1
|
Lu Z, Lin Q, Zhang H. Characterization of the Complete Mitochondrial Genome of Agelas nakamurai from the South China Sea. Int J Mol Sci 2023; 25:357. [PMID: 38203529 PMCID: PMC10779334 DOI: 10.3390/ijms25010357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/21/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
The Agelas genus sponges are widely distributed and provide shelter for organisms that inhabit reefs. However, there is a lack of research on the genetic diversity of the Agelas sponges. Additionally, only one Agelas mitochondrial genome has been documented, leaving the characteristics of the Agelas genus's mitogenome in need of further clarification. To address this research gap, we utilized Illumina HiSeq4000 sequencing and de novo assembly to ascertain the complete mitochondrial genome of Agelas sp. specimens, sourced from the South China Sea. Our analysis of the cox1 barcoding similarity and phylogenetic relationship reveals that taxonomically, the Agelas sp. corresponds to Agelas nakamurai. The mitogenome of Agelas nakamurai is 20,885 bp in length, encoding 14 protein-coding genes, 24 transfer RNA genes, and 2 ribosomal RNA genes. Through a comparison of the mitochondrial genes, we discovered that both Agelas nakamurai and Agelas schmidti have an identical gene arrangement. Furthermore, we observed a deletion in the trnD gene and duplication and remodeling of the trnL gene in the Agelas nakamurai's mitogenome. Our evolutionary analysis also identified lineage-specific positive selection sites in the nad3 and nad5 genes of the Agelas sponges' mitogenome. These findings shed light on the gene rearrangement events and positive selection sites in the mitogenome of Agelas nakamurai, providing valuable molecular insights into the evolutionary processes of this genus.
Collapse
Affiliation(s)
- Zijian Lu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510000, China;
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510000, China
- University of Chinese Academy of Sciences, Beijing 100000, China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510000, China;
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510000, China
- University of Chinese Academy of Sciences, Beijing 100000, China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510000, China;
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510000, China
- University of Chinese Academy of Sciences, Beijing 100000, China
| |
Collapse
|
2
|
Zhang Y, Li Z, Zhang Y, Sun K, Ren N, Li M. Acute toxic effects of diclofenac exposure on freshwater crayfish (Procambarus clarkii): Insights from hepatopancreatic pathology, molecular regulation and intestinal microbiota. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 244:114068. [PMID: 36108435 DOI: 10.1016/j.ecoenv.2022.114068] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/27/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
In this study, we exposed adult male crayfish (Procambarus clarkii) to different concentrations of diclofenac (DCF) for 96 h. In the meantime, we investigated the alternations of hepatopancreatic pathology, molecular regulation and intestinal microbiota of P. clarkii exposed to DCF. The results demonstrated DCF led to histological changes including epithelium vacuolization and tubule lumen dilatation in the hepatopancreas. Transcriptome sequencing analysis showed that 642 and 586 genes were differentially expressed in the hepatopancreas of P. clarkii exposed to 1 and 10 mg/L DCF, respectively. DCF could affect the functions of antioxidation, immunity and metabolism of hepatopancreas by inducing the abnormal expressions of immune- and redox-related genes. GO enrichment results demonstrated that 10 mg/L DCF exposure could modulate the processes of molting, amino sugar metabolism, protein hydrolysis and intracellular protein translocation of P. clarkii. Additionally, the abundances of bacterial families including Shewanellaceae, Bacteroidaceae, Vibrionaceae, Erysipelotrichaceae, Aeromonadaceae, Moraxellaceae, etc. in the intestine were significantly changed after DCF exposure, and the disruption of intestinal flora might further cause abnormal intestinal metabolism in P. clarkii. This study provides novel mechanistic insights into the toxic effects of anti-inflammatory drugs on aquatic crustaceans.
