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Millet A, Ledo JH, Tavazoie SF. An exhausted-like microglial population accumulates in aged and APOE4 genotype Alzheimer's brains. Immunity 2024; 57:153-170.e6. [PMID: 38159571 PMCID: PMC10805152 DOI: 10.1016/j.immuni.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/04/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
The dominant risk factors for late-onset Alzheimer's disease (AD) are advanced age and the APOE4 genetic variant. To examine how these factors alter neuroimmune function, we generated an integrative, longitudinal single-cell atlas of brain immune cells in AD model mice bearing the three common human APOE alleles. Transcriptomic and chromatin accessibility analyses identified a reactive microglial population defined by the concomitant expression of inflammatory signals and cell-intrinsic stress markers whose frequency increased with age and APOE4 burden. An analogous population was detectable in the brains of human AD patients, including in the cortical tissue, using multiplexed spatial transcriptomics. This population, which we designate as terminally inflammatory microglia (TIM), exhibited defects in amyloid-β clearance and altered cell-cell communication during aducanumab treatment. TIM may represent an exhausted-like state for inflammatory microglia in the AD milieu that contributes to AD risk and pathology in APOE4 carriers and the elderly, thus presenting a potential therapeutic target for AD.
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Affiliation(s)
- Alon Millet
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA; Tri-Institutional Program in Computational Biology and Medicine, The Rockefeller University, New York, NY 10065, USA
| | - Jose Henrique Ledo
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA; Department of Pathology and Laboratory of Medicine, Department of Neuroscience, South Carolina Alzheimer's Disease Research Center, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA; Tri-Institutional Program in Computational Biology and Medicine, The Rockefeller University, New York, NY 10065, USA.
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Soto-Sánchez J, Pérez-Mora S, Ospina-Villa JD, Zavala-Ocampo LM. Esters of Quinoxaline-7-Carboxylate 1,4-di- N-Oxide as Potential Inhibitors of Glycolytic Enzymes of Entamoeba histolytica: In silico Approach. Curr Comput Aided Drug Des 2024; 20:155-169. [PMID: 37076964 DOI: 10.2174/1573409919666230417135204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/10/2023] [Accepted: 03/07/2023] [Indexed: 04/21/2023]
Abstract
BACKGROUND Esters of quinoxaline-7-carboxylate 1,4-di-N-oxide (7-carboxylate QdNOs) derivatives are compounds that inhibit the growth of Entamoeba histolytica, the causative agent of amebiasis. Although these compounds cause changes in the redistribution of glycogen deposits within the parasite, it is unknown whether these compounds interact with enzymes of the glycolytic pathway. OBJECTIVE The aim of this study was to test the binding affinity of these compounds to pyrophosphate- dependent phosphofructokinase (PPi-PFK), triosephosphate isomerase (TIM), and pyruvate phosphate dikinase (PPDK) from E. histolytica as a possible mechanism of action. METHODS The molecular docking study of the 7-carboxylate QdNOs derivatives and the proteins was performed using AutoDock/Vina software. Molecular dynamics simulation was performed for 100 ns. RESULTS Among all the selected compounds, T-072 exhibited the best binding affinity to EhPPi- PFK and EhTIM proteins, while T-006 interacted best with EhPPDK. ADMET analysis revealed that T-072 was non-toxic, while T-006 could become harmful to the host. In addition, molecular dynamics showed that T-072 has stable interaction with EhPPi-PFK and EhTIM. CONCLUSION Including all aspects, these data indicated that these compounds might inhibit the activity of key enzymes in energy metabolism leading to parasite death. Furthermore, these compounds may be a good starting point for the future development of new potent antiamebic agents.
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Affiliation(s)
- Jacqueline Soto-Sánchez
- Sección de Estudios de Posgrado e Investigación, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, México
| | - Salvador Pérez-Mora
- Sección de Estudios de Posgrado e Investigación, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, México
| | | | - Lizeth Mariel Zavala-Ocampo
- Laboratorio de Productos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
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Shi D, Fang G, Chen Q, Li J, Ruan X, Lian X. Six-hour time-restricted feeding inhibits lung cancer progression and reshapes circadian metabolism. BMC Med 2023; 21:417. [PMID: 37924048 PMCID: PMC10625271 DOI: 10.1186/s12916-023-03131-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND Accumulating evidence has suggested an oncogenic effect of diurnal disruption on cancer progression. To test whether targeting circadian rhythm by dietary strategy suppressed lung cancer progression, we adopted 6-h time-restricted feeding (TRF) paradigm to elucidate whether and how TRF impacts lung cancer progression. METHODS This study used multiple lung cancer cell lines, two xenograft mouse models, and a chemical-treated mouse lung cancer model. Stable TIM-knockdown and TIM-overexpressing A549 cells were constructed. Cancer behaviors in vitro were determined by colony formation, EdU proliferation, wound healing, transwell migration, flow cytometer, and CCK8 assays. Immunofluorescence, pathology examinations, and targeted metabolomics were also used in tumor cells and tissues. mCherry-GFP-LC3 plasmid was used to detect autophagic flux. RESULTS We found for the first time that compared to normal ad libitum feeding, 6-h TRF inhibited lung cancer progression and reprogrammed the rhythms of metabolites or genes involved in glycolysis and the circadian rhythm in tumors. After TRF intervention, only timeless (TIM) gene among five lung cancer-associated clock genes was found to consistently align rhythm of tumor cells to that of tumor tissues. Further, we demonstrated that the anti-tumor effect upon TRF was partially mediated by the rhythmic downregulation of the TIM and the subsequent activation of autophagy. Combining TRF with TIM inhibition further enhanced the anti-tumor effect, comparable to treatment efficacy of chemotherapy in xenograft model. CONCLUSIONS Six-hour TRF inhibits lung cancer progression and reshapes circadian metabolism, which is partially mediated by the rhythmic downregulation of the TIM and the subsequent upregulation of autophagy.
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Affiliation(s)
- Dan Shi
- Center for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P.R. China.
- Department of Nutrition and Food Hygiene, School of Public Health, Chongqing Medical University, Chongqing, 400016, P.R. China.
- Research Center for Environment and Population Health, School of Public Health, Chongqing Medical University, Chongqing, 400016, P. R. China.
- Nutrition Innovation Platform-Sichuan and Chongqing, School of Public Health, Chongqing Medical University, Chongqing, China.
| | - Gaofeng Fang
- Center for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P.R. China
- Department of Nutrition and Food Hygiene, School of Public Health, Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Qianyao Chen
- Center for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P.R. China
- Department of Nutrition and Food Hygiene, School of Public Health, Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Jianling Li
- Center for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P.R. China
- Department of Nutrition and Food Hygiene, School of Public Health, Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Xiongzhong Ruan
- Center for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P.R. China.
| | - Xuemei Lian
- Center for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P.R. China.
- Department of Nutrition and Food Hygiene, School of Public Health, Chongqing Medical University, Chongqing, 400016, P.R. China.
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Svagusa T, Sikiric S, Milavic M, Sepac A, Seiwerth S, Milicic D, Gasparovic H, Biocina B, Rudez I, Sutlic Z, Manola S, Varvodic J, Udovicic M, Urlic M, Ivankovic S, Plestina S, Paic F, Kulic A, Bakovic P, Sedlic F. Heart failure in patients is associated with downregulation of mitochondrial quality control genes. Eur J Clin Invest 2023; 53:e14054. [PMID: 37403271 DOI: 10.1111/eci.14054] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/27/2023] [Accepted: 06/15/2023] [Indexed: 07/06/2023]
Abstract
BACKGROUND Mitochondrial dysfunction is one of key factors causing heart failure. We performed a comprehensive analysis of expression of mitochondrial quality control (MQC) genes in heart failure. METHODS Myocardial samples were obtained from patients with ischemic and dilated cardiomyopathy in a terminal stage of heart failure and donors without heart disease. Using quantitative real-time PCR, we analysed a total of 45 MQC genes belonging to mitochondrial biogenesis, fusion-fission balance, mitochondrial unfolded protein response (UPRmt), translocase of the inner membrane (TIM) and mitophagy. Protein expression was analysed by ELISA and immunohistochemistry. RESULTS The following genes were downregulated in ischemic and dilated cardiomyopathy: COX1, NRF1, TFAM, SIRT1, MTOR, MFF, DNM1L, DDIT3, UBL5, HSPA9, HSPE1, YME1L, LONP1, SPG7, HTRA2, OMA1, TIMM23, TIMM17A, TIMM17B, TIMM44, PAM16, TIMM22, TIMM9, TIMM10, PINK1, PARK2, ROTH1, PARL, FUNDC1, BNIP3, BNIP3L, TPCN2, LAMP2, MAP1LC3A and BECN1. Moreover, MT-ATP8, MFN2, EIF2AK4 and ULK1 were downregulated in heart failure from dilated, but not ischemic cardiomyopathy. VDAC1 and JUN were only genes that exhibited significantly different expression between ischemic and dilated cardiomyopathy. Expression of PPARGC1, OPA1, JUN, CEBPB, EIF2A, HSPD1, TIMM50 and TPCN1 was not significantly different between control and any form of heart failure. TOMM20 and COX proteins were downregulated in ICM and DCM. CONCLUSIONS Heart failure in patients with ischemic and dilated cardiomyopathy is associated with downregulation of large number of UPRmt, mitophagy, TIM and fusion-fission balance genes. This indicates multiple defects in MQC and represents one of potential mechanisms underlying mitochondrial dysfunction in patients with heart failure.
