1
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Zhuang F, Huang S, Liu L. MALSU1-mediated regulation of mitochondrial function governs proliferation and doxorubicin resistance in triple-negative breast cancer cells. Mol Cell Biochem 2024:10.1007/s11010-024-05053-6. [PMID: 38896203 DOI: 10.1007/s11010-024-05053-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
Triple-negative breast cancer (TNBC) poses a formidable challenge in oncology due to its aggressive nature and limited treatment options. Although doxorubicin, a widely used chemotherapeutic agent, shows efficacy in TNBC treatment, acquired resistance remains a significant obstacle. Our study explores the role of MALSU1, a regulator of mitochondrial translation, in TNBC and its impact on cell proliferation and doxorubicin resistance. We observed increased MALSU1 expression in TNBC, correlating with poor patient prognosis. MALSU1 knockdown in TNBC cells significantly reduced proliferation, indicating its pivotal role in sustaining cell growth. Mechanistically, MALSU1 depletion resulted in decreased activities of mitochondrial respiratory chain complexes, cellular ATP levels, and mitochondrial respiration. Notably, exogenous addition of normal mitochondria restored proliferation and mitochondrial respiration in MALSU1-depleted TNBC cells. Importantly, MALSU1 knockdown enhanced the sensitivity of doxorubicin-resistant TNBC cells to doxorubicin treatment. Furthermore, pharmacological inhibition of mitochondrial translation using tigecycline and chloramphenicol mimicked the effects of MALSU1 knockdown, suggesting mitochondrial translation as a potential therapeutic target. Taken together, our findings not only elucidate the intricate role of MALSU1 in TNBC biology and doxorubicin resistance but also lay the groundwork for future investigations targeting MALSU1 and/or mitochondrial translation as a promising avenue for developing innovative therapeutic strategies against TNBC.
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Affiliation(s)
- Feifei Zhuang
- Department of Medical Oncology, Yantaishan Hospital, Yantai, Shandong Province, China
| | - Shaoyan Huang
- Department of Medical Oncology, Yantaishan Hospital, Yantai, Shandong Province, China
| | - Lei Liu
- Department of Medical Oncology, Yantaishan Hospital, Yantai, Shandong Province, China.
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2
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McShane E, Churchman LS. Central dogma rates in human mitochondria. Hum Mol Genet 2024; 33:R34-R41. [PMID: 38779776 PMCID: PMC11112385 DOI: 10.1093/hmg/ddae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 12/28/2023] [Accepted: 02/29/2024] [Indexed: 05/25/2024] Open
Abstract
In human cells, the nuclear and mitochondrial genomes engage in a complex interplay to produce dual-encoded oxidative phosphorylation (OXPHOS) complexes. The coordination of these dynamic gene expression processes is essential for producing matched amounts of OXPHOS protein subunits. This review focuses on our current understanding of the mitochondrial central dogma rates, highlighting the striking differences in gene expression rates between mitochondrial and nuclear genes. We synthesize a coherent model of mitochondrial gene expression kinetics, highlighting the emerging principles and emphasizing where more precise measurements would be beneficial. Such an understanding is pivotal for grasping the unique aspects of mitochondrial function and its role in cellular energetics, and it has profound implications for aging, metabolic disorders, and neurodegenerative diseases.