Collapse
Affiliation(s)
- Yu Zhang
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, College of Resources and Environment, Jilin Agricultural University, Changchun 130118, China
| | - Zheyu Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yanxiang Zhang
- School of Environmental and Material Engineering, Yantai University, Yantai 264005, China
| | - Kai Sun
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Mingtang Li
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, College of Resources and Environment, Jilin Agricultural University, Changchun 130118, China
| |
Collapse
|
3
|
Ye J, Tian X, Wang Q, Zheng J, Yang Y, Xu B, Zhang S, Yuan F, Yang Z. Monkfish Peptides Mitigate High Fat Diet-Induced Hepatic Steatosis in Mice. Mar Drugs 2022; 20:md20050312. [PMID: 35621963 PMCID: PMC9147042 DOI: 10.3390/md20050312] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 02/05/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a hepatic metabolic syndrome usually accompanied by fatty degeneration and functional impairment. The aim of the study was to determine whether monkfish peptides (LPs) could ameliorate high-fat diet (HFD)-induced NAFLD and its underlying mechanisms. NAFLD was induced in mice by giving them an HFD for eight weeks, after which LPs were administered in various dosages. In comparison to the HFD control group: body weight in the LP-treated groups decreased by 23–28%; triacylglycerol levels in the blood decreased by 16–35%; and low-density lipoproteins levels in the blood decreased by 23–51%. Additionally, we found that LPs elevated the activity of hepatic antioxidant enzymes and reduced the inflammatory reactions within fatty liver tissue. Investigating the effect on metabolic pathways, we found that in LP-treated mice: the levels of phospho-AMP-activated protein kinase (p-AMPK), and phospho-acetyl CoA carboxylase (p-ACC) in the AMP-activated protein kinase (AMPK) pathway were up-regulated and the levels of downstream sterol regulatory element-binding transcription factor 1 (SREBP-1) were down-regulated; lipid oxidation increased and free fatty acid (FFA) accumulation decreased (revealed by the increased carnitine palmitoyltransferase-1 (CPT-1) and the decreased fatty acid synthase (FASN) expression, respectively); the nuclear factor erythroid-2-related factor 2 (Nrf2) antioxidant pathway was activated; and the levels of heme oxygenase-1 (HO-1) and nicotinamide quinone oxidoreductase 1 (NQO1) were increased. Overall, all these findings demonstrated that LPs can improve the antioxidant capacity of liver to alleviate NAFLD progression mainly through modulating the AMPK and Nrf2 pathways, and thus it could be considered as an effective candidate in the treatment of human NAFLD.
Collapse
Affiliation(s)
- Jiena Ye
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
| | - Xiaoxiao Tian
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
| | - Qiongfen Wang
- Zhoushan Institute for Food and Drug Control, Zhoushan 316000, China;
| | - Jiawen Zheng
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
| | - Yanzhuo Yang
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
| | - Baogui Xu
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
| | - Shuai Zhang
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
| | - Falei Yuan
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
- Correspondence: (F.Y.); (Z.Y.)
| | - Zuisu Yang
- Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; (J.Y.); (X.T.); (J.Z.); (Y.Y.); (B.X.); (S.Z.)
- Correspondence: (F.Y.); (Z.Y.)
| |
Collapse
|
4
|
Mazumder GA, Uddin A, Chakraborty S. Analysis of codon usage pattern of mitochondrial ND genes in Platyhelminthes. Mol Biochem Parasitol 2020; 238:111294. [PMID: 32592756 DOI: 10.1016/j.molbiopara.2020.111294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 01/24/2023]
Abstract
Codon usage bias (CUB) is the nonrandom usage of synonymous codons in which some codons are more preferred to others.CUB can be determined by mutation pressure and selection. Various approaches have been used to understand the pattern of CUB in the mitochondrial ND (MT-ND or ND) genes involved in complex I of respiratory chain in five different classes of Platyhelminthes as no work was reported yet. The present study revealed that the CUB varies across MT-ND genes and the coding sequences showed the richness of A and T. Correspondence analysis implied the effect of mutational pressure and also the pattern of codon usage was different in different classes of platyhelminthes for MT-ND genes. Highly significant correlation was observed between overall nucleotide composition and its 3rd codon position in most of the homogeneous nucleotides such as A% and A3%, T% and T3%, G% and G3%, C% and C3%, GC% and GC3% and also some significant correlations observed among heterogeneous nucleotides in all the five classes for MT-ND genes suggested the role of mutational pressure as well as natural selection in affecting the CUB. Neutrality plot suggested that the contributions of natural selection and mutational pressure varied across different classes of platyhelminthes and also differed in different MT-ND genes.