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Affiliation(s)
- T Svagusa
- Department of Cardiovascular Diseases, Dubrava Clinical Hospital, Zagreb, Croatia
| | - S Sikiric
- Department of Pathology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - M Milavic
- Department of Pathology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - A Sepac
- Department of Pathology, University of Zagreb School of Medicine, Zagreb, Croatia
- Department of Pathology and Cytology, University Hospital Center Zagreb, Zagreb, Croatia
| | - S Seiwerth
- Department of Pathology, University of Zagreb School of Medicine, Zagreb, Croatia
- Department of Pathology and Cytology, University Hospital Center Zagreb, Zagreb, Croatia
| | - D Milicic
- Department of Internal Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
- Department of Cardiovascular Diseases, University Hospital Center Zagreb, Zagreb, Croatia
| | - H Gasparovic
- Department of Surgery, University of Zagreb School of Medicine, Zagreb, Croatia
- Department of Cardiac Surgery, University Hospital Center Zagreb, Zagreb, Croatia
| | - B Biocina
- Department of Surgery, University of Zagreb School of Medicine, Zagreb, Croatia
- Department of Cardiac Surgery, University Hospital Center Zagreb, Zagreb, Croatia
| | - I Rudez
- Department of Surgery, University of Zagreb School of Medicine, Zagreb, Croatia
- Department of Cardiac and Transplant Surgery, Dubrava Clinical Hospital, Zagreb, Croatia
| | - Z Sutlic
- Department of Surgery, University of Zagreb School of Medicine, Zagreb, Croatia
- Department of Cardiac and Transplant Surgery, Dubrava Clinical Hospital, Zagreb, Croatia
| | - S Manola
- Department of Cardiovascular Diseases, Dubrava Clinical Hospital, Zagreb, Croatia
| | - J Varvodic
- Department of Cardiac and Transplant Surgery, Dubrava Clinical Hospital, Zagreb, Croatia
| | - M Udovicic
- Department of Cardiovascular Diseases, Dubrava Clinical Hospital, Zagreb, Croatia
- Department of Internal Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
| | - M Urlic
- Department of Cardiac Surgery, University Hospital Center Zagreb, Zagreb, Croatia
| | - S Ivankovic
- Department of Cardiac Surgery, University Hospital Center Split, Split, Croatia
| | - S Plestina
- Department of Pathophysiology, University of Zagreb School of Medicine, Zagreb, Croatia
- Department of Oncology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - F Paic
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - A Kulic
- Department of Oncology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - P Bakovic
- Department of Pathophysiology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - F Sedlic
- Department of Pathophysiology, University of Zagreb School of Medicine, Zagreb, Croatia
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Herviou P, Balvay A, Bellet D, Bobet S, Maudet C, Staub J, Alric M, Leblond-Bourget N, Delorme C, Rabot S, Denis S, Payot S. Transfer of the Integrative and Conjugative Element ICE St3 of Streptococcus thermophilus in Physiological Conditions Mimicking the Human Digestive Ecosystem. Microbiol Spectr 2023; 11:e0466722. [PMID: 36995244 PMCID: PMC10269554 DOI: 10.1128/spectrum.04667-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/12/2023] [Indexed: 03/31/2023] Open
Abstract
Metagenome analyses of the human microbiome suggest that horizontal gene transfer (HGT) is frequent in these rich and complex microbial communities. However, so far, only a few HGT studies have been conducted in vivo. In this work, three different systems mimicking the physiological conditions encountered in the human digestive tract were tested, including (i) the TNO gastro-Intestinal tract Model 1 (TIM-1) system (for the upper part of the intestine), (ii) the ARtificial COLon (ARCOL) system (to mimic the colon), and (iii) a mouse model. To increase the likelihood of transfer by conjugation of the integrative and conjugative element studied in the artificial digestive systems, bacteria were entrapped in alginate, agar, and chitosan beads before being placed in the different gut compartments. The number of transconjugants detected decreased, while the complexity of the ecosystem increased (many clones in TIM-1 but only one clone in ARCOL). No clone was obtained in a natural digestive environment (germfree mouse model). In the human gut, the richness and diversity of the bacterial community would offer more opportunities for HGT events to occur. In addition, several factors (SOS-inducing agents, microbiota-derived factors) that potentially increase in vivo HGT efficiency were not tested here. Even if HGT events are rare, expansion of the transconjugant clones can happen if ecological success is fostered by selecting conditions or by events that destabilize the microbial community. IMPORTANCE The human gut microbiota plays a key role in maintaining normal host physiology and health, but its homeostasis is fragile. During their transit in the gastrointestinal tract, bacteria conveyed by food can exchange genes with resident bacteria. New traits acquired by HGT (e.g., new catabolic properties, bacteriocins, antibiotic resistance) can impact the gut microbial composition and metabolic potential. We showed here that TIM-1, a system mimicking the upper digestive tract, is a useful tool to evaluate HGT events in conditions closer to the physiological ones. Another important fact pointed out in this work is that Enterococcus faecalis is a good candidate for foreign gene acquisition. Due to its high ability to colonize the gut and acquire mobile genetic elements, this commensal bacterium could serve as an intermediate for HGT in the human gut.
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Affiliation(s)
- Pauline Herviou
- Université Clermont-Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
| | - Aurélie Balvay
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Deborah Bellet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Sophie Bobet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Claire Maudet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Johan Staub
- Université de Lorraine, INRAE, DynAMic, Nancy, France
| | - Monique Alric
- Université Clermont-Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
| | | | - Christine Delorme
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Sylvie Rabot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Sylvain Denis
- Université Clermont-Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
| | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, Nancy, France
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Duque-Soto C, Quintriqueo-Cid A, Rueda-Robles A, Robert P, Borrás-Linares I, Lozano-Sánchez J. Evaluation of Different Advanced Approaches to Simulation of Dynamic In Vitro Digestion of Polyphenols from Different Food Matrices-A Systematic Review. Antioxidants (Basel) 2022; 12:101. [PMID: 36670962 PMCID: PMC9854833 DOI: 10.3390/antiox12010101] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
Phenolic compounds have become interesting bioactive antioxidant compounds with implications for obesity, cancer and inflammatory gastrointestinal pathologies. As the influence of digestion and gut microbiota on antioxidant behavior is yet to be completely elucidated, and due to limitations associated to in vivo studies, dynamic in vitro gastrointestinal models have been promoted. A systematic review was conducted of different databases (PubMed, Web of Science and Scopus) following PRISMA guidelines to assess different dynamic digestion models and assay protocols used for phenolic compound research regarding bioaccesibility and interaction with colonic microbiota. Of 284 records identified, those including dynamic multicompartmental digestion models for the study of phenolic compound bioaccesibility, bioactivity and the effects of microbiota were included, with 57 studies meeting the inclusion criteria. Different conditions and experimental configurations as well as administered doses, sample treatments and microbiological assays of dynamic digestion studies on polyphenols were recorded and compared to establish their relevance for the dynamic in vitro digestion of phenolic compounds. While similarities were observed in certain experimental areas, a high variability was found in others, such as administered doses. A description of considerations on the study of the digestion of phenolic compounds is proposed to enhance comparability in research.
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Affiliation(s)
- Carmen Duque-Soto
- Department of Food Science and Nutrition, Faculty of Farmacy, University of Granada, 18071 Granada, Spain
| | - Alejandra Quintriqueo-Cid
- Department of Food Science and Nutrition, Faculty of Farmacy, University of Granada, 18071 Granada, Spain
- Departamento de Ciencia de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380492, Chile
| | - Ascensión Rueda-Robles
- Department of Food Science and Nutrition, Faculty of Farmacy, University of Granada, 18071 Granada, Spain
| | - Paz Robert
- Departamento de Ciencia de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380492, Chile
| | - Isabel Borrás-Linares
- Department of Analytical Chemistry, Faculty of Science, University of Granada, 18071 Granada, Spain
| | - Jesús Lozano-Sánchez
- Department of Food Science and Nutrition, Faculty of Farmacy, University of Granada, 18071 Granada, Spain
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Abstract
The circadian rhythm is generated at the cellular level by a molecular clock system that involves specific genes. Studies have revealed that circadian clock disruption is a control point in cancer progression. Colorectal cancer (CRC) is one of the cancers closely associated with circadian disruption. In the present review, the involvement of the circadian clock in CRC development was summarized. Abnormal expression of certain clock genes has been found in patients with CRC and their correlation with clinicopathological features has also been explored. The period and cryptochrome 2 (Cry2), Sirtuin1 (SIRT1) and neuronal PAS domain protein 2 (NPAS2) genes were reported to have tumour suppressor properties. Conversely, Cry1, brain and muscle ARNT-like-1, circadian locomotor output cycles kaput (CLOCK) and timeless may aggravate CRC progression, but these findings are not consistent and require to be confirmed by further research. Circadian scheduling also indicated advantages in chemotherapy treatments for patients with CRC by increasing the maximum tolerated doses and decreasing toxicities. Dysfunction of the molecular CLOCK system disrupted cellular processes to accelerate colon tumorigenesis, such as metabolism, cell cycle, DNA damage repair, proliferation and apoptosis, epithelial-mesenchymal transition and stemness. The clock gene network and how the dynamics of the system influence CRC were discussed.