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Affiliation(s)
- Erik McShane
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, United States
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, United States
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3
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Santonoceto G, Jurkiewicz A, Szczesny RJ. RNA degradation in human mitochondria: the journey is not finished. Hum Mol Genet 2024; 33:R26-R33. [PMID: 38779774 DOI: 10.1093/hmg/ddae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria are vital organelles present in almost all eukaryotic cells. Although most of the mitochondrial proteins are nuclear-encoded, mitochondria contain their own genome, whose proper expression is necessary for mitochondrial function. Transcription of the human mitochondrial genome results in the synthesis of long polycistronic transcripts that are subsequently processed by endonucleases to release individual RNA molecules, including precursors of sense protein-encoding mRNA (mt-mRNA) and a vast amount of antisense noncoding RNAs. Because of mitochondrial DNA (mtDNA) organization, the regulation of individual gene expression at the transcriptional level is limited. Although transcription of most protein-coding mitochondrial genes occurs with the same frequency, steady-state levels of mature transcripts are different. Therefore, post-transcriptional processes are important for regulating mt-mRNA levels. The mitochondrial degradosome is a complex composed of the RNA helicase SUV3 (also known as SUPV3L1) and polynucleotide phosphorylase (PNPase, PNPT1). It is the best-characterized RNA-degrading machinery in human mitochondria, which is primarily responsible for the decay of mitochondrial antisense RNA. The mechanism of mitochondrial sense RNA decay is less understood. This review aims to provide a general picture of mitochondrial genome expression, with a particular focus on mitochondrial RNA (mtRNA) degradation.
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Affiliation(s)
- Giulia Santonoceto
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
| | - Aneta Jurkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
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4
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Lei T, Rui Y, Xiaoshuang Z, Jinglan Z, Jihong Z. Mitochondria transcription and cancer. Cell Death Discov 2024; 10:168. [PMID: 38589371 PMCID: PMC11001877 DOI: 10.1038/s41420-024-01926-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
Mitochondria are major organelles involved in several processes related to energy supply, metabolism, and cell proliferation. The mitochondria function is transcriptionally regulated by mitochondria DNA (mtDNA), which encodes the key proteins in the electron transport chain that is indispensable for oxidative phosphorylation (OXPHOS). Mitochondrial transcriptional abnormalities are closely related to a variety of human diseases, such as cardiovascular diseases, and diabetes. The mitochondria transcription is regulated by the mtDNA, mitochondrial RNA polymerase (POLRMT), two transcription factors (TFAM and TF2BM), one transcription elongation (TEFM), and one known transcription termination factor (mTERFs). Dysregulation of these factors directly leads to altered expression of mtDNA in tumor cells, resulting in cellular metabolic reprogramming and mitochondrial dysfunction. This dysregulation plays a role in modulating tumor progression. Therefore, understanding the role of mitochondrial transcription in cancer can have implications for cancer diagnosis, prognosis, and treatment. Targeting mitochondrial transcription or related pathways may provide potential therapeutic strategies for cancer treatment. Additionally, assessing mitochondrial transcriptional profiles or biomarkers in cancer cells or patient samples may offer diagnostic or prognostic information.
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Affiliation(s)
- Tang Lei
- Medical School, Kunming University of Science and Technology, Kunming, China
| | - Yu Rui
- Medical School, Kunming University of Science and Technology, Kunming, China
| | - Zhou Xiaoshuang
- Medical School, Kunming University of Science and Technology, Kunming, China
| | - Zhang Jinglan
- Medical School, Kunming University of Science and Technology, Kunming, China
| | - Zhang Jihong
- Medical School, Kunming University of Science and Technology, Kunming, China.
- Yunnan Province Clinical Research Center for Hematologic Disease, Kunming, China.
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5
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Sun Z, Jiao A, Zhao Y, Han T, Zhang H, Gao Q. Isoliquiritin can cause mitochondrial dysfunction and regulate Nrf2 to affect the development of mouse oocytes. Food Chem Toxicol 2024; 185:114445. [PMID: 38311047 DOI: 10.1016/j.fct.2024.114445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/07/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024]
Abstract
IsoliQuirtigenin (ILG) has been widely studied in somatic cells and tissues, but less in reproductive development. It is a kind of widely used food additive. In this study, it was found that ILG could significantly increase the levels of ROS,GSH and MMP in mouse oocytes (P < 0.01). In order to explore the cause of this phenomenon, it was found that the abnormal distribution of mitochondria and ATP synthesis levels were significantly increased (P < 0.05). At this time, we made a reasonable hypothesis that ILG affected mitochondrial function. In subsequent studies, it was found that the endogenous ROS accumulation level in mitochondria was significantly increased. After continuous RT-PCR screening, it was found that the expression of Nrf2 was significantly inhibited (P < 0.01). Its upstream and downstream FOXO3 GPX1, CAT, SOD2, SIRT1 gene also appear different degree of significant change (P < 0.05), in which the lower expression of NADP + (P < 0.05) illustrates the mitochondrial ATP synthesis electronic chain were suppressed, it also has the reason, By inhibiting electron chain and ATP synthesis, ILG leads to oocyte apoptosis and initiation of autophagy, reducing oocyte and its subsequent developmental potential.
