPAP), is responsible for producing the poly(A) tails in mammalian mitochondria. The crystal structure of human PAPD1 was reported recently, offering molecular insights into its catalysis. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Jeong Ho Chang
- Department of Biological Sciences, Columbia University, New York, NY10027, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY10027, USA
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Burkard G, Keller EB. Poly(A) polymerase and poly(g) polymerase in wheat chloroplasts. Proc Natl Acad Sci U S A 2010; 71:389-93. [PMID: 16592140 PMCID: PMC388011 DOI: 10.1073/pnas.71.2.389] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Extracts of wheat chloroplasts contain a poly(A) polymerase which can polymerize AMP residues from ATP onto an RNA primer. Whole extracts of wheat leaves also contain another poly(A) polymerase which is present in much larger amount and is probably derived from the nuclei. Both polymerases can utilize as primer poly(A), poly(C), transfer RNA, and ribosomal RNA, but only the chloroplast polymerase can utilize poly(U) and poly(G). Both enzymes have a specific requirement for ATP. Extracts of wheat chloroplasts contain, in addition to the poly(A) polymerase, a poly(G) polymerase which can polymerize GMP residues from GTP onto primers such as poly(G), poly(A), or ribosomal RNA. The poly(G) polymerase cannot utilize ATP but can slowly polymerize CMP from CTP. When the two chloroplast polymerases are present together in an in vitro incubation with ATP plus GTP and poly(A), the polymerization product is a mixed poly(A,G) tract.
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Affiliation(s)
- G Burkard
- Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14850
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Borowski LS, Szczesny RJ, Brzezniak LK, Stepien PP. RNA turnover in human mitochondria: more questions than answers? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1066-70. [PMID: 20117077 DOI: 10.1016/j.bbabio.2010.01.028] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 01/19/2010] [Accepted: 01/25/2010] [Indexed: 01/16/2023]
Abstract
Protein complexes responsible for RNA degradation play important role in three key aspects of RNA metabolism: they control stability of physiologically functional transcripts, remove the unnecessary RNA processing intermediates and destroy aberrantly formed RNAs. In mitochondria the post-transcriptional events seem to play a major role in regulation of gene expression, therefore RNA turnover is of particular importance. Despite many years of research, the details of this process are still a challenge. This review summarizes emerging landscape of interplay between the Suv3p helicase (SUPV3L1, Suv3), poly(A) polymerase and polynucleotide phosphorylase in controlling RNA degradation in human mitochondria.
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Affiliation(s)
- Lukasz S Borowski
- Institute of Genetics and Biotechnology, Faculty of Biology, Warsaw University, Pawinskiego 5a, 02-106 Warsaw, Poland
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Littauer UZ, Soreq H. The regulatory function of poly(A) and adjacent 3' sequences in translated RNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1982; 27:53-83. [PMID: 7048421 DOI: 10.1016/s0079-6603(08)60597-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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9
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Rascati R, Parsons P. Biosynthesis of cytochrome c oxidase by isolated rat liver mitochondria. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(17)37813-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Verdier G. Poly(adenylic acid)-containing RNA of Euglena gracilis during chloroplast development. I. Analysis of their complexity by hybridization to complementary DNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 93:573-80. [PMID: 105904 DOI: 10.1111/j.1432-1033.1979.tb12857.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Karpetsky TP, Boguski MS, Levy CC. Structures, properties, and possible biologic functions of polyadenylic acid. Subcell Biochem 1979; 6:1-116. [PMID: 377581 DOI: 10.1007/978-1-4615-7945-8_1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Eaton BT, Randlett DJ. Origin of the actinomycin D insensitive RNA species in Aedes albopictus cells. Nucleic Acids Res 1978; 5:1301-14. [PMID: 652522 PMCID: PMC342078 DOI: 10.1093/nar/5.4.1301] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In the presence of actinomycin D or a combination of actinomycin D and either camptothecin or alpha-amanatin. Aedes albopictus cells synthesize a variety of single stranded RNA species. These actinomycin D resistant species are ethidium bromide sensitive and they are present in the cell cytoplasm in an RNase resistant structure which has the sedimentation and buoyant density characteristics of mitochondria. Twelve actinomycin D insensitive RNA species can be detected by electrophoresis in 7M urea and 11 of these bind to oligo(dT)-cellulose. An identical set of oligo(dT)-cellulose binding RNA species is obtained when A. albopictus cells are labeled in the presence of camptothecin alone. The actinomycin D insensitive RNA species which bind to oligo(dT)-cellulose hybridize to mitochondrial DNA. These data indicate that the actinomycin D insensitive RNA species have a mitochondrial origin and are not associated with the replication of an inapparent contaminating virus.