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Affiliation(s)
- Xiwu Rao
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, P.R. China
| | - Lizhu Lin
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, P.R. China
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Wang J, Yu C, Zhuang J, Qi W, Jiang J, Liu X, Zhao W, Cao Y, Wu H, Qi J, Zhao RC. The role of phosphatidylserine on the membrane in immunity and blood coagulation. Biomark Res 2022; 10:4. [PMID: 35033201 PMCID: PMC8760663 DOI: 10.1186/s40364-021-00346-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 12/17/2022] Open
Abstract
The negatively charged aminophospholipid, phosphatidylserine (PtdSer), is located in the inner leaflet of the plasma membrane in normal cells, and may be exposed to the outer leaflet under some immune and blood coagulation processes. Meanwhile, Ptdser exposed to apoptotic cells can be recognized and eliminated by various immune cells, whereas on the surface of activated platelets Ptdser interacts with coagulation factors prompting enhanced production of thrombin which significantly facilitates blood coagulation. In the case where PtdSer fails in exposure or mistakenly occurs, there are occurrences of certain immunological and haematological diseases, such as the Scott syndrome and Systemic lupus erythematosus. Besides, viruses (e.g., Human Immunodeficiency Virus (HIV), Ebola virus (EBOV)) can invade host cells through binding the exposed PtdSer. Most recently, the Corona Virus Disease 2019 (COVID-19) has been similarly linked to PtdSer or its receptors. Therefore, it is essential to comprehensively understand PtdSer and its functional characteristics. Therefore, this review summarizes Ptdser, its eversion mechanism; interaction mechanism, particularly with its immune receptors and coagulation factors; recognition sites; and its function in immune and blood processes. This review illustrates the potential aspects for the underlying pathogenic mechanism of PtdSer-related diseases, and the discovery of new therapeutic strategies as well.
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Affiliation(s)
- Jiao Wang
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China.
| | - Changxin Yu
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Junyi Zhuang
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Wenxin Qi
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Jiawen Jiang
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Xuanting Liu
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Wanwei Zhao
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Yiyang Cao
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Hao Wu
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Jingxuan Qi
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Robert Chunhua Zhao
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China.
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, No. 5 Dongdansantiao, Beijing, 100005, China.
- Centre of Excellence in Tissue Engineering, Chinese Academy of Medical Sciences, Beijing, China.
- Beijing Key Laboratory of New Drug Development and Clinical Trial of Stem Cell Therapy (BZ0381), Beijing, China.
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9
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Xing X, Gu F, Hua L, Cui X, Li D, Wu Z, Zhang R. TIMELESS Promotes Tumor Progression by Enhancing Macrophages Recruitment in Ovarian Cancer. Front Oncol 2021; 11:732058. [PMID: 34490127 PMCID: PMC8417241 DOI: 10.3389/fonc.2021.732058] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/29/2021] [Indexed: 01/11/2023] Open
Abstract
Objective Ovarian cancer (OV) is the most fatal and frequent type of gynecological malignancy worldwide. TIMELESS (TIM), as a circadian clock gene, has been found to be highly expressed and predictive of poor prognosis in various cancers. However, the function of TIM in OV is not known. This study was designed to investigate the biological functions and underlying mechanisms of TIM during OV progression. Methods Cell viability assay, cell migration assay, immunohistochemistry staining, qPCR analyses, and tumor xenograft model were used to identify the functions of TIM in OV. Bioinformatics analyses, including GEPIA, cBioPortal, GeneMANIA, and TIMER, were used to analyze the gene expression, genetic alteration, and immune cell infiltration of TIM in OV. Results TIM is highly expressed in OV patients. TIM knockdown inhibited OV cell proliferation, migration, and invasion both in vitro and in vivo. Genetic alteration of TIM was identified in patients with OV. TIM co-expression network indicates that TIM had a wide effect on the immune cell infiltration and activation in OV. Further analysis and experimental verification revealed that TIM was positively correlated with macrophages infiltration in OV. Conclusions Our study unveiled a novel function of highly expressed TIM associated with immune cell especially macrophages infiltration in OV. TIM may serve as a potential prognostic biomarker and immunotherapy target for OV patients.
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Affiliation(s)
- Xin Xing
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Fei Gu
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Lanyu Hua
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoxiao Cui
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Dongxue Li
- Shanghai Cancer Institute, Shanghai, China
| | - Zhiyong Wu
- Gynecology Department, Shanghai Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Rong Zhang
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
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10
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Chaudhuri M, Tripathi A, Gonzalez FS. Diverse Functions of Tim50, a Component of the Mitochondrial Inner Membrane Protein Translocase. Int J Mol Sci 2021; 22:7779. [PMID: 34360547 PMCID: PMC8346121 DOI: 10.3390/ijms22157779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022] Open
Abstract
Mitochondria are essential in eukaryotes. Besides producing 80% of total cellular ATP, mitochondria are involved in various cellular functions such as apoptosis, inflammation, innate immunity, stress tolerance, and Ca2+ homeostasis. Mitochondria are also the site for many critical metabolic pathways and are integrated into the signaling network to maintain cellular homeostasis under stress. Mitochondria require hundreds of proteins to perform all these functions. Since the mitochondrial genome only encodes a handful of proteins, most mitochondrial proteins are imported from the cytosol via receptor/translocase complexes on the mitochondrial outer and inner membranes known as TOMs and TIMs. Many of the subunits of these protein complexes are essential for cell survival in model yeast and other unicellular eukaryotes. Defects in the mitochondrial import machineries are also associated with various metabolic, developmental, and neurodegenerative disorders in multicellular organisms. In addition to their canonical functions, these protein translocases also help maintain mitochondrial structure and dynamics, lipid metabolism, and stress response. This review focuses on the role of Tim50, the receptor component of one of the TIM complexes, in different cellular functions, with an emphasis on the Tim50 homologue in parasitic protozoan Trypanosoma brucei.
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Affiliation(s)
- Minu Chaudhuri
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN 37208, USA; (A.T.); (F.S.G.)
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11
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Luessing J, Sakhteh M, Sarai N, Frizzell L, Tsanov N, Ramberg KO, Maretto S, Crowley PB, Lowndes NF. The nuclear kinesin KIF18B promotes 53BP1-mediated DNA double-strand break repair. Cell Rep 2021; 35:109306. [PMID: 34192545 DOI: 10.1016/j.celrep.2021.109306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/29/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
53BP1 is recruited to chromatin in the vicinity of DNA double-strand breaks (DSBs). We identify the nuclear kinesin, KIF18B, as a 53BP1-interacting protein and define its role in 53BP1-mediated DSB repair. KIF18B is a molecular motor protein involved in destabilizing astral microtubules during mitosis. It is primarily nuclear throughout the interphase and is constitutively chromatin bound. Our observations indicate a nuclear function during the interphase for a kinesin previously implicated in mitosis. We identify a central motif in KIF18B, which we term the Tudor-interacting motif (TIM), because of its interaction with the Tudor domain of 53BP1. TIM enhances the interaction between the 53BP1 Tudor domain and dimethylated lysine 20 of histone H4. TIM and the motor function of KIF18B are both required for efficient 53BP1 focal recruitment in response to damage and for fusion of dysfunctional telomeres. Our data suggest a role for KIF18B in efficient 53BP1-mediated end-joining of DSBs.
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12
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Palmer CS, Anderson AJ, Stojanovski D. Mitochondrial protein import dysfunction: mitochondrial disease, neurodegenerative disease and cancer. FEBS Lett 2021; 595:1107-1131. [PMID: 33314127 DOI: 10.1002/1873-3468.14022] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/12/2020] [Accepted: 10/17/2020] [Indexed: 12/13/2022]
Abstract
The majority of proteins localised to mitochondria are encoded by the nuclear genome, with approximately 1500 proteins imported into mammalian mitochondria. Dysfunction in this fundamental cellular process is linked to a variety of pathologies including neuropathies, cardiovascular disorders, myopathies, neurodegenerative diseases and cancer, demonstrating the importance of mitochondrial protein import machinery for cellular function. Correct import of proteins into mitochondria requires the co-ordinated activity of multimeric protein translocation and sorting machineries located in both the outer and inner mitochondrial membranes, directing the imported proteins to the destined mitochondrial compartment. This dynamic process maintains cellular homeostasis, and its dysregulation significantly affects cellular signalling pathways and metabolism. This review summarises current knowledge of the mammalian mitochondrial import machinery and the pathological consequences of mutation of its components. In addition, we will discuss the role of mitochondrial import in cancer, and our current understanding of the role of mitochondrial import in neurodegenerative diseases including Alzheimer's disease, Huntington's disease and Parkinson's disease.