Collapse
Affiliation(s)
| | - Arif Uddin
- Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, 788150 Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, 788011 Assam, India.
| |
Collapse
|
5
|
Wang L, Cheng B, Li H, Wang Y. Proteomics analysis of preadipocytes between fat and lean broilers. Br Poult Sci 2019; 60:522-529. [PMID: 31132862 DOI: 10.1080/00071668.2019.1621989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
1. Reducing excessive chicken body fat deposition is a main goal of the poultry industry. Preadipocytes are important in adipose tissue growth and development. 2. To discover proteins related to chicken fat deposition, two-dimensional fluorescence difference gel electrophoresis (2-D DIGE) was used to identify differentially expressed proteins in preadipocytes derived from Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF). 3. A total of 46 differentially expressed protein spots were found in the preadipocytes between fat and lean broilers. Matrix-assisted laser desorption-ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) analysis showed the protein spots corresponded to 33 different proteins. The proteins were mainly related to biological oxidation, cell proliferation, cytoskeleton, lipid metabolism, molecular chaperone, protein synthesis and signal transduction. 4. From the perspective of protein expression, these results lay a foundation for further study of the genetic mechanism of broiler adipose tissue growth and development.
Collapse
Affiliation(s)
- L Wang
- Ministry of Agriculture and Rural Affairs, Key Laboratory of Chicken Genetics and Breeding , Harbin , P. R. China.,Department of Education of Heilongjiang Province, Key Laboratory of Animal Genetics, Breeding and Reproduction , Harbin , P. R. China.,College of Animal Science and Technology, Northeast Agricultural University , Harbin , P. R. China
| | - B Cheng
- Ministry of Agriculture and Rural Affairs, Key Laboratory of Chicken Genetics and Breeding , Harbin , P. R. China.,Department of Education of Heilongjiang Province, Key Laboratory of Animal Genetics, Breeding and Reproduction , Harbin , P. R. China.,College of Animal Science and Technology, Northeast Agricultural University , Harbin , P. R. China
| | - H Li
- Ministry of Agriculture and Rural Affairs, Key Laboratory of Chicken Genetics and Breeding , Harbin , P. R. China.,Department of Education of Heilongjiang Province, Key Laboratory of Animal Genetics, Breeding and Reproduction , Harbin , P. R. China.,College of Animal Science and Technology, Northeast Agricultural University , Harbin , P. R. China
| | - Y Wang
- Ministry of Agriculture and Rural Affairs, Key Laboratory of Chicken Genetics and Breeding , Harbin , P. R. China.,Department of Education of Heilongjiang Province, Key Laboratory of Animal Genetics, Breeding and Reproduction , Harbin , P. R. China.,College of Animal Science and Technology, Northeast Agricultural University , Harbin , P. R. China
| |
Collapse
|
6
|
Zhang Y, Li Z, Kholodkevich S, Sharov A, Feng Y, Ren N, Sun K. Cadmium-induced oxidative stress, histopathology, and transcriptome changes in the hepatopancreas of freshwater crayfish (Procambarus clarkii). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 666:944-955. [PMID: 30970501 DOI: 10.1016/j.scitotenv.2019.02.159] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/01/2019] [Accepted: 02/10/2019] [Indexed: 05/06/2023]
Abstract