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Grohmann K, Amairic F, Crews S, Attardi G. Failure to detect "cap" structures in mitochondrial DNA-coded poly(A)-containing RNA from HeLa cells. Nucleic Acids Res 1978; 5:637-51. [PMID: 643614 PMCID: PMC342012 DOI: 10.1093/nar/5.3.637] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The structure of the 5'-termini has been investigated in mitochondrial DNA-coded poly(A)-containing RNA from HeLa cells. For this purpose, mitochondrial RNA isolated from cells labeled for 3 hours with [32P]orthophosphate in the presence of 20 microgram/ml camptothecin, and selected for poly(A) content by two passages through oligo(dT)-cellulose, was digested either with the nuclease P1 or with a mixture of RNases: the digestion products were then fractionated by two-dimensional electrophoresis. No "cap" structures were detected under conditions where the presence of such structures in one out of five to ten RNA molecules would have been recognized. It is, therefore, likely that "cap" structures are completely absent in HeLa cell mitochondrial poly(A)-containing RNA.
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Puckett L, Darnell JE. Essential factors in the kinetic analysis of RNA synthesis in HeLa cells. J Cell Physiol 1977; 90:521-34. [PMID: 853064 DOI: 10.1002/jcp.1040900315] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Further evidence of mRNA in HeLa cells with a half-life two hours or less is given. A kinetic model of RNA synthesis in HeLa cells is described in which equilibration of label occurs first into the acid soluble pool (evidence is given that this pool feeds RNA synthesis) and thence in nuclear and cytoplasmic molecules. The measured accumulation of label in nuclear and cytoplasmic poly (A) is examined with the model and parameters were found which are consistent with the quantitative transfer of nuclear poly(A) to the cytoplasm. The strengths and limitations of the model are discussed.
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Gaitskhoki VS, Kisselev OI, Klimov NA. Polyribosomes and messenger RNA from rat liver mitochondria. Mol Cell Biochem 1977; 14:101-8. [PMID: 857143 DOI: 10.1007/bf01734172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Rat liver mitochondrial polyribosomes were isolated free from cytoplasmic ribonucleoprotein contaminations in a number of criteria (sedimentation and buoyant density patterns, ribosomal RNA composition). Heterogeneous poly A containing RNA from mitochondrial polysomes was purified by two-stage cellulose chromatography. This RNA was in vitro labelled with 125I up to specific activity approximately 10(6)-10(7) cts.min-1.microng-1 and used for hybridization experiments with separate complementary strands of mitochondrial DNA and nuclear DNA fragments. The proportions of mitochondrial poly A containing RNA that is complementary to heavy and light strands of mtDNA were respectively 31.5% and 8.3%. Besides, a significant RNA fraction was complementary to unique sequences of nuclear DNA (2-3 copies per haploid genome). The hybrids that were formed possessed a high Tm indicative of a perfect base pairing. A dual intracellular origin of mitochondrial messenger RNA is discussed.
