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Bouda E, Stapon A, Garcia-Diaz M. Mechanisms of mammalian mitochondrial transcription. Protein Sci 2019; 28:1594-1605. [PMID: 31309618 DOI: 10.1002/pro.3688] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 01/06/2023]
Abstract
Numerous age-related human diseases have been associated with deficiencies in cellular energy production. Moreover, genetic alterations resulting in mitochondrial dysfunction are the cause of inheritable disorders commonly known as mitochondrial diseases. Many of these deficiencies have been directly or indirectly linked to deficits in mitochondrial gene expression. Transcription is an essential step in gene expression and elucidating the molecular mechanisms involved in this process is critical for understanding defects in energy production. For the past five decades, substantial efforts have been invested in the field of mitochondrial transcription. These efforts have led to the discovery of the main protein factors responsible for transcription as well as to a basic mechanistic understanding of the transcription process. They have also revealed various mechanisms of transcriptional regulation as well as the links that exist between the transcription process and downstream processes of RNA maturation. Here, we review the knowledge gathered in early mitochondrial transcription studies and focus on recent findings that shape our current understanding of mitochondrial transcription, posttranscriptional processing, as well as transcriptional regulation in mammalian systems.
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Affiliation(s)
- Emilie Bouda
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
| | - Anthony Stapon
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
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Park JY, Lee TS, Song IH, Cho YL, Chae JR, Yun M, Kang H, Lee JH, Lim JH, Cho WG, Kang WJ. Hybridization-based aptamer labeling using complementary oligonucleotide platform for PET and optical imaging. Biomaterials 2016; 100:143-51. [PMID: 27258484 DOI: 10.1016/j.biomaterials.2016.05.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 05/12/2016] [Accepted: 05/17/2016] [Indexed: 11/29/2022]
Abstract
Aptamers are promising next-generation ligands used in molecular imaging and theragnosis. Aptamers are synthetic nucleic acids that can be held together with complementary sequences by base-pair hybridization. In this study, the complementary oligonucleotide (cODN) hybridization-based aptamer conjugation platform was developed to use aptamers as the molecular imaging agent. The cODN was pre-labeled with fluorescent dye or radioisotope and hybridized with a matched sequence containing aptamers in aqueous conditions. The cODN platform-hybridized aptamers exhibited good serum stability and specific binding affinity towards target cancer cells both in vitro and in vivo. These results suggest that the newly designed aptamer conjugation platform offers great potential for the versatile application of aptamers as molecular imaging agents.
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Affiliation(s)
- Jun Young Park
- Department of Nuclear Medicine, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Department of Anatomy, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Republic of Korea
| | - Tae Sup Lee
- Molecular Imaging Research Center, Research Institute of Radiological and Medical Sciences, Korea Institute of Radiological and Medical Sciences, 75 Nowon-ro, Nowon-gu, Seoul 01812, Republic of Korea
| | - In Ho Song
- Molecular Imaging Research Center, Research Institute of Radiological and Medical Sciences, Korea Institute of Radiological and Medical Sciences, 75 Nowon-ro, Nowon-gu, Seoul 01812, Republic of Korea
| | - Ye Lim Cho
- Department of Nuclear Medicine, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Ju Ri Chae
- Department of Nuclear Medicine, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Mijin Yun
- Department of Nuclear Medicine, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hyungu Kang
- R&D Strategic Planning, Bundang CHA Medical Center, 59 Yatap-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13496, Republic of Korea
| | - Jung Hwan Lee
- APGEN Inc, 220, Yeongsin-ro, Yeongdeungpo-gu, Seoul 07228, Republic of Korea
| | - Jong Hoon Lim
- APGEN Inc, 220, Yeongsin-ro, Yeongdeungpo-gu, Seoul 07228, Republic of Korea
| | - Won Gil Cho
- Department of Anatomy, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Republic of Korea.
| | - Won Jun Kang
- Department of Nuclear Medicine, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
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Fukamachi S, Bartoov B, Freeman KB. Synthesis of ribonucleic acid by isolated rat liver mitochondria. Biochem J 1972; 128:299-309. [PMID: 4404394 PMCID: PMC1173765 DOI: 10.1042/bj1280299] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Rat liver mitochondria isolated in sucrose-N-tris(hydroxymethyl)methyl-2-aminoethane-sulphonic acid (TES) incorporated [(3)H]UTP into RNA for 1h. Incorporation was inhibited 50% by 1mug of actinomycin D/ml, 1mug of acriflavine/ml and 0.5mug of ethidium bromide/ml but was insensitive to rifampicin, rifamycin SV, streptovarcin and deoxyribonuclease. After the first 10min of incubation, the synthesis was insensitive to ribonuclease. RNA synthesis by mitochondria isolated in sucrose-EDTA was insensitive to actinomycin D and sensitive to ribonuclease during the first 10min of the incubation but thereafter the sensitivities were the same as for mitochondria isolated in sucrose-TES. In a hypo-osmotic medium the relative extent of incorporation of the four ribonucleoside triphosphates into RNA was CTP>UTP=ATP>>GTP. In an iso-osmotic medium the incorporation of CTP and GTP decreased. All four nucleotides were incorporated into RNA in a DNA-dependent process, as indicated by the inhibition by actinomycin D. In addition, CTP and ATP were incorporated into the CCA end of mitochondrial tRNA. ATP was also incorporated into an unidentified acid-insoluble compound, which hydrolysed in alkali to a product that was not ATP, ADP or 5'- or 2(3')-AMP. Atractyloside inhibited the incorporation of ATP into RNA with 50% inhibition at 2-3nmol/mg of protein. The [(3)H]UTP-labelled RNA had peaks of 16S and 13S characteristic of mitochondrial rRNA. In addition a peak at 20-21S was observed as well as heterogeneous RNA sedimenting throughout the gradient. The synthesis of all these species was inhibited by actinomycin D, indicating that rat liver mitochondrial DNA codes for mitochondrial rRNA as well as other as yet unidentified species.
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Aloni Y, Attardi G. Symmetrical in vivo transcription of mitochondrial DNA in HeLa cells. Proc Natl Acad Sci U S A 1971; 68:1757-61. [PMID: 5288761 PMCID: PMC389287 DOI: 10.1073/pnas.68.8.1757] [Citation(s) in RCA: 154] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
RNA.DNA hybridization experiments utilizing separated strands of HeLa mitochondrial DNA and mit-RNA from HeLa cells exposed to short pulses of [5-(3)H]uridine have shown that the labeled RNA hybridizes with both the light (L) and the heavy (H) strand, though to a different relative extent depending upon the labeling time. Thus, hybridization of pulse-labeled RNA is about equal with the two strands when the pulse is very short (1-5 min), and becomes more and more predominant with the H strand with increasing pulse length. Pulse-labeled fast-sedimenting mit-RNA forms RNase-resistant double-stranded structures up to more than 5 mum long when self-annealed or annealed with an excess of unlabeled mit-RNA. These observations and the previous evidence of complete transcription of the H strand strongly suggest that mit-DNA is transcribed in HeLa cells symmetrically over a considerable portion of its length, with the transcript of the L strand being rapidly degraded or otherwise removed from the mitochondrial fraction.
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Szybalski W, Kubinski H, Hradecna Z, Summers W. [30] Analytical and preparative separation of the complementary DNA strands. Methods Enzymol 1971. [DOI: 10.1016/s0076-6879(71)21032-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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