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Affiliation(s)
- Zhaoyang Sun
- Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Yanbian University, Yanji, 133002, China; College of Agriculture, Yanbian University, Yanji, 133002, China; Jilin Engineering Research Center of Yanbian Yellow Cattle Resources Reservation, Yanji, 133002, China
| | - Anhui Jiao
- Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Yanbian University, Yanji, 133002, China; College of Agriculture, Yanbian University, Yanji, 133002, China; Jilin Engineering Research Center of Yanbian Yellow Cattle Resources Reservation, Yanji, 133002, China
| | - Yuhan Zhao
- Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Yanbian University, Yanji, 133002, China; College of Agriculture, Yanbian University, Yanji, 133002, China; Jilin Engineering Research Center of Yanbian Yellow Cattle Resources Reservation, Yanji, 133002, China
| | - Tiancang Han
- Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Yanbian University, Yanji, 133002, China; College of Agriculture, Yanbian University, Yanji, 133002, China; Jilin Engineering Research Center of Yanbian Yellow Cattle Resources Reservation, Yanji, 133002, China
| | - Hongbo Zhang
- Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Yanbian University, Yanji, 133002, China; College of Agriculture, Yanbian University, Yanji, 133002, China; Jilin Engineering Research Center of Yanbian Yellow Cattle Resources Reservation, Yanji, 133002, China
| | - Qingshan Gao
- Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Yanbian University, Yanji, 133002, China; College of Agriculture, Yanbian University, Yanji, 133002, China; Jilin Engineering Research Center of Yanbian Yellow Cattle Resources Reservation, Yanji, 133002, China.
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6
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Tran TAT, Iwata Y, Hoang LT, Kitajima S, Yoneda-Nakagawa S, Oshima M, Sakai N, Toyama T, Yamamura Y, Yamazaki H, Hara A, Shimizu M, Sako K, Minami T, Yuasa T, Horikoshi K, Hayashi D, Kajikawa S, Wada T. Protective Role of MAVS Signaling for Murine Lipopolysaccharide-Induced Acute Kidney Injury. Immunohorizons 2024; 8:1-18. [PMID: 38169549 PMCID: PMC10835654 DOI: 10.4049/immunohorizons.2300069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024] Open
Abstract
Despite treatment advances, acute kidney injury (AKI)-related mortality rates are still high in hospitalized adults, often due to sepsis. Sepsis and AKI could synergistically worsen the outcomes of critically ill patients. TLR4 signaling and mitochondrial antiviral signaling protein (MAVS) signaling are innate immune responses essential in kidney diseases, but their involvement in sepsis-associated AKI (SA-AKI) remains unclear. We studied the role of MAVS in kidney injury related to the TLR4 signaling pathway using a murine LPS-induced AKI model in wild-type and MAVS-knockout mice. We confirmed the importance of M1 macrophage in SA-AKI through in vivo assessment of inflammatory responses. The TLR4 signaling pathway was upregulated in activated bone marrow-derived macrophages, in which MAVS helped maintain the LPS-suppressed TLR4 mRNA level. MAVS regulated redox homeostasis via NADPH oxidase Nox2 and mitochondrial reverse electron transport in macrophages to alleviate the TLR4 signaling response to LPS. Hypoxia-inducible factor 1α (HIF-1α) and AP-1 were key regulators of TLR4 transcription and connected MAVS-dependent reactive oxygen species signaling with the TLR4 pathway. Inhibition of succinate dehydrogenase could partly reduce inflammation in LPS-treated bone marrow-derived macrophages without MAVS. These findings highlight the renoprotective role of MAVS in LPS-induced AKI by regulating reactive oxygen species generation-related genes and maintaining redox balance. Controlling redox homeostasis through MAVS signaling may be a promising therapy for SA-AKI.