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Affiliation(s)
- Catherine S Palmer
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Alexander J Anderson
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
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13
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Saxena R, Saribas S, Jadiya P, Tomar D, Kaminski R, Elrod JW, Safak M. Human neurotropic polyomavirus, JC virus, agnoprotein targets mitochondrion and modulates its functions. Virology 2021; 553:135-153. [PMID: 33278736 PMCID: PMC7847276 DOI: 10.1016/j.virol.2020.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/12/2020] [Indexed: 01/18/2023]
Abstract
JC virus encodes an important regulatory protein, known as Agnoprotein (Agno). We have recently reported Agno's first protein-interactome with its cellular partners revealing that it targets various cellular networks and organelles, including mitochondria. Here, we report further characterization of the functional consequences of its mitochondrial targeting and demonstrated its co-localization with the mitochondrial networks and with the mitochondrial outer membrane. The mitochondrial targeting sequence (MTS) of Agno and its dimerization domain together play major roles in this targeting. Data also showed alterations in various mitochondrial functions in Agno-positive cells; including a significant reduction in mitochondrial membrane potential, respiration rates and ATP production. In contrast, a substantial increase in ROS production and Ca2+ uptake by the mitochondria were also observed. Finally, findings also revealed a significant decrease in viral replication when Agno MTS was deleted, highlighting a role for MTS in the function of Agno during the viral life cycle.
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Affiliation(s)
- Reshu Saxena
- Department of Neuroscience, Laboratory of Molecular Neurovirology, MERB-757, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Sami Saribas
- Department of Neuroscience, Laboratory of Molecular Neurovirology, MERB-757, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Pooja Jadiya
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, USA
| | - Dhanendra Tomar
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, USA
| | - Rafal Kaminski
- Department of Neuroscience, Laboratory of Molecular Neurovirology, MERB-757, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - John W Elrod
- Center for Translational Medicine, Lewis Katz School of Medicine at Temple University, USA
| | - Mahmut Safak
- Department of Neuroscience, Laboratory of Molecular Neurovirology, MERB-757, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA.
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14
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Chaudhuri M, Darden C, Soto Gonzalez F, Singha UK, Quinones L, Tripathi A. Tim17 Updates: A Comprehensive Review of an Ancient Mitochondrial Protein Translocator. Biomolecules 2020; 10:E1643. [PMID: 33297490 PMCID: PMC7762337 DOI: 10.3390/biom10121643] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023] Open
Abstract
The translocases of the mitochondrial outer and inner membranes, the TOM and TIMs, import hundreds of nucleus-encoded proteins into mitochondria. TOM and TIMs are multi-subunit protein complexes that work in cooperation with other complexes to import proteins in different sub-mitochondrial destinations. The overall architecture of these protein complexes is conserved among yeast/fungi, animals, and plants. Recent studies have revealed unique characteristics of this machinery, particularly in the eukaryotic supergroup Excavata. Despite multiple differences, homologues of Tim17, an essential component of one of the TIM complexes and a member of the Tim17/Tim22/Tim23 family, have been found in all eukaryotes. Here, we review the structure and function of Tim17 and Tim17-containing protein complexes in different eukaryotes, and then compare them to the single homologue of this protein found in Trypanosoma brucei, a unicellular parasitic protozoan.
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Affiliation(s)
- Minu Chaudhuri
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, 1005 Dr. D.B. Todd, Jr., Blvd, Nashville, TN 37208, USA; (C.D.); (F.S.G.); (U.K.S.); (L.Q.); (A.T.)
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15
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Wei X, Li R, Qiao S, Chen XX, Xing G, Zhang G. Porcine Reproductive and Respiratory Syndrome Virus Utilizes Viral Apoptotic Mimicry as an Alternative Pathway To Infect Host Cells. J Virol 2020; 94:e00709-20. [PMID: 32522856 DOI: 10.1128/JVI.00709-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/03/2020] [Indexed: 12/29/2022] Open
Abstract
PRRS has caused huge economic losses to pig farming worldwide. Its causative agent, PRRSV, infects host cells through low pH-dependent clathrin-mediated endocytosis and CD163 is indispensable during the process. Whether there exist alternative infection pathways for PRRSV arouses our interest. Here, we found that PRRSV exposed PS on its envelope and disguised as apoptotic debris. The PS receptor TIM-1/4 recognized PRRSV and induced the downstream signaling pathway to mediate viral infection via CD163-dependent macropinocytosis. The current work deepens our understanding of PRRSV infection and provides clues for the development of drugs and vaccines against the virus. Porcine reproductive and respiratory syndrome (PRRS), caused by PRRS virus (PRRSV), has led to enormous economic losses in global swine industry. Infection by PRRSV is previously shown to be via low pH-dependent clathrin-mediated endocytosis, and CD163 functions as an essential receptor during viral infection. Despite much research focusing on it, PRRSV infection remains to be fully elucidated. In this study, we demonstrated that PRRSV externalized phosphatidylserine (PS) on the envelope as viral apoptotic mimicry and infected host cells through T-cell immunoglobulin and mucin domain (TIM)-induced and CD163-involved macropinocytosis as an alternative pathway. In detail, we identified that PS receptor TIM-1/4 recognized and interacted with PRRSV as viral apoptotic mimicry and subsequently induced macropinocytosis by the downstream Rho GTPases Rac1, cell division control protein 42 (Cdc42), and p21-activated kinase 1 (Pak1). Altogether, these results expand our knowledge of PRRSV infection, which will support implications for the prevention and control of PRRS. IMPORTANCE PRRS has caused huge economic losses to pig farming worldwide. Its causative agent, PRRSV, infects host cells through low pH-dependent clathrin-mediated endocytosis and CD163 is indispensable during the process. Whether there exist alternative infection pathways for PRRSV arouses our interest. Here, we found that PRRSV exposed PS on its envelope and disguised as apoptotic debris. The PS receptor TIM-1/4 recognized PRRSV and induced the downstream signaling pathway to mediate viral infection via CD163-dependent macropinocytosis. The current work deepens our understanding of PRRSV infection and provides clues for the development of drugs and vaccines against the virus.
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16
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Abstract
Immunotherapy for cancer is making impressive strides at improving survival of a subset of cancer patients. To increase the breadth of patients that benefit from immunotherapy, new strategies that combat the immunosuppressive microenvironment of tumors are needed. Phosphatidylserine (PS) signaling is exploited by tumors to enhance tumor immune evasion and thus strategies to inhibit PS-mediated immune suppression have potential to increase the efficacy of immunotherapy. PS is a membrane lipid that flips to the outer surface of the cell membrane during apoptosis and/or cell stress. Externalized PS can drive efferocytosis or engage PS receptors (PSRs) to promote local immune suppression. In the tumor microenvironment (TME) PS-mediated immune suppression is often termed apoptotic mimicry. Monoclonal antibodies (mAbs) targeting PS or PSRs have been developed and are in preclinical and clinical testing. The TIM (T-cell/transmembrane, immunoglobulin, and mucin) and TAM (Tyro3, AXL, and MerTK) family of receptors are PSRs that have been shown to drive PS-mediated immune suppression in tumors. This review will highlight the development of mAbs targeting PS, TIM-3 and the TAM receptors. Video Abstract
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Affiliation(s)
- Adam S Dayoub
- Division of Surgical Oncology, Department of Surgery, Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390-8593, USA
| | - Rolf A Brekken
- Division of Surgical Oncology, Department of Surgery, Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390-8593, USA. .,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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17
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Oliveira LG, Peron JPS. Viral receptors for flaviviruses: Not only gatekeepers. J Leukoc Biol 2019; 106:695-701. [PMID: 31063609 DOI: 10.1002/jlb.mr1118-460r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 12/20/2022] Open
Abstract
Arboviruses have been a huge threat for human health since the discovery of yellow fever virus in 1901. Arboviruses are arthropod born viruses, mainly transmitted by mosquitoes and ticks, responsible for more than thousands of deaths annually. The Flavivirideae family is probably the most clinically relevant, as it is composed of very important agents, such as dengue, yellow fever, West Nile, Japanese encephalitis, and, recently, Zika virus. Intriguingly, despite their structural and genomic similarities, flaviviruses may cause conditions ranging from mild infections with fever, cutaneous rash, and headache, to very severe cases, such as hemorrhagic fever, encephalitis, Guillain-Barré syndrome, and microcephaly. These differences may greatly rely on viral burden, tissue tropism, and mechanisms of immune evasion that may depend on both viral and host genetic factors. Unfortunately, very little is known about the biology of these factors, and how they orchestrate these differences. In this context, viral structural proteins and host cellular receptors may have a great relevance, as their interaction dictates not only viral tissue tropism, but also a plethora on intracellular mechanisms that may greatly account for either failure or success of infection. A great number of viral receptors have been described so far, although there is still a huge gap in understanding their overall role during infection. Here we discuss some important aspects triggered after the interaction of flaviviruses and host membrane receptors, and how they change the overall outcome of the infection.