Cadmium (Cd) is a common contaminant in environment. Crayfish are considered suitable for indicating the impact of heavy metals on the environment. However, there is limited information on the mechanisms causing damage to the hepatopancreas of Procambarus clarkii exposed to Cd. We exposed adult male P. clarkii to 2.0, 5.0, and 10.0 mg/L Cd for 24, 48, and 72 h to explore Cd toxicity. Afterwards, we measured bioaccumulations in the hepatopancreas and determined malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT), and glutathione S-transferase (GST). Additionally, the hepatopancreas histopathology was analyzed and the transcriptome analysis of the P. clarkii hepatopancreas under Cd stress was conducted. The results revealed that hepatopancreas could accumulate Cd in a time- and dose-dependent manner. Cd induced significant changes in MDA content and antioxidant enzyme activity. Severe histological alterations were observed in crayfish hepatopancreas. After 72 h exposure to 2.0, 5.0, and 10.0 mg/L Cd, transcriptome analysis identified 1061, 747, and 1086 differentially expressed genes (DEGs), respectively. Exposure to 5.0 mg/L Cd inhibited heme binding, tetrapyrrole binding, iron ion binding and activity of oxidoreductase and sulfotransferase, while exposure to 10.0 mg/L Cd enhanced the export of matters from nucleus. In the hepatopancreas treated with 10.0 mg/L Cd, pathways related to diseases and immune system were significantly enriched. Meanwhile, 31, 31, 24, 7, and 12 identified DEGs were associated with the oxidation-reduction process, immune system, ion homeostasis, digestion and absorption, and ATPases, respectively. Our study provides comprehensive information for exploring the toxic mechanisms of Cd and candidate biomarkers for aquatic Cd risk evaluation.
Collapse
Affiliation(s)
- Yu Zhang
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zheyu Li
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Sergey Kholodkevich
- Institute of Earth Sciences, Saint-Petersburg State University, Saint-Petersburg 199034, Russia
| | - Andrey Sharov
- Institute of Earth Sciences, Saint-Petersburg State University, Saint-Petersburg 199034, Russia
| | - Yujie Feng
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nanqi Ren
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Kai Sun
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| |
Collapse
|
7
|
Strangers in strange lands: mitochondrial proteins found at extra-mitochondrial locations. Biochem J 2019; 476:25-37. [DOI: 10.1042/bcj20180473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/23/2018] [Accepted: 11/27/2018] [Indexed: 12/18/2022]
Abstract
Abstract
The mitochondrial proteome is estimated to contain ∼1100 proteins, the vast majority of which are nuclear-encoded, with only 13 proteins encoded by the mitochondrial genome. The import of these nuclear-encoded proteins into mitochondria was widely believed to be unidirectional, but recent discoveries have revealed that many these ‘mitochondrial’ proteins are exported, and have extra-mitochondrial activities divergent from their mitochondrial function. Surprisingly, three of the exported proteins discovered thus far are mitochondrially encoded and have significantly different extra-mitochondrial roles than those performed within the mitochondrion. In this review, we will detail the wide variety of proteins once thought to only reside within mitochondria, but now known to ‘emigrate’ from mitochondria in order to attain ‘dual citizenship’, present both within mitochondria and elsewhere.