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Affiliation(s)
- Trang Anh Thi Tran
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
| | - Yasunori Iwata
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
- Division of Infection Control, Kanazawa University Hospital, Kanazawa, Japan
| | - Linh Thuy Hoang
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
| | - Shinji Kitajima
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
- Division of Blood Purification, Kanazawa University Hospital, Kanazawa, Japan
| | | | - Megumi Oshima
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
| | - Norihiko Sakai
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
- Division of Blood Purification, Kanazawa University Hospital, Kanazawa, Japan
| | - Tadashi Toyama
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
| | - Yuta Yamamura
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
| | - Hiroka Yamazaki
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
| | - Akinori Hara
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
| | - Miho Shimizu
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
| | - Keisuke Sako
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
| | - Taichiro Minami
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
| | - Takahiro Yuasa
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
| | - Keisuke Horikoshi
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
| | - Daiki Hayashi
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
| | - Sho Kajikawa
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
| | - Takashi Wada
- Department of Nephrology and Rheumatology, Kanazawa University, Kanazawa, Japan
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7
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Dinh N, Bonnefoy N. Schizosaccharomyces pombe as a fundamental model for research on mitochondrial gene expression: Progress, achievements and outlooks. IUBMB Life 2023. [PMID: 38117001 DOI: 10.1002/iub.2801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
Schizosaccharomyces pombe (fission yeast) is an attractive model for mitochondrial research. The organism resembles human cells in terms of mitochondrial inheritance, mitochondrial transport, sugar metabolism, mitogenome structure and dependence of viability on the mitogenome (the petite-negative phenotype). Transcriptions of these genomes produce only a few polycistronic transcripts, which then undergo processing as per the tRNA punctuation model. In general, the machinery for mitochondrial gene expression is structurally and functionally conserved between fission yeast and humans. Furthermore, molecular research on S. pombe is supported by a considerable number of experimental techniques and database resources. Owing to these advantages, fission yeast has significantly contributed to biomedical and fundamental research. Here, we review the current state of knowledge regarding S. pombe mitochondrial gene expression, and emphasise the pertinence of fission yeast as both a model and tool, especially for studies on mitochondrial translation.
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Affiliation(s)
- Nhu Dinh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette cedex, France
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8
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Potter A, Cabrera-Orefice A, Spelbrink JN. Let's make it clear: systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling. Nucleic Acids Res 2023; 51:10619-10641. [PMID: 37615582 PMCID: PMC10602928 DOI: 10.1093/nar/gkad697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/18/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
Complexome profiling (CP) is a powerful tool for systematic investigation of protein interactors that has been primarily applied to study the composition and dynamics of mitochondrial protein complexes. Here, we further optimized this method to extend its application to survey mitochondrial DNA- and RNA-interacting protein complexes. We established that high-resolution clear native gel electrophoresis (hrCNE) is a better alternative to preserve DNA- and RNA-protein interactions that are otherwise disrupted when samples are separated by the widely used blue native gel electrophoresis (BNE). In combination with enzymatic digestion of DNA, our CP approach improved the identification of a wide range of protein interactors of the mitochondrial gene expression system without compromising the detection of other multiprotein complexes. The utility of this approach was particularly demonstrated by analysing the complexome changes in human mitochondria with impaired gene expression after transient, chemically induced mitochondrial DNA depletion. Effects of RNase on mitochondrial protein complexes were also evaluated and discussed. Overall, our adaptations significantly improved the identification of mitochondrial DNA- and RNA-protein interactions by CP, thereby unlocking the comprehensive analysis of a near-complete mitochondrial complexome in a single experiment.