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Affiliation(s)
- Lilian G Oliveira
- Neuroimmune Interactions Laboratory, Institute of Biomedical Sciences, Department of Immunology, University of Sao Paulo, São Paulo, Brazil
| | - Jean Pierre Schatzmann Peron
- Immunopathology and Alergy PostGraduate Program, School of Medicine, University of São Paulo, Brazil.,Scientific Platform Pasteur, USP, São Paulo, Brazil
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18
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Li M, Waheed AA, Yu J, Zeng C, Chen HY, Zheng YM, Feizpour A, Reinhard BM, Gummuluru S, Lin S, Freed EO, Liu SL. TIM-mediated inhibition of HIV-1 release is antagonized by Nef but potentiated by SERINC proteins. Proc Natl Acad Sci U S A 2019; 116:5705-14. [PMID: 30842281 DOI: 10.1073/pnas.1819475116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The T cell Ig and mucin domain (TIM) proteins inhibit release of HIV-1 and other enveloped viruses by interacting with cell- and virion-associated phosphatidylserine (PS). Here, we show that the Nef proteins of HIV-1 and other lentiviruses antagonize TIM-mediated restriction. TIM-1 more potently inhibits the release of Nef-deficient relative to Nef-expressing HIV-1, and ectopic expression of Nef relieves restriction. HIV-1 Nef does not down-regulate the overall level of TIM-1 expression, but promotes its internalization from the plasma membrane and sequesters its expression in intracellular compartments. Notably, Nef mutants defective in modulating membrane protein endocytic trafficking are incapable of antagonizing TIM-mediated inhibition of HIV-1 release. Intriguingly, depletion of SERINC3 or SERINC5 proteins in human peripheral blood mononuclear cells (PBMCs) attenuates TIM-1 restriction of HIV-1 release, in particular that of Nef-deficient viruses. In contrast, coexpression of SERINC3 or SERINC5 increases the expression of TIM-1 on the plasma membrane and potentiates TIM-mediated inhibition of HIV-1 production. Pulse-chase metabolic labeling reveals that the half-life of TIM-1 is extended by SERINC5 from <2 to ∼6 hours, suggesting that SERINC5 stabilizes the expression of TIM-1. Consistent with a role for SERINC protein in potentiating TIM-1 restriction, we find that MLV glycoGag and EIAV S2 proteins, which, like Nef, antagonize SERINC-mediated diminishment of HIV-1 infectivity, also effectively counteract TIM-mediated inhibition of HIV-1 release. Collectively, our work reveals a role of Nef in antagonizing TIM-1 and highlights the complex interplay between Nef and HIV-1 restriction by TIMs and SERINCs.
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19
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Murphy S, Henry M, Meleady P, Ohlendieck K. Utilization of dried and long-term stored polyacrylamide gels for the advanced proteomic profiling of mitochondrial contact sites from rat liver. Biol Methods Protoc 2018; 3:bpy008. [PMID: 32161802 PMCID: PMC6994098 DOI: 10.1093/biomethods/bpy008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/07/2018] [Accepted: 07/24/2018] [Indexed: 11/25/2022] Open
Abstract
Following subcellular fractionation, the complexity of proteins derived from a particular cellular compartment is often evaluated by gel electrophoretic analysis. For the proteomic cataloguing of these distinct protein populations and their biochemical characterization, gel electrophoretic protein separation can be conveniently combined with liquid chromatography mass spectrometry. Here we describe a gel-enhanced liquid chromatography mass spectrometry (GeLC-MS)/MS approach with a new bioanalytical focus on the proteomic profiling of mitochondrial contact sites from rat liver using the highly sensitive Orbitrap Fusion Tribrid mass spectrometer for optimum protein identification following extraction from dried and long-term stored gels. Mass spectrometric analysis identified 964 protein species in the mitochondrial contact site fraction, whereby 459 proteins were identified by ≥3 unique peptides. This included mitochondrial components of the supramolecular complexes that form the ATP synthase, the respiratory chain, ribosomal subunits and the cytochrome P450 system, as well as crucial components of the translocase complexes translocase of the inner membrane (TIM) and translocase of the outer membrane (TOM) of the two mitochondrial membranes. Proteomics also identified contact site markers, such as glutathione transferase, monoamine oxidase and the pore protein voltage dependent anion channel (VDAC)-1. Hence, this report demonstrates that the GeLC-MS/MS method can be used to study complex mixtures of proteins that have been embedded and stored in dried polyacrylamide gels for a long period of time. Careful re-swelling and standard in-gel digestion is suitable to produce peptide profiles from old gels that can be used to extract sophisticated proteomic maps and enable the subsequent bioinformatics analysis of the distribution of protein function and the determination of potential protein clustering within the contact site system.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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20
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Dasilva G, Boller M, Medina I, Storch J. Relative levels of dietary EPA and DHA impact gastric oxidation and essential fatty acid uptake. J Nutr Biochem 2017; 55:68-75. [PMID: 29413491 DOI: 10.1016/j.jnutbio.2017.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 09/12/2017] [Accepted: 11/13/2017] [Indexed: 01/31/2023]
Abstract
Previous research showed that increasing the proportion of docosahexaenoic acid (DHA) in marine lipid supplements significantly reduces associated health benefits compared with balanced eicosapentaenoic acid (EPA):DHA supplementation Dasilva et al., 2015 [1]. It was therefore hypothesized that the EPA and DHA molecules might have differential resistance to oxidation during gastric digestion and that the oxidation level achieved could be inversely correlated with intestinal absorption and, hence, with the resultant health benefits. Accordingly, we tested this proposed mechanism of action by investigating the degree of oxidation in the stomach, and the levels of bioaccessible lipids, of varying molar proportions of DHA and EPA (2:1, 1:1 and 1:2) using the dynamic gastrointestinal tract model TIM-1. In addition, small intestine enterocyte absorption and metabolism were simulated by Caco-2 cell monolayers that were incubated with these same varying proportions of DHA and EPA, and comparing oxidized and nonoxidized polyunsaturated fatty acids (PUFAs). The results show an inverse correlation between lipid oxidation products in the stomach and the levels of bioaccessible lipids. The balanced 1:1 EPA:DHA diet resulted in lower oxidation of PUFAs during stomach digestion relative to the other ratios tested. Finally, cell-based studies showed significantly lower assimilation of oxidized EPA and DHA substrates compared to nonoxidized PUFAs, as well as significant differences between the net uptake of EPA and DHA. Overall, the present work suggests that the correct design of diets and/or supplements containing marine lipids can strongly influence the stability and bioaccessibility of PUFAs during gastrointestinal digestion and subsequent absorption. This could modulate their health benefits related with inflammation, oxidative stress and metabolic disorders.
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Affiliation(s)
- Gabriel Dasilva
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas (IIM-CSIC), E-36208 Vigo, Spain; Department of Analytical Chemistry, Nutrition and Bromatology and Research Institute for Food Analysis (I.I.A.A.), University of Santiago de Compostela, E-15782, Spain.
| | - Matthew Boller
- Department of Nutritional Sciences and Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ, USA
| | - Isabel Medina
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas (IIM-CSIC), E-36208 Vigo, Spain
| | - Judith Storch
- Department of Nutritional Sciences and Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ, USA
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21
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Appelhans T, Busch KB. Dynamic imaging of mitochondrial membrane proteins in specific sub-organelle membrane locations. Biophys Rev 2017; 9:345-352. [PMID: 28819924 DOI: 10.1007/s12551-017-0287-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/25/2017] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are cellular organelles with multifaceted tasks and thus composed of different sub-compartments. The inner mitochondrial membrane especially has a complex nano-architecture with cristae protruding into the matrix. Related to their function, the localization of mitochondrial membrane proteins is more or less restricted to specific sub-compartments. In contrast, it can be assumed that membrane proteins per se diffuse unimpeded through continuous membranes. Fluorescence recovery after photobleaching is a versatile technology used in mobility analyses to determine the mobile fraction of proteins, but it cannot provide data on subpopulations or on confined diffusion behavior. Fluorescence correlation spectroscopy is used to analyze single molecule diffusion, but no trajectory maps are obtained. Single particle tracking (SPT) technologies in live cells, such as tracking and localization microscopy (TALM), do provide nanotopic localization and mobility maps of mitochondrial proteins in situ. Molecules can be localized with a precision of between 10 and 20 nm, and single trajectories can be recorded and analyzed; this is sufficient to reveal significant differences in the spatio-temporal behavior of diverse mitochondrial proteins. Here, we compare diffusion coefficients obtained by these different technologies and discuss trajectory maps of diverse mitochondrial membrane proteins obtained by SPT/TALM. We show that membrane proteins in the outer membrane generally display unhindered diffusion, while the mobility of inner membrane proteins is restricted by the inner membrane architecture, resulting in significantly lower diffusion coefficients. Moreover, tracking analysis could discern proteins in the inner boundary membrane from proteins preferentially diffusing in cristae membranes, two sub-compartments of the inner mitochondrial membrane. Thus, by evaluating trajectory maps it is possible to assign proteins to different sub-compartments of the same membrane.
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Affiliation(s)
- Timo Appelhans
- Mitochondrial Dynamics Group, School of Biology, University of Osnabrück, 49076, Osnabrück, Germany
| | - Karin B Busch
- Mitochondrial Dynamics Group, School of Biology, University of Osnabrück, 49076, Osnabrück, Germany. .,Institute of Molecular Cell Biology, School of Biology, Westfälische Wilhelms-University of Münster, 48149, Münster, Germany.