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Attardi G, Costantino P, Lynch D, Mitchel C, Murphy W, Ojala D. Molecular and genetic approaches to the analysis of the informational content of the mitochondrial genome in mammalian cells. Mol Cell Biochem 1977; 14:151-64. [PMID: 854029 DOI: 10.1007/bf01734179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Our laboratory has been involved in the last few years in investigations aiming at analysing by molecular approaches the informational content of the mitochondrial genome in mammalian cells and the mechanisms and control of its expression, H eLa cells and other mammalian cell lines have been utilized for these studies. These investigations, as well as work carried out in other laboratories, have yielded a considerable amount of information concerning the mechanism, products and regulation of transcription of mitochondrial DNA (mit-DNA), the apparatus and products of mitochondria-specific protein synthesis in animal cells, and the number and topology of the sites on mit-DNA which code for the primary gene products identified so far. It is the purpose of the present report to summarize the latest observations in this area, as well as some recent results on the isolation and characterization of chloramphenicol-resistant variants of a human cell line. Reference is made to previous review articles 1,2,3 for the earlier work.
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Richter D, Isono K. The mechanism of protein synthesis-initiation, elongation and termination in translation of genetic messeges. Curr Top Microbiol Immunol 1977; 76:83-125. [PMID: 334484 DOI: 10.1007/978-3-642-66653-7_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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19
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Koch G. Synthesis of the mitochondrial inner membrane in cultured Xenopus laevis oocytes. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33064-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Abstract
Hybridization experiments with chloroplast DNA and 125I-labeled RNA from maize seedlings suggest that chloroplasts and etioplasts contain detectable amounts of RNA that contains poly(adenylic aicd) (poly (A)) and was transcribed from chloroplast DNA. About 6% of the total poly(A)-containing RNA isolated from maize seedlings hybridized to chloroplast DNA. Poly(A)-containing RNA could also be isolated directly from purified chloroplasts that were treated with ribonucleases to reduce cytoplasmic contamination. At least 65% of this poly(A)-containing RNA hybridized to chloroplast DNA. Chloroplast poly(A) tracts average about 45 nucleotides in length, one-half the average size of poly(A) tracts from whole cells. The poly (A) tracts themselves are probably added to plastid RNAs following their transcription, because maize chloroplast DNA was found not to contain poly(dT).
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Jacob ST, Rose KM, Munro HN. Response of poly(adenylic acid) polymerase in rat liver nuclei and mitochondria to stravation and re-feeding with amino acids. Biochem J 1976; 158:161-7. [PMID: 985420 PMCID: PMC1163955 DOI: 10.1042/bj1580161] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Poly(adenylic acid) polymerase was extracted from liver nuclei and mitochondria of rats either fed ad libitum, starved overnight or starved and then re-fed with a complete amino acid mixture for 1-3 h. The enzymes were partially purified and assayed by using exogenous primers. Starvation resulted in an 80% decrease in the total activity of the purified nuclear enzyme, and the mitochondrial enzyme activity diminished to almost zero after overnight starvation. Measurements of the protein content of whole nuclei or mitochondria and of the enzyme extracts from these organelles indicated that the decrease in enzyme activity on starvation was not caused by incomplete extraction of the enzyme from the starved animals. Re-feeding the animals with the complete amino acid mixture increased the total activity of poly(A) polymerase from the nuclei and mitochondria by 1.9-fold and 63-fold respectively. Under these conditions, the total protein content of the nuclei and mitochondria increased by only 13 and 32% respectively. These data indicate that poly(A) polymerase is one of the cellular proteins specifically regulated by amino acid supply.