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Affiliation(s)
- Alisa Potter
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Functional Proteomics, Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
| | - Johannes N Spelbrink
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
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9
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Bayazit MB, Francois A, McGrail E, Accornero F, Stratton MS. mt-tRNAs in the polymerase gamma mutant heart. THE JOURNAL OF CARDIOVASCULAR AGING 2023; 3:41. [PMID: 38235059 PMCID: PMC10793997 DOI: 10.20517/jca.2023.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Introduction Mice harboring a D257A mutation in the proofreading domain of the mitochondrial DNA polymerase, Polymerase Gamma (POLG), experience severe metabolic dysfunction and display hallmarks of accelerated aging. We previously reported a mitochondrial unfolded protein response (UPTmt) - like (UPRmt-like) gene and protein expression pattern in the right ventricular tissue of POLG mutant mice. Aim We sought to determine if POLG mutation altered the expression of genes encoded by the mitochondria in a way that might also reduce proteotoxic stress. Methods and Results The expression of genes encoded by the mitochondrial DNA was interrogated via RNA-seq and northern blot analysis. A striking, location-dependent effect was seen in the expression of mitochondrial-encoded tRNAs in the POLG mutant as assayed by RNA-seq. These expression changes were negatively correlated with the tRNA partner amino acid's amyloidogenic potential. Direct measurement by northern blot was conducted on candidate mt-tRNAs identified from the RNA-seq. This analysis confirmed reduced expression of MT-TY in the POLG mutant but failed to show increased expression of MT-TP, which was dramatically increased in the RNA-seq data. Conclusion We conclude that reduced expression of amyloid-associated mt-tRNAs is another indication of adaptive response to severe mitochondrial dysfunction in the POLG mutant. Incongruence between RNA-seq and northern blot measurement of MT-TP expression points towards the existence of mt-tRNA post-transcriptional modification regulation in the POLG mutant that alters either polyA capture or cDNA synthesis in RNA-seq library generation. Together, these data suggest that 1) evolution has distributed mt-tRNAs across the circular mitochondrial genome to allow chromosomal location-dependent mt-tRNA regulation (either by expression or PTM) and 2) this regulation is cognizant of the tRNA partner amino acid's amyloidogenic properties.
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Affiliation(s)
- M. Bilal Bayazit
- Department of Physiology & Cell Biology, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Ashley Francois
- Department of Physiology & Cell Biology, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Erin McGrail
- Department of Physiology & Cell Biology, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Federica Accornero
- Department of Physiology & Cell Biology, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Matthew S. Stratton
- Department of Physiology & Cell Biology, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
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10
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Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K. Structures illustrate step-by-step mitochondrial transcription initiation. Nature 2023; 622:872-879. [PMID: 37821701 PMCID: PMC10600007 DOI: 10.1038/s41586-023-06643-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 09/13/2023] [Indexed: 10/13/2023]
Abstract
Transcription initiation is a key regulatory step in gene expression during which RNA polymerase (RNAP) initiates RNA synthesis de novo, and the synthesized RNA at a specific length triggers the transition to the elongation phase. Mitochondria recruit a single-subunit RNAP and one or two auxiliary factors to initiate transcription. Previous studies have revealed the molecular architectures of yeast1 and human2 mitochondrial RNAP initiation complexes (ICs). Here we provide a comprehensive, stepwise mechanism of transcription initiation by solving high-resolution cryogenic electron microscopy (cryo-EM) structures of yeast mitochondrial RNAP and the transcription factor Mtf1 catalysing two- to eight-nucleotide RNA synthesis at single-nucleotide addition steps. The growing RNA-DNA is accommodated in the polymerase cleft by template scrunching and non-template reorganization, creating stressed intermediates. During early initiation, non-template strand scrunching and unscrunching destabilize the short two- and three-nucleotide RNAs, triggering abortive synthesis. Subsequently, the non-template reorganizes into a base-stacked staircase-like structure supporting processive five- to eight-nucleotide RNA synthesis. The expanded non-template staircase and highly scrunched template in IC8 destabilize the promoter interactions with Mtf1 to facilitate initiation bubble collapse and promoter escape for the transition from initiation to the elongation complex (EC). The series of transcription initiation steps, each guided by the interplay of multiple structural components, reveal a finely tuned mechanism for potential regulatory control.