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22
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Lavin Y, Kobayashi S, Leader A, Amir EAD, Elefant N, Bigenwald C, Remark R, Sweeney R, Becker CD, Levine JH, Meinhof K, Chow A, Kim-Shulze S, Wolf A, Medaglia C, Li H, Rytlewski JA, Emerson RO, Solovyov A, Greenbaum BD, Sanders C, Vignali M, Beasley MB, Flores R, Gnjatic S, Pe'er D, Rahman A, Amit I, Merad M. Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses. Cell 2017; 169:750-765.e17. [PMID: 28475900 PMCID: PMC5737939 DOI: 10.1016/j.cell.2017.04.014] [Citation(s) in RCA: 803] [Impact Index Per Article: 114.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/26/2017] [Accepted: 04/11/2017] [Indexed: 12/15/2022]
Abstract
To guide the design of immunotherapy strategies for patients with early stage lung tumors, we developed a multiscale immune profiling strategy to map the immune landscape of early lung adenocarcinoma lesions to search for tumor-driven immune changes. Utilizing a barcoding method that allows a simultaneous single-cell analysis of the tumor, non-involved lung, and blood cells, we provide a detailed immune cell atlas of early lung tumors. We show that stage I lung adenocarcinoma lesions already harbor significantly altered T cell and NK cell compartments. Moreover, we identified changes in tumor-infiltrating myeloid cell (TIM) subsets that likely compromise anti-tumor T cell immunity. Paired single-cell analyses thus offer valuable knowledge of tumor-driven immune changes, providing a powerful tool for the rational design of immune therapies. VIDEO ABSTRACT.
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Affiliation(s)
- Yonit Lavin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Soma Kobayashi
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew Leader
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - El-Ad David Amir
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Naama Elefant
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel
| | - Camille Bigenwald
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Romain Remark
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert Sweeney
- Department of Thoracic Surgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christian D Becker
- Division of Pulmonology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jacob H Levine
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Klaus Meinhof
- Division of Pulmonology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew Chow
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seunghee Kim-Shulze
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrea Wolf
- Department of Thoracic Surgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chiara Medaglia
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel
| | - Hanjie Li
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel
| | | | | | - Alexander Solovyov
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benjamin D Greenbaum
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | - Mary Beth Beasley
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raja Flores
- Department of Thoracic Surgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sacha Gnjatic
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Adeeb Rahman
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ido Amit
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel
| | - Miriam Merad
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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23
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Lopez-Zavala AA, Carrasco-Miranda JS, Ramirez-Aguirre CD, López-Hidalgo M, Benitez-Cardoza CG, Ochoa-Leyva A, Cardona-Felix CS, Diaz-Quezada C, Rudiño-Piñera E, Sotelo-Mundo RR, Brieba LG. Structural insights from a novel invertebrate triosephosphate isomerase from Litopenaeus vannamei. Biochim Biophys Acta 2016; 1864:1696-1706. [PMID: 27614148 DOI: 10.1016/j.bbapap.2016.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/17/2016] [Accepted: 09/03/2016] [Indexed: 01/12/2023]
Abstract
Triosephosphate isomerase (TIM; EC 5.3.1.1) is a key enzyme involved in glycolysis and gluconeogenesis. Glycolysis is one of the most regulated metabolic pathways, however little is known about the structural mechanisms for its regulation in non-model organisms, like crustaceans. To understand the structure and function of this enzyme in invertebrates, we obtained the crystal structure of triosephosphate isomerase from the marine Pacific whiteleg shrimp (Litopenaeus vannamei, LvTIM) in complex with its inhibitor 2-phosphogyceric acid (2-PG) at 1.7Å resolution. LvTIM assembles as a homodimer with residues 166-176 covering the active site and residue Glu166 interacting with the inhibitor. We found that LvTIM is the least stable TIM characterized to date, with the lowest range of melting temperatures, and with the lowest activation enthalpy associated with the thermal unfolding process reported. In TIMs dimer stabilization is maintained by an interaction of loop 3 by a set of hydrophobic contacts between subunits. Within these contacts, the side chain of a hydrophobic residue of one subunit fits into a cavity created by a set of hydrophobic residues in the neighboring subunit, via a "ball and socket" interaction. LvTIM presents a Cys47 at the "ball" inter-subunit contact indicating that the character of this residue is responsible for the decrease in dimer stability. Mutational studies show that this residue plays a role in dimer stability but is not a solely determinant for dimer formation.
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Affiliation(s)
- Alonso A Lopez-Zavala
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico; Departamento de Ciencias Quimico Biologicas, Universidad de Sonora, Blvd. Luis Encinas y Rosales S/N, Col. Centro, Hermosillo, Sonora 83000, Mexico
| | - Jesus S Carrasco-Miranda
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico
| | - Claudia D Ramirez-Aguirre
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico
| | - Marisol López-Hidalgo
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-Instituto Politecnico Nacional, Ave. Guillermo Massieu Helguera, No. 239, Fracc. "La Escalera", Ticoman, Ciudad de México, 07320, Mexico
| | - Claudia G Benitez-Cardoza
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-Instituto Politecnico Nacional, Ave. Guillermo Massieu Helguera, No. 239, Fracc. "La Escalera", Ticoman, Ciudad de México, 07320, Mexico
| | - Adrian Ochoa-Leyva
- Departamento de Microbiologia Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Cesar S Cardona-Felix
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico; Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas (CICIMAR-IPN), Av. Instituto Politécnico Nacional. s/n., 23096, La Paz, Baja California Sur 23096, Mexico; Cátedras CONACyT, Dirección Adjunta de Desarrollo Científico, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Ciudad de Mexico, 03940, Mexico
| | - Corina Diaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad #2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Rogerio R Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico.
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico.
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24
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Mendieta-Moreno JI, Marcos-Alcalde I, Trabada DG, Gómez-Puertas P, Ortega J, Mendieta J. A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules. Adv Protein Chem Struct Biol 2015; 100:67-88. [PMID: 26415841 DOI: 10.1016/bs.apcsb.2015.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2.
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Affiliation(s)
- Jesús I Mendieta-Moreno
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain; Molecular Modelling Group, Center of Molecular Biology "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Iñigo Marcos-Alcalde
- Molecular Modelling Group, Center of Molecular Biology "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Daniel G Trabada
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Paulino Gómez-Puertas
- Molecular Modelling Group, Center of Molecular Biology "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - José Ortega
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain.
| | - Jesús Mendieta
- Molecular Modelling Group, Center of Molecular Biology "Severo Ochoa" (CSIC-UAM), Madrid, Spain; Biomol-Informatics SL, Campus UAM, Madrid, Spain
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25
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Abstract
Cancer transformation involves reprograming of mitochondrial function to avert cell death mechanisms, monopolize energy metabolism, accelerate mitotic proliferation, and promote metastasis. Mitochondrial ion channels have emerged as promising therapeutic targets because of their connection to metabolic and apoptotic functions. This mini review discusses how mitochondrial channels may be associated with cancer transformation and expands on the possible involvement of mitochondrial protein import complexes in pathophysiological process.
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Affiliation(s)
- Stephen M Madamba
- Department of Natural Sciences, Baruch College, City University of New York , New York, NY , USA ; City University of New York Graduate Center , New York, NY , USA
| | - Kevin N Damri
- Department of Natural Sciences, Baruch College, City University of New York , New York, NY , USA
| | - Laurent M Dejean
- Department of Chemistry, College of Science and Mathematics, California State University Fresno , Fresno, CA , USA
| | - Pablo M Peixoto
- Department of Natural Sciences, Baruch College, City University of New York , New York, NY , USA ; City University of New York Graduate Center , New York, NY , USA ; Department of Basic Sciences, New York University College of Dentistry , New York, NY , USA
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26
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Murcha MW, Narsai R, Devenish J, Kubiszewski-Jakubiak S, Whelan J. MPIC: a mitochondrial protein import components database for plant and non-plant species. Plant Cell Physiol 2015; 56:e10. [PMID: 25435547 DOI: 10.1093/pcp/pcu186] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In the 2 billion years since the endosymbiotic event that gave rise to mitochondria, variations in mitochondrial protein import have evolved across different species. With the genomes of an increasing number of plant species sequenced, it is possible to gain novel insights into mitochondrial protein import pathways. We have generated the Mitochondrial Protein Import Components (MPIC) Database (DB; http://www.plantenergy.uwa.edu.au/applications/mpic) providing searchable information on the protein import apparatus of plant and non-plant mitochondria. An in silico analysis was carried out, comparing the mitochondrial protein import apparatus from 24 species representing various lineages from Saccharomyces cerevisiae (yeast) and algae to Homo sapiens (human) and higher plants, including Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice) and other more recently sequenced plant species. Each of these species was extensively searched and manually assembled for analysis in the MPIC DB. The database presents an interactive diagram in a user-friendly manner, allowing users to select their import component of interest. The MPIC DB presents an extensive resource facilitating detailed investigation of the mitochondrial protein import machinery and allowing patterns of conservation and divergence to be recognized that would otherwise have been missed. To demonstrate the usefulness of the MPIC DB, we present a comparative analysis of the mitochondrial protein import machinery in plants and non-plant species, revealing plant-specific features that have evolved.
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Affiliation(s)
- Monika W Murcha
- Australian Research Council Centre of Excellence in Plant Energy Biology, Bayliss Building M316, University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - Reena Narsai
- Department of Botany, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora 3083, Victoria, Australia
| | - James Devenish
- Australian Research Council Centre of Excellence in Plant Energy Biology, Bayliss Building M316, University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - Szymon Kubiszewski-Jakubiak
- Australian Research Council Centre of Excellence in Plant Energy Biology, Bayliss Building M316, University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - James Whelan
- Department of Botany, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora 3083, Victoria, Australia
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27
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Abstract
TIM proteins are known to promote viral entry into host cells. Unexpectedly, a recent study has shown that TIM proteins also inhibit HIV-1 release from the host cell by directly binding to phosphatidylserine exposed on the virus surface, providing details on a new role of TIM proteins in HIV replication.