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Lewis FS, Rutman RJ, Avadhani NG. Messenger ribonucleic acid metabolism in mammalian mitochondria. Discrete poly(adenylic acid) lacking messenger ribonucleic acid species associated with mitochondrial polysomes. Biochemistry 1976; 15:3367-72. [PMID: 986158 DOI: 10.1021/bi00660a031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The mRNA species released from mitochondrial polysomes prepared by the Mg2+ precipitation technique have been further characterized using various analytical techniques. Mitochondrial polysomes were dissociated by treatment with puromycin and chemically labeled with (3H) dimethyl sulfate. About 51% of steady-state mitochondrial mRNA bind to oligo(dT)-cellulose indicating the presence of poly(adenylic acid)(poly(A)) in this fraction. The poly(A)-containing mRNAs resolve into discrete bands of 9-16 Se, while the RNA fraction unable to bind to oligo(dT)-cellulose representing poly(A)-lacking mRNA contains 8-12 Se species. About 90% of poly(A) lacking RNA hybridizes with mitochondrial DNA and less than 7% hybridizes with nuclear DNA. The extent of hybridization of poly(A)-lacking RNA with mitochondrial DNA was not significantly affected by the presence of excess mitochondrial rRNA, cytoplasmic rRNA, or a tenfold concentration of poly(A)-containing RNA isolated from total mitochondrial RNA. Possible differences in sequence properties between poly(A)-containing and -lacking mitochondrial mRNAs were further verified using a solid phase-bound cDNA procedure. Poly(A)-containing mRNA released from mitochondrial polysomes shows over 85% sequance homology with oligo(dT)-cellulose-bound cDNA prepared against total mitochondrial poly(A)-lacking mitochondrial mRNA hybridizes with the cDNA providing direct evidence for the distinct sequence properties of the two mRNA species.
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Cupello A, Rosadini G. Poly(A) associated RNA from mitochondria and microsomes of rat brain. EXPERIENTIA 1976; 32:872-4. [PMID: 954966 DOI: 10.1007/bf02003738] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Rat brain mitochondria contain a significant proportion of poly(A) associated RNA which is higher than that found in microsomes from the same source. When steady state poly(A) RNA of brain mitochondria was analyzed by microelectrophoresis, it displayed a characteristic separation pattern with a large amount of "free" poly(A).
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Aujame L, Freeman KB. The synthesis of polyadenylic acid-containing ribonucleic acid by isolated mitochondria from Ehrlich ascites cells. Biochem J 1976; 156:499-506. [PMID: 986139 PMCID: PMC1163781 DOI: 10.1042/bj1560499] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The synthesis of poly(A)-containing RNA by isolated mitochondria from Ehrlich ascites cells was studied. Isolated mitochondria incorporate [3H]AMP or [3H]UTP into an RNA species that adsorbs on oligo (dT)-cellulose columns or Millipore filters. Hydrolysis of the poly(A)-containing RNA with pancreatic and T1 ribonucleases released a poly(A) sequence that had an electrophoretic mobility slightly faster than 4SE. In comparison, ascites-cell cytosolic poly(A)-containing RNA had a poly(A) tail that had an electrophoretic mobility of about 7SE. Sensitivity of the incorporation of [3H]AMP into poly(A)-containing RNA to ethidium bromide and to atractyloside and lack of sensitivity to immobilized ribonuclease added to the mitochondria after incubation indicated that the site of incorporation was mitochondrial. The poly(A)-containing RNA sedimented with a peak of about 18S, with much material of higher s value. After denaturation at 70 degrees C for 5 min the poly(A)-containing RNA separated into two components of 12S and 16S on a 5-20% (w/v) sucrose density gradient at 4 degrees C, or at 4 degrees and 25 degrees C in the presence of formaldehyde. Poly(A)-containing RNA synthesized in the presence of ethidium bromide sedimented at 5-10S in a 15-33% (w/v) sucrose density gradient at 24 degrees C. The poly(A) tail of this RNA was smaller than that synthesized in the absence of ethidium bromide. The size of the poly(A)-containing RNA (approx. 1300 nucleotides) is about the length necessary for that of mRNA species for the products of mitochondrial protein synthesis observed by ourselves and others.