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Affiliation(s)
- Quinten Goovaerts
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Jiayu Shen
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Brent De Wijngaert
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Urmimala Basu
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.
| | - Kalyan Das
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.
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11
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Grotehans N, McGarry L, Nolte H, Xavier V, Kroker M, Narbona‐Pérez ÁJ, Deshwal S, Giavalisco P, Langer T, MacVicar T. Ribonucleotide synthesis by NME6 fuels mitochondrial gene expression. EMBO J 2023; 42:e113256. [PMID: 37439264 PMCID: PMC10505918 DOI: 10.15252/embj.2022113256] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 06/07/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023] Open
Abstract
Replication of the mitochondrial genome and expression of the genes it encodes both depend on a sufficient supply of nucleotides to mitochondria. Accordingly, dysregulated nucleotide metabolism not only destabilises the mitochondrial genome, but also affects its transcription. Here, we report that a mitochondrial nucleoside diphosphate kinase, NME6, supplies mitochondria with pyrimidine ribonucleotides that are necessary for the transcription of mitochondrial genes. Loss of NME6 function leads to the depletion of mitochondrial transcripts, as well as destabilisation of the electron transport chain and impaired oxidative phosphorylation. These deficiencies are rescued by an exogenous supply of pyrimidine ribonucleosides. Moreover, NME6 is required for the maintenance of mitochondrial DNA when the access to cytosolic pyrimidine deoxyribonucleotides is limited. Our results therefore reveal an important role for ribonucleotide salvage in mitochondrial gene expression.
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Affiliation(s)
- Nils Grotehans
- Max Planck Institute for Biology of AgeingCologneGermany
| | | | - Hendrik Nolte
- Max Planck Institute for Biology of AgeingCologneGermany
| | | | - Moritz Kroker
- Max Planck Institute for Biology of AgeingCologneGermany
| | | | - Soni Deshwal
- Max Planck Institute for Biology of AgeingCologneGermany
| | | | - Thomas Langer
- Max Planck Institute for Biology of AgeingCologneGermany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
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12
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Macrophage Mitochondrial Biogenesis and Metabolic Reprogramming Induced by Leishmania donovani Require Lipophosphoglycan and Type I Interferon Signaling. mBio 2022; 13:e0257822. [PMID: 36222510 PMCID: PMC9764995 DOI: 10.1128/mbio.02578-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogen-specific rewiring of host cell metabolism creates the metabolically adapted microenvironment required for pathogen replication. Here, we investigated the mechanisms governing the modulation of macrophage mitochondrial properties by the vacuolar pathogen Leishmania. We report that induction of oxidative phosphorylation and mitochondrial biogenesis by Leishmania donovani requires the virulence glycolipid lipophosphoglycan, which stimulates the expression of key transcriptional regulators and structural genes associated with the electron transport chain. Leishmania-induced mitochondriogenesis also requires a lipophosphoglycan-independent pathway involving type I interferon (IFN) receptor signaling. The observation that pharmacological induction of mitochondrial biogenesis enables an avirulent lipophosphoglycan-defective L. donovani mutant to survive in macrophages supports the notion that mitochondrial biogenesis contributes to the creation of a metabolically adapted environment propitious to the colonization of host cells by the parasite. This study provides novel insight into the complex mechanism by which Leishmania metacyclic promastigotes alter host cell mitochondrial biogenesis and metabolism during the colonization process. IMPORTANCE To colonize host phagocytes, Leishmania metacyclic promastigotes subvert host defense mechanisms and create a specialized intracellular niche adapted to their replication. This is accomplished through the action of virulence factors, including the surface coat glycoconjugate lipophosphoglycan. In addition, Leishmania induces proliferation of host cell mitochondria as well as metabolic reprogramming of macrophages. These metabolic alterations are crucial to the colonization process of macrophages, as they may provide metabolites required for parasite growth. In this study, we describe a new key role for lipophosphoglycan in the stimulation of oxidative phosphorylation and mitochondrial biogenesis. We also demonstrate that host cell pattern recognition receptors Toll-like receptor 4 (TLR4) and endosomal TLRs mediate these Leishmania-induced alterations of host cell mitochondrial biology, which also require type I IFN signaling. These findings provide new insight into how Leishmania creates a metabolically adapted environment favorable to their replication.