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Affiliation(s)
- Jiri Vlach
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294.
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28
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Gao H, Zheng Z, Mao Y, Wang W, Qiao Y, Zhou L, Liu F, He H, Zhao X. Identification of tumor antigens that elicit a humoral immune response in the sera of Chinese esophageal squamous cell carcinoma patients by modified serological proteome analysis. Cancer Lett 2013; 344:54-61. [PMID: 24157810 DOI: 10.1016/j.canlet.2013.10.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/11/2013] [Accepted: 10/14/2013] [Indexed: 12/01/2022]
Abstract
Our aim was to identify novel tumor-associated antigens from the esophageal squamous cell carcinoma (ESCC) cell line EC0156, and related autoantibodies in sera from patients with ESCC. We used modified serological proteome analysis, involving one- and two-dimensional electrophoresis, Western blot, and MALDI-TOF/TOF-MS to identify 6 ESCC-associated antigens. From these, 105 kDa heat shock protein (HSP105) and triosephosphate isomerase (TIM) were further evaluated and we determined they could induce autoantibody responses in ESCC sera and are highly expressed in ESCC tissues. Anti-HSP105 and anti-TIM autoantibodies were found in 39.1% (18/46) and 34.8% (16/46) of patients with ESCC, respectively, but only in two controls. A receiver operating characteristic curve constructed with HSP105 and TIM gave a sensitivity of 54.3% and 95% (38/40) specificity in discriminating ESCC from matched controls. Interestingly, we found that autoantibodies against TIM in ESCC serum mainly reacted with glycosylated but not deglycosylated TIM. The preliminary results suggest the potential utility of screening autoantibodies in sera for use as biomarkers for cancer diagnosis.
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Affiliation(s)
- Hongjun Gao
- Clinical Laboratory of China Meitan General Hospital, Beijing, PR China
| | - Zhaoxu Zheng
- Department of Abdominal Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Yousheng Mao
- Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Wei Wang
- Department of Thoracic Surgery, Navy General Hospital of Chinese PLA, Beijing, PR China
| | - Yuanyuan Qiao
- Center for Basic Medical Science, Navy General Hospital of Chinese PLA, Beijing, PR China
| | - Lanping Zhou
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Fang Liu
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Hongzhi He
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Xiaohang Zhao
- Center for Basic Medical Science, Navy General Hospital of Chinese PLA, Beijing, PR China; State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China.
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29
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Murcha MW, Wang Y, Narsai R, Whelan J. The plant mitochondrial protein import apparatus - the differences make it interesting. Biochim Biophys Acta Gen Subj 2013; 1840:1233-45. [PMID: 24080405 DOI: 10.1016/j.bbagen.2013.09.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/17/2013] [Accepted: 09/18/2013] [Indexed: 12/25/2022]
Abstract
BACKGROUND Mitochondria play essential roles in the life and death of almost all eukaryotic cells, ranging from single-celled to multi-cellular organisms that display tissue and developmental differentiation. As mitochondria only arose once in evolution, much can be learned from studying single celled model systems such as yeast and applying this knowledge to other organisms. However, two billion years of evolution have also resulted in substantial divergence in mitochondrial function between eukaryotic organisms. SCOPE OF REVIEW Here we review our current understanding of the mechanisms of mitochondrial protein import between plants and yeast (Saccharomyces cerevisiae) and identify a high level of conservation for the essential subunits of plant mitochondrial import apparatus. Furthermore, we investigate examples whereby divergence and acquisition of functions have arisen and highlight the emerging examples of interactions between the import apparatus and components of the respiratory chain. MAJOR CONCLUSIONS After more than three decades of research into the components and mechanisms of mitochondrial protein import of plants and yeast, the differences between these systems are examined. Specifically, expansions of the small gene families that encode the mitochondrial protein import apparatus in plants are detailed, and their essential role in seed viability is revealed. GENERAL SIGNIFICANCE These findings point to the essential role of the inner mitochondrial protein translocases in Arabidopsis, establishing their necessity for seed viability and the crucial role of mitochondrial biogenesis during germination. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research.
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Affiliation(s)
- Monika W Murcha
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia.
| | - Yan Wang
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Reena Narsai
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia; Computational Systems Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building M316, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia; Department of Botany, School of Life Science, La Trobe University, Bundoora 3086, Victoria, Australia
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30
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Yamamoto K, Wilson DK. Identification, characterization, and crystal structure of an aldo-keto reductase (AKR2E4) from the silkworm Bombyx mori. Arch Biochem Biophys 2013; 538:156-63. [PMID: 24012638 DOI: 10.1016/j.abb.2013.08.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 08/29/2013] [Accepted: 08/31/2013] [Indexed: 10/26/2022]
Abstract
A new member of the aldo-keto reductase (AKR) superfamily with 3-dehydroecdysone reductase activity was found in the silkworm Bombyx mori upon induction by the insecticide diazinon. The amino acid sequence showed that this enzyme belongs to the AKR2 family, and the protein was assigned the systematic name AKR2E4. In this study, recombinant AKR2E4 was expressed, purified to near homogeneity, and kinetically characterized. Additionally, its ternary structure in complex with NADP(+) and citrate was refined at 1.3Å resolution to elucidate substrate binding and catalysis. The enzyme is a 33-kDa monomer and reduces dicarbonyl compounds such as isatin and 17α-hydroxy progesterone using NADPH as a cosubstrate. No NADH-dependent activity was detected. Robust activity toward the substrate inhibitor 3-dehydroecdysone was observed, which suggests that this enzyme plays a role in regulation of the important molting hormone ecdysone. This structure constitutes the first insect AKR structure determined. Bound NADPH is located at the center of the TIM- or (β/α)8-barrel, and residues involved in catalysis are conserved.
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Affiliation(s)
- Kohji Yamamoto
- Faculty of Agriculture, Kyushu University Graduate School, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
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31
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Tee KL, Wong TS. Polishing the craft of genetic diversity creation in directed evolution. Biotechnol Adv 2013; 31:1707-21. [PMID: 24012599 DOI: 10.1016/j.biotechadv.2013.08.021] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 08/31/2013] [Accepted: 08/31/2013] [Indexed: 12/25/2022]
Abstract
Genetic diversity creation is a core technology in directed evolution where a high quality mutant library is crucial to its success. Owing to its importance, the technology in genetic diversity creation has seen rapid development over the years and its application has diversified into other fields of scientific research. The advances in molecular cloning and mutagenesis since 2008 were reviewed. Specifically, new cloning techniques were classified based on their principles of complementary overhangs, homologous sequences, overlapping PCR and megaprimers and the advantages, drawbacks and performances of these methods were highlighted. New mutagenesis methods developed for random mutagenesis, focused mutagenesis and DNA recombination were surveyed. The technical requirements of these methods and the mutational spectra were compared and discussed with references to commonly used techniques. The trends of mutant library preparation were summarised. Challenges in genetic diversity creation were discussed with emphases on creating "smart" libraries, controlling the mutagenesis spectrum and specific challenges in each group of mutagenesis methods. An outline of the wider applications of genetic diversity creation includes genome engineering, viral evolution, metagenomics and a study of protein functions. The review ends with an outlook for genetic diversity creation and the prospective developments that can have future impact in this field.
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Affiliation(s)
- Kang Lan Tee
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, England, United Kingdom
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32
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Abstract
A unique organelle for studying membrane biochemistry is the mitochondrion whose functionality depends on a coordinated supply of proteins and lipids. Mitochondria are capable of synthesizing several lipids autonomously such as phosphatidylglycerol, cardiolipin and in part phosphatidylethanolamine, phosphatidic acid and CDP-diacylglycerol. Other mitochondrial membrane lipids such as phosphatidylcholine, phosphatidylserine, phosphatidylinositol, sterols and sphingolipids have to be imported. The mitochondrial lipid composition, the biosynthesis and the import of mitochondrial lipids as well as the regulation of these processes will be main issues of this review article. Furthermore, interactions of lipids and mitochondrial proteins which are highly important for various mitochondrial processes will be discussed. Malfunction or loss of enzymes involved in mitochondrial phospholipid biosynthesis lead to dysfunction of cell respiration, affect the assembly and stability of the mitochondrial protein import machinery and cause abnormal mitochondrial morphology or even lethality. Molecular aspects of these processes as well as diseases related to defects in the formation of mitochondrial membranes will be described.
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Affiliation(s)
- Susanne E Horvath
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, A-8010 Graz, Austria
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Vlachakis D, Pavlopoulou A, Kazazi D, Kossida S. Unraveling microalgal molecular interactions using evolutionary and structural bioinformatics. Gene 2013; 528:109-19. [PMID: 23900196 DOI: 10.1016/j.gene.2013.07.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/08/2013] [Accepted: 07/18/2013] [Indexed: 10/26/2022]
Abstract
Microalgae are unicellular microorganisms indispensible for environmental stability and life on earth, because they produce approximately half of the atmospheric oxygen, with simultaneously feeding on the harmful greenhouse gas carbon dioxide. Using gene fusion analysis, a series of five fusion/fission events was identified, that provided the basis for critical insights to their evolutionary history. Moreover, the three-dimensional structures of both the fused and the component proteins were predicted, allowing us to envisage putative protein-protein interactions that are invaluable for the efficient usage, handling and exploitation of microalgae. Collectively, our proposed approach on the five fusion/fission alga protein events contributes towards the expansion of the microalgae knowledgebase, bridging protein evolution of the ancient microalgal species and the rapidly evolving, modern, bioinformatics field.