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Hieter PA, LeGendre SM, Levy CC. Stabilization of an RNA molecule by 3'-terminal poly (A)-induced inhibition of RNase activity. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33435-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Rosen D, Edelman M. Poly(A)-associated RNA from the mitochondrial fraction of the fungus Trichoderma. EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 63:525-32. [PMID: 944128 DOI: 10.1111/j.1432-1033.1976.tb10256.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Total RNA was extracted from purified mitochondrial and cytoplasmic fractions of germinating conidia of Trichoderma viride and bound to oligo(dT)-cellulose at 22 and 4 degrees C. Under chromatographic conditions which retained very short poly(A) segments (i.e., 4 degrees C), up to 10% of short-term 32PO4-lebeled RNA from the mitochondrial fraction were selectively bound. The poly(A)-associated RNAs from the mitochondrial and cytoplasmic fractions showed the following characteristics. (a) On polyacrylamide gels mitochondrial fraction RNA had a distinctive pattern with a major peak at about 22 S and a smaller one at about 29 S; in contrast, cytoplasmic fraction RNA was heterogenously distributed along the gel. (b) The poly(A) segment released by RNAase digestion of mitochondrial fraction poly(A)-associated RNA migrated on polyacrylamide gels as molecules 20-25-nucleotides long, while that of the cytoplasmic fraction showed an apparent size of 50-60 nucleotides. (c) Mitochondrial fraction RNA bound to oligo(dT)-cellulose in the cold had a guanine + cytosine content of 21% versus 34% for bulk mitochondrial RNA and 48% for cytoplasmic poly(A)-associated RNA; the oligo(dT)-bound RNAs were further identified by their high percentages of adenine residues (46% for the mitochondria and 30% for the cytoplasm). (d) The poly(A)-associated RNA fraction was translated, in vitro, in a cell-free protein-synthesizing system from wheat germ. The products induced by cytoplasmic RNA showed a complex pattern on polyacrylamide gels of many polypeptides ranging in molecular weights from 10000 to 40000. The pattern induced by mitochondrial fraction RNA however, was much simpler, revealing two discrete, main products: a major one at Mr approximately 13000 and a minor one at Mr approximately 20000.
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Abstract
Qualitative and quantitative ultrastructural studies were performed on mitochondria of leukemic monoblasts from 15 patients with acute monoblastic leukemia. Similar comparative observations were made on mitochondria of myeloblasts from 14 hematologically normal controls. No significant quantitative differences were noted between normal and leukemic mitochondria. Area measurements were approximately equal. Qualitative differences between the two groups consisted of increased numbers of irregularly shaped mitochondria, damaged mitochondrial membranes, mitochondria with damaged matrix, and small granules in mitochondria in the leukemic group. Leukemic cells exhibited nuclear-mitochondrial contact and virus-like particles within damaged mitochondria. To confirm the presence of virus-like particles and to aid in our understanding of nuclear-mitochondrial interaction, a C-type virus producer MSV-MLV infected rat embryo cell culture was used for additional analysis. Mitochondrial abnormalities and increased frequency of virus in damaged mitochondria, often attached to mitochondrial membranes, were noted. Several lysosomes exhibited accumulations of virus and budding into lysosomes from lysosomal membranes. Mitochondria are important organelles in glycolytic-oxidative phosphorylation pathways, and carry extranuclear genetic information. Further studies of morphologic and biochemical abnormalities of leukemic mitochondria and the interaction between the mitochondria and the nuclei in leukemic cells are needed to provide researchers with data on extranuclear factors operating in oncogenesis.