Collapse
|
8
|
Mao X, Shi Y, Liang X, Cai M, Yang X, Chen S, Jia X, Wang J, Hu S, Lai S. Genetic diversities of MT-ND3 and MT-ND4L genes are associated with high-altitude adaptation. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1544040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Xudong Mao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yu Shi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaohu Liang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingcheng Cai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xue Yang
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Shiyi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Songjia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
9
|
Wang Z, Tang D, Sun L, Shi X, Liu R, Guo H, Tang B. Comparative transcriptome analysis in the hepatopancreas of Helice tientsinensis exposed to the toxic metal cadmium. Genes Genomics 2018; 41:417-429. [DOI: 10.1007/s13258-018-0774-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/03/2018] [Indexed: 12/24/2022]
|
10
|
Pramod RK, Velayutham D, P K S, P S B, Zachariah A, Zachariah A, B C, S S S, P G, Dhinoth Kumar B, Iype S, Gupta R, Santhosh S, Thomas G. Complete mitogenome reveals genetic divergence and phylogenetic relationships among Indian cattle ( Bos indicus) breeds. Anim Biotechnol 2018; 30:219-232. [PMID: 29938580 DOI: 10.1080/10495398.2018.1476376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Indigenous cattle of India belong to the species, Bos indicus and they possess various adaptability and production traits. However, little is known about the genetic diversity and origin of these breeds. To investigate the status, we sequenced and analyzed the whole mitochondrial DNA (mtDNA) of seven Indian cattle breeds. In total, 49 single-nucleotide variants (SNVs) were identified among the seven breeds analyzed. We observed a common synonymous SNV in the COII gene (m.7583G > A) of all the breeds studied. The phylogenetic analysis and genetic distance estimation showed the close genetic relationship among the Indian cattle breeds, whereas distinct genetic differences were observed between Bos indicus and Bos taurus cattle. Our results indicate a common ancestor for European Zwergzebu breed and South Indian cattle. The estimated divergence time demonstrated that the Bos indicus and Bos taurus cattle lineages diverged 0.92 million years ago. Our study also demonstrates that ancestors of present zebu breeds originated in South and North India separately ∼30,000 to 20,000 years ago. In conclusion, the identified genetic variants and results of the phylogenetic analysis may provide baseline information to develop appropriate strategies for management and conservation of Indian cattle breeds.
Collapse
Affiliation(s)
| | | | - Sajesh P K
- a AgriGenome Labs Pvt. Ltd., Smart City Kochi , India
| | - Beena P S
- a AgriGenome Labs Pvt. Ltd., Smart City Kochi , India
| | | | - Arun Zachariah
- c Department of Forest and Wildlife , Wayanad , Kerala , India
| | - Chandramohan B
- d National Institute of Science Education and Research , Jatni , India
| | - Sujith S S
- a AgriGenome Labs Pvt. Ltd., Smart City Kochi , India
| | - Ganapathi P
- e Bargur Cattle Research Station, Tamil Nadu Veterinary Animal Sciences University , Chennai , India
| | | | | | - Ravi Gupta
- f Medgenome Labs Pvt. Ltd. , Narayana Health City , Bommasandra , Bengaluru , India
| | - Sam Santhosh
- g SciGenom Research Foundation , Cheruthuruthy , India
| | - George Thomas
- g SciGenom Research Foundation , Cheruthuruthy , India
| |
Collapse
|
11
|
Yang H, Peng Y, Shi Y, Tian J, Wang J, Peng X, Xie C, Xu X, Song Q, Wang Z, Lv Z. Transcriptome assembly and expression profiling of the molecular responses to cadmium toxicity in cerebral ganglia of wolf spider Pardosa pseudoannulata (Araneae: Lycosidae). ECOTOXICOLOGY (LONDON, ENGLAND) 2018; 27:198-208. [PMID: 29299797 PMCID: PMC5847060 DOI: 10.1007/s10646-017-1885-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/05/2017] [Indexed: 05/23/2023]
Abstract
Cadmium (Cd) is a heavy metal that can cause irreversible toxicity to animals, and is an environmental pollutant in farmlands. Spiders are considered to be an excellent model for investigating the impacts of heavy metals on the environment. To date, the changes at the molecular level in the cerebral ganglia of spiders are poorly understood. Cd exposure leads to strong damage in the nervous system, such as apoptosis and necrosis of nerve cells, therefore we conducted a transcriptomic analysis of Pardosa pseudoannulata cerebral ganglia under Cd stress to profile differential gene expression (DGE). We obtained a total of 123,328 assembled unigenes, and 1441 Cd stress-associated DEGs between the Cd-treated and control groups. Expression profile analysis demonstrated that many genes involved in calcium signaling, cGMP-PKG signaling, tyrosine metabolism, phototransduction-fly, melanogenesis and isoquinoline alkaloid biosynthesis were up-regulated under Cd stress, whereas oxidative phosphorylation-related, nervous disease-associated, non-alcoholic fatty liver disease-associated, and ribosomal-associated genes were down-regulated. Here, we provide a comprehensive set of DEGs influenced by Cd stress, and heavy metal stress, and provide new information for elucidating the neurotoxic mechanisms of Cd stress in spiders.