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Affiliation(s)
- Dimitrios Vlachakis
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece
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Rocha RA, de la Fuente B, Clemente MJ, Ruiz A, Vélez D, Devesa V. Factors affecting the bioaccessibility of fluoride from seafood products. Food Chem Toxicol 2013; 59:104-10. [PMID: 23747712 DOI: 10.1016/j.fct.2013.05.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 05/27/2013] [Accepted: 05/28/2013] [Indexed: 11/24/2022]
Abstract
Fluoride is considered important for health because of its beneficial effect on the prevention of dental caries and on bone development in the child population. However, excessive intake has negative effects. The main pathway for exposure is oral, through consumption of drinking water, and some food products. Therefore its bioaccessibility (quantity of the element solubilized during the digestive process) is a parameter to be considered when estimating the risk/benefit associated with this element. The aim of the present study was to evaluate the influence of the digestion phase, gastrointestinal digestion factors (pH, pepsin and bile salt concentrations) and the presence of cations on the bioaccessibility of fluoride from seafood products. The results show that the solubilization of fluoride takes place entirely during the gastric phase. Its bioaccessibility is strongly influenced by conditions that favor the formation of insoluble complexes of fluoride with other elements present in the matrix. The factors that are most influential in reducing its bioaccessibility are the increase in pH in the gastric phase, the presence of cations, especially in the intestinal phase, and a low concentration of bile salts.
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Affiliation(s)
- R A Rocha
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Paterna, Valencia, Spain
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Abstract
Over the years it has become crystal clear that a variety of processes encode time-of-day information, ranging from gene expression, protein stability, or subcellular localization of key proteins, to the fine tuning of network properties and modulation of input signals, ultimately ensuring that physiology and behavior are properly synchronized to a changing environment. The purpose of this review is to put forward examples (as opposed to generate a comprehensive revision of all the available literature) in which the circadian system displays a remarkable degree of plasticity, from cell autonomous to circuit-based levels. In the literature, the term circadian plasticity has been used to refer to different concepts. The obvious one, more literally, refers to any change that follows a circadian (circa=around, diem=day) pattern, i.e. a daily change of a given parameter. The discovery of daily remodeling of neuronal structures will be referred herein as structural circadian plasticity, and represents an additional and novel phenomenon modified daily. Finally, any plasticity that has to do with a circadian parameter would represent a type of circadian plasticity; as an example, adjustments that allow organisms to adapt their daily behavior to the annual changes in photoperiod is a form of circadian plasticity at a higher organizational level, which is an emergent property of the whole circadian system. Throughout this work we will revisit these types of changes by reviewing recent literature delving around circadian control of clock outputs, from the most immediate ones within pacemaker neurons to the circadian modulation of rest-activity cycles.
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Affiliation(s)
- N I Muraro
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir, IIB-BA-CONICET, Buenos Aires, Argentina
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36
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Kim HY, Chang YJ, Chuang YT, Lee HH, Kasahara DI, Martin T, Hsu JT, Savage PB, Shore SA, Freeman GJ, Dekruyff RH, Umetsu DT. T-cell immunoglobulin and mucin domain 1 deficiency eliminates airway hyperreactivity triggered by the recognition of airway cell death. J Allergy Clin Immunol 2013; 132:414-25.e6. [PMID: 23672783 DOI: 10.1016/j.jaci.2013.03.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/21/2013] [Accepted: 03/25/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Studies of asthma have been limited by a poor understanding of how nonallergic environmental exposures, such as air pollution and infection, are translated in the lung into inflammation and wheezing. OBJECTIVE Our goal was to understand the mechanism of nonallergic asthma that leads to airway hyperreactivity (AHR), a cardinal feature of asthma independent of adaptive immunity. METHOD We examined mouse models of experimental asthma in which AHR was induced by respiratory syncytial virus infection or ozone exposure using mice deficient in T-cell immunoglobulin and mucin domain 1 (TIM1/HAVCR1), an important asthma susceptibility gene. RESULTS TIM1(-/-) mice did not have airways disease when infected with RSV or when repeatedly exposed to ozone, a major component of air pollution. On the other hand, the TIM1(-/-) mice had allergen-induced experimental asthma, as previously shown. The RSV- and ozone-induced pathways were blocked by treatment with caspase inhibitors, indicating an absolute requirement for programmed cell death and apoptosis. TIM-1-expressing, but not TIM-1-deficient, natural killer T cells responded to apoptotic airway epithelial cells by secreting cytokines, which mediated the development of AHR. CONCLUSION We defined a novel pathway in which TIM-1, a receptor for phosphatidylserine expressed by apoptotic cells, drives the development of asthma by sensing and responding to injured and apoptotic airway epithelial cells.
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Affiliation(s)
- Hye Young Kim
- Division of Immunology and Allergy, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Shah SA, Erdmann S, Mojica FJ, Garrett RA. Protospacer recognition motifs: mixed identities and functional diversity. RNA Biol 2013; 10:891-9. [PMID: 23403393 PMCID: PMC3737346 DOI: 10.4161/rna.23764] [Citation(s) in RCA: 227] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 01/21/2013] [Accepted: 01/24/2013] [Indexed: 02/07/2023] Open
Abstract
Protospacer adjacent motifs (PAMs) were originally characterized for CRISPR-Cas systems that were classified on the basis of their CRISPR repeat sequences. A few short 2-5 bp sequences were identified adjacent to one end of the protospacers. Experimental and bioinformatical results linked the motif to the excision of protospacers and their insertion into CRISPR loci. Subsequently, evidence accumulated from different virus- and plasmid-targeting assays, suggesting that these motifs were also recognized during DNA interference, at least for the recently classified type I and type II CRISPR-based systems. The two processes, spacer acquisition and protospacer interference, employ different molecular mechanisms, and there is increasing evidence to suggest that the sequence motifs that are recognized, while overlapping, are unlikely to be identical. In this article, we consider the properties of PAM sequences and summarize the evidence for their dual functional roles. It is proposed to use the terms protospacer associated motif (PAM) for the conserved DNA sequence and to employ spacer acqusition motif (SAM) and target interference motif (TIM), respectively, for acquisition and interference recognition sites.
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Affiliation(s)
- Shiraz A. Shah
- Archaea Centre; Department of Biology, University of Copenhagen; Copenhagen, Denmark
| | - Susanne Erdmann
- Archaea Centre; Department of Biology, University of Copenhagen; Copenhagen, Denmark
| | - Francisco J.M. Mojica
- Departamento de Fisiología; Genética y Microbiología; Facultad de Ciencias; Universidad de Alicante; Alicante, Spain
| | - Roger A. Garrett
- Archaea Centre; Department of Biology, University of Copenhagen; Copenhagen, Denmark
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Kozlov G, Vinaik R, Gehring K. Triosephosphate isomerase is a common crystallization contaminant of soluble His-tagged proteins produced in Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:499-502. [PMID: 23695562 DOI: 10.1107/s1744309113010841] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 04/20/2013] [Indexed: 11/10/2022]
Abstract
Attempts to crystallize several mammalian proteins overexpressed in Escherichia coli revealed a common contaminant, triosephosphate isomerase, a protein involved in glucose metabolism. Even with triosephosphate isomerase present in very small amounts, similarly shaped crystals appeared in the crystallization drops in a number of polyethylene glycol-containing conditions. All of the target proteins were His-tagged and their purification involved immobilized metal-affinity chromatography (IMAC), a step that was likely to lead to triosephosphate isomerase contamination. Analysis of the triosephosphate isomerase crystals led to the structure of E. coli triosephosphate isomerase at 1.85 Å resolution, which is a significant improvement over the previous structure.
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Affiliation(s)
- Guennadi Kozlov
- Department of Biochemistry, Groupe de Recherche axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montréal, Québec H3G 0B1, Canada
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Lionaki E, Tavernarakis N. Oxidative stress and mitochondrial protein quality control in aging. J Proteomics 2013; 92:181-94. [PMID: 23563202 DOI: 10.1016/j.jprot.2013.03.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 02/22/2013] [Accepted: 03/25/2013] [Indexed: 12/17/2022]
Abstract
Mitochondrial protein quality control incorporates an elaborate network of chaperones and proteases that survey the organelle for misfolded or unfolded proteins and toxic aggregates. Repair of misfolded or aggregated protein and proteolytic removal of irreversibly damaged proteins are carried out by the mitochondrial protein quality control system. Initial maturation and folding of the nuclear or mitochondrial-encoded mitochondrial proteins are mediated by processing peptidases and chaperones that interact with the protein translocation machinery. Mitochondrial proteins are subjected to cumulative oxidative damage. Thus, impairment of quality control processes may cause mitochondrial dysfunction. Aging has been associated with a marked decline in the effectiveness of mitochondrial protein quality control. Here, we present an overview of the chaperones and proteases involved in the initial folding and maturation of new, incoming precursor molecules, and the subsequent repair and removal of oxidized aggregated proteins. In addition, we highlight the link between mitochondrial protein quality control mechanisms and the aging process. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Eirini Lionaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 71110, Crete, Greece
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