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Saccone C, Quagliariello E. Biochemical studies of mitochondrial transcription and translation. INTERNATIONAL REVIEW OF CYTOLOGY 1976; 43:125-65. [PMID: 131112 DOI: 10.1016/s0074-7696(08)60068-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Mahler HR, Raff RA. The evolutionary origin of the mitochondrion: a nonsymbiotic model. INTERNATIONAL REVIEW OF CYTOLOGY 1976; 43:1-124. [PMID: 131111 DOI: 10.1016/s0074-7696(08)60067-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Wheeler AM, Hartley MR. Major mRNA species from spinach chloroplasts do not contain poly(A). Nature 1975; 257:66-7. [PMID: 1161008 DOI: 10.1038/257066a0] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Abstract
Total yeast mitochondrial RNA was shown to possess messenger RNA activity when injected into oocytes of the frog Xenopus laevis. The specific polypeptides formed were precipitated by mitochondrial antisera. A comparison was made of the molecular weights of the proteins obtained form this system with those made by mitochondria in vivo in the presence of cycloheximide. No RNA containing poly(A) sequences was detected in yeast mitochondria.
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Brandhorst BP, McConkey EH. Relationship between nuclear and cytoplasmic poly(adenylic acid). Proc Natl Acad Sci U S A 1975; 72:3580-4. [PMID: 1059146 PMCID: PMC433039 DOI: 10.1073/pnas.72.9.3580] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The kinetics of accumulation of radioactive poly(A) in the nucleus and cytoplasm of mouse L cells have been determined using labeling conditions in which the cellular ATP pool is shown to have a nearly constant specific radioactivity. Most or all nuclear poly(A) accumulates with kinetics very similar to those of heterogeneous nuclear RNA, having a half-time of about 25 min. There is little or no lag before attainment of a maximal rate of accumulation of cytoplasmic poly(A). These data are consistent with a variety of models in which nuclear poly(A) does or does not all serve as a precursor of cytoplasmic poly(A). In either type of model there must be a class of poly(A) either synthesized in the cytoplasm or passing through a small nuclear pool separate from the main pool of nuclear poly(A).
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Abstract
The endosymbiont and episome theories about the origin of mitochondria are reviewed. Biochemical and genetic data, relevant to these theories are discussed. An alternative theory is also proposed; this theory is that nuclear and mitochondrial DNAs developed from compartmentalized duplicate prokaryote DNAs.
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DeLarco J, Nakagawa S, Abramowitz A, Bromwell K, Gurogg G. Polyadenylic acid-containing RNA from rat brain synaptosomes. J Neurochem 1975; 25:131-7. [PMID: 1141910 DOI: 10.1111/j.1471-4159.1975.tb12239.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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37
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Levy CC, Schmukler M, Frank JJ, Karpetsky TP, Jewett PB, Hieter PA, LeGendre SM, Dorr RG. Possible role for poly(A) as an inhibitor of endonuclease activity in eukaryotic cells. Nature 1975; 256:340-2. [PMID: 1143339 DOI: 10.1038/256340a0] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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38
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Nakazato H, Venkatesan S, Edmonds M. Polyadenylic acid sequences in E. coli messenger RNA. Nature 1975; 256:144-6. [PMID: 1097936 DOI: 10.1038/256144a0] [Citation(s) in RCA: 95] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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39
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Kisselev OI, Gaitskhoki BS, Klimov NA. Messenger RNA-containing ribonucleoprotein from mitochondrial polyribosomes of rat liver. Mol Biol Rep 1975; 2:143-9. [PMID: 1160879 DOI: 10.1007/bf00357545] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A ribonucleoprotein was released from carefully purified rat liver mitochondrial polyribosomes after dissociation with 1 M potassium chloridepuromycin. This ribonucleoprotein was characterized by a sedimentation coefficient ranging from 10-14 S and buoyant density of 1.48 g cm(-3) in cesium chloride equilibrium centrifugation differing in these parameters from the subunits of mitochondrial ribosomes. Poly(A)-containing RNA constituted more than 30% of the total RNA content in this non-ribosomal ribonucleoprotein.