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Kiyama T, Chen CK, Zhang A, Mao CA. Differential Susceptibility of Retinal Neurons to the Loss of Mitochondrial Biogenesis Factor Nrf1. Cells 2022; 11:cells11142203. [PMID: 35883647 PMCID: PMC9321222 DOI: 10.3390/cells11142203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022] Open
Abstract
The retina, the accessible part of the central nervous system, has served as a model system to study the relationship between energy utilization and metabolite supply. When the metabolite supply cannot match the energy demand, retinal neurons are at risk of death. As the powerhouse of eukaryotic cells, mitochondria play a pivotal role in generating ATP, produce precursors for macromolecules, maintain the redox homeostasis, and function as waste management centers for various types of metabolic intermediates. Mitochondrial dysfunction has been implicated in the pathologies of a number of degenerative retinal diseases. It is well known that photoreceptors are particularly vulnerable to mutations affecting mitochondrial function due to their high energy demand and susceptibility to oxidative stress. However, it is unclear how defective mitochondria affect other retinal neurons. Nuclear respiratory factor 1 (Nrf1) is the major transcriptional regulator of mitochondrial biogenesis, and loss of Nrf1 leads to defective mitochondria biogenesis and eventually cell death. Here, we investigated how different retinal neurons respond to the loss of Nrf1. We provide in vivo evidence that the disruption of Nrf1-mediated mitochondrial biogenesis results in a slow, progressive degeneration of all retinal cell types examined, although they present different sensitivity to the deletion of Nrf1, which implicates differential energy demand and utilization, as well as tolerance to mitochondria defects in different neuronal cells. Furthermore, transcriptome analysis on rod-specific Nrf1 deletion uncovered a previously unknown role of Nrf1 in maintaining genome stability.
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Affiliation(s)
- Takae Kiyama
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin St., MSB 7.024, Houston, TX 77030, USA; (T.K.); (A.Z.)
| | - Ching-Kang Chen
- Department of Ophthalmology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
| | - Annie Zhang
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin St., MSB 7.024, Houston, TX 77030, USA; (T.K.); (A.Z.)
| | - Chai-An Mao
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin St., MSB 7.024, Houston, TX 77030, USA; (T.K.); (A.Z.)
- The MD Anderson Cancer Center/UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Correspondence:
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Reiner A, Kühl I. Highlight: Young research groups in Germany – 4th edition. Biol Chem 2022. [DOI: 10.1515/hsz-2022-0207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Andreas Reiner
- Department of Biology and Biotechnology , Ruhr University Bochum , Universitätsstrasse 150, D-44801 Bochum , Germany
| | - Inge Kühl
- Department of Cell Biology , Institute of Integrative Biology of the Cell (I2BC), UMR9198, CEA, CNRS, Université Paris-Saclay , F-91190 Gif-sur-Yvette , France
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