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Lande MA, Adesnik M, Sumida M, Tashiro Y, Sabatini DD. Direct association of messenger RNA with microsomal membranes in human diploid fibroblasts. J Biophys Biochem Cytol 1975; 65:513-28. [PMID: 1133114 PMCID: PMC2109435 DOI: 10.1083/jcb.65.3.513] [Citation(s) in RCA: 72] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Messenger RNA (mRNA) of membrane-bound polysomes in a membrane fraction of WI-38 cells remains associated with the microsomal membranes even after ribosomes and their nascent polypeptide chains are removed by using puromycin in a high salt buffer or by disassembling the ribosomes in a medium of high ionic strength lacking magnesium. mRNA either was specifically labeled in the presence of actinomycin D, or it was recognized by virtue of its affinity for oligo-dT. Poly A segments in bound mRNAs have an electrophoretic mobility in acrylamide gels which is characteristic of cytoplasmic mRNAs and corresponds to 150-200 adenyl residues. Extensive RNase treatment did not lead to release of the poly A segments of membrane-associated mRNA molecules either from an intact membrane fraction or from a membrane fraction previously stripped of ribosomes. On the other hand, RNase treatment led to the release and digestion of the nonpoly A segments of the mRNA molecules, indicating that the site of attachment of mRNA to the ER membranes is located near or at the 3' end of the molecule which contains the poly A. A direct association of mRNAs and endoplasmic reticulum membranes is considered in a modelto explain the assembly of bound polysomes and protein synthesis in a membrane-associated apparatus.
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41
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Ohta N, Sanders M, Newton A. Poly(adenylic acid) sequences in the RNA of Caulobacter crescenus. Proc Natl Acad Sci U S A 1975; 72:2343-6. [PMID: 1094464 PMCID: PMC432754 DOI: 10.1073/pnas.72.6.2343] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Poly(adenylic acid) sequences have been isolated from the Gram-negative bacterium Caulobacter crescentus. Most of these A-rich tracts are associated with large RNA molecules that constitute an important fraction of the unstable RNA in these bacteria, and, as estimated by poly(U) filter binding, they are not present in the 16S or 23S ribosomal RNA. Preliminary estimates of size from polyacrylamide gel electrophoresis suggest that the majority of the A-rich tracts ranges from 15 to approximately 50 residues in length.
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42
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Abstract
The content, size, and mechanism of synthesis of 3'-terminal poly(A) on the various intracellular species of poliovirus RNA have been examined. All viral RNA species bound to poly(U) filters and contained RNase-resistant stretches of poly(A) which could be analyzed by electrophoresis in polyacrylamide gels. At 3 h after infection, the poly(A) on virion RNA, relicative intermediate RNA, polyribosomal RNA, and total cytoplasmic 35S RNA was heterogeneous in size with an average length of 75 nucleotides. By 6 h after infection many of the intracellular RNA's had poly(A) of over 150 nucleotides in length, but the poly(A) in virion RNA did not increase in size suggesting that the amount of poly(A) which can be encapsidated is limited. At all times, the double-stranded poliovirus RNA molecules had poly(A) of 150 to 200 nucleotides. Investigation of the kinetics of poly(A) appearance in the replicative intermediate and in finished 35S molecules indicated that poly(A) is the last portion of the 35S RNA to be synthesized; no nascent poly(A) could be detected in the replicative intermediate. Although this result indicates that poliovirus RNA is synthesized 5' leads to 3' like other RNA's, it also suggests that much of the poly(A) found in the replicative intermediate is an artifact possibly arising from the binding of finished 35S RNA molecules to the replicative intermediate during extraction. The addition of poly(A) to 35S RNA molecules was not sensitive to guanidene.
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43
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Rose KM, Morris HP, Jacob ST. Mitochondrial poly(A) polymerase from a poorly differentiated hepatoma: purification and characteristics. Biochemistry 1975; 14:1025-32. [PMID: 235943 DOI: 10.1021/bi00676a022] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Poly(A) polymerase (EC 2.7.7.19) solubilized from mitochondria of a poorly differentiated rat tumor, Morris hepatoma 3924A, was purified more than 1000-fold by successive column chromatography on phosphocellulose, DEAE-Sephadex, and hydroxylapatite. Purified enzyme catalyzed the incorporation of ATP into poly(A) only upon addition of an exogenous primer. Of several primers tested, synthetic poly(A) was the most effective. The enzyme utilized mitochondrial RNA as a primer at least five times as efficiently as nuclear RNA. The enzyme required Mn2+, and had a pH optimum of 7.8-8.2. The enzyme utilized ATP exclusively as a substrate; the calculated K-m for ATP was 28 muM. The polymerization reaction was not inhibited by RNase, ethidium bromide, distamycin, or alpha-amanitin. The reaction was sensitive to O-n-octyloxime of 3-formylrifamycin SV (AF/013). As estimated from glycerol gradient centrifugation and acrylamide gel electrophoresis in the presence of sodium dodecyl sulfate, the molecular weight of the enzyme was 60,000. The product was covalently linked to the polynucleotide primer and the average length of the poly(A) formed was 600 nucleotides.
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46
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47
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48
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Puckett L, Chambers S, Darnell JE. Short-lived messenger RNA in HeLa cells and its impace on the kinetics of accumulation of cytoplasmic polyadenylate. Proc Natl Acad Sci U S A 1975; 72:389-93. [PMID: 1054512 PMCID: PMC432311 DOI: 10.1073/pnas.72.1.389] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Accumulation of [3H]adenine in the acid-soluble pool and in nuclear and cytoplasmic poly(A) of HeLa cells shows that the nuclear poly(A) rises along a curve similar to that of the acid-soluble pool. By use of a [3H]guanosine pulse-chase experiment in adenine-grown cells, at least 35-50% of the pulse-labeled mRNA was found to have a half-life of about 1-2 hr. A mathematical model involving nuclear poly(A) synthesis and conservative transport to the cytoplasm has been derived from the new information about mRNA with a short half-life. This model predicts curves similar to those found for nuclear and cytoplasmic accumulation of poly(A). Thus, there is no necessity on kinetic grounds to invoke either nuclear turnover or cytoplasmic synthesis of poly(A).
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Groot GS, Flavell RA, Van Ommen GJ, Grivell LA. Yeast mitochondrial RNA does not contain poly(A). Nature 1974; 252:167-9. [PMID: 4424381 DOI: 10.1038/252167a0] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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50
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Sippel AE, Stavrianopoulos JG, Schutz G, Feigelson P. Translational properties of rabbit globin mRNA after specific removal of poly(A) with ribonuclease H. Proc Natl Acad Sci U S A 1974; 71:4635-9. [PMID: 4531006 PMCID: PMC433943 DOI: 10.1073/pnas.71.11.4635] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Highly purified RNase H (RNA.DNA hybrid ribonucleotidohydrolase, EC 3.1.4.34) from calf thymus was used to specifically remove the poly(A) sequences of purified rabbit globin mRNA after its hybridization with poly(dT). The deadenylylated globin mRNA was repurified by a one-step procedure including a nitrocellulose column. The poly(A) size and the content of unmodified mRNA were determined by hybridization with [(3)H]-poly(U), and it could be shown that the RNase H digestion method effectively removes this terminal poly(A) sequence. No difference in activity was found between mRNAs with and without poly(A) to initiate, elongate, terminate, and release newly synthesized globin chains in exogenous-mRNA-dependent, cell-free, protein-synthesizing systems from wheat embryo, ascites Krebs II cells, and rat liver. Furthermore, poly(A)-free globin mRNA competed with the same efficiency as authentic globin mRNA against chick ovalbumin mRNA when translated under total mRNA saturation conditions. It is apparent that the 3'-terminal poly(A) sequence is not necessary to maintain the translationally active secondary and tertiary configuration of the globin mRNA molecule. Preincubation of intact and deadenylylated globin mRNA in the Krebs II ascites translational system indicates that the presence of the poly(A) sequence may stabilize the translationally active mRNA molecule.
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