Collapse
Affiliation(s)
- Huilin Yang
- College of Orient Science & Technology, Hunan Agriculture University, No. 1 Nongda Road, Changsha, 410128, Hunan, China
- College of Bioscience and Biotechnology, Hunan Agriculture University, No. 1 Nongda Road, Changsha, 410128, Hunan, China
| | - Yuande Peng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Yixue Shi
- College of Bioscience and Biotechnology, Hunan Agriculture University, No. 1 Nongda Road, Changsha, 410128, Hunan, China
| | - Jianxiang Tian
- College of Continuing Education, Hunan Agriculture University, No. 1 Nongda Road, Changsha, 410128, Hunan, China
| | - Juan Wang
- College of Bioscience and Biotechnology, Hunan Agriculture University, No. 1 Nongda Road, Changsha, 410128, Hunan, China
| | - Xianjin Peng
- College of Life Science, Hunan Normal University, Changsha, 410006, Hunan, China
| | - Chunliang Xie
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Xiang Xu
- College of Life Science, Hunan Normal University, Changsha, 410006, Hunan, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Zhi Wang
- College of Bioscience and Biotechnology, Hunan Agriculture University, No. 1 Nongda Road, Changsha, 410128, Hunan, China.
| | - Zhiyue Lv
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
| |
Collapse
|
12
|
Li K, Sun J, Yang J, Roberts SM, Zhang X, Cui X, Wei S, Ma LQ. Molecular Mechanisms of Perfluorooctanoate-Induced Hepatocyte Apoptosis in Mice Using Proteomic Techniques. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:11380-11389. [PMID: 28885018 DOI: 10.1021/acs.est.7b02690] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The stability of perfluorooctanoate (PFOA) coupled with its wide use cause serious concerns regarding its potential risk to human health. The molecular mechanisms of PFOA-induced hepatotoxicity relevant to human health was investigated using both in vivo (mouse model) and in vitro (human hepatocyte cells, HL-7702) techniques. Both male and female Balb/c mice were administered PFOA at 0.05, 0.5, or 2.5 mg/kg-d for 28-d, with serum PFOA concentrations after exposure being found at environmentally relevant levels. Liver samples were examined for histology and proteomic change using iTRAQ and Western Blotting, showing dose-dependent hepatocyte apoptosis and peroxisome proliferation. At high doses, genotoxicity resulting from ROS hypergeneration was due to suppression of Complex I subunits in the electron transport chain and activation of PPARα in both genders. However, at 0.05 mg/kg-d, Complex I suppression occurred only in females, making them more sensitive to PFOA-induced apoptosis. In vitro assays using HL-7702 cells confirmed that apoptosis was also induced through a similar mechanism. The dose/gender-dependent toxicity mechanisms help to explain some epidemiological phenomena, i.e., liver cancer is not often associated with PFOA exposure in professional workers. Our results demonstrated that a proteomic approach is a robust tool to explore molecular mechanisms of toxic chemicals at environmentally relevant levels.
Collapse
Affiliation(s)
- Kan Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Jie Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Jingping Yang
- School of the Medicine, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Stephen M Roberts
- Center for Environmental and Human Toxicology, University of Florida , Gainesville, Florida 32611, United States
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Xinyi Cui
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Si Wei
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Lena Q Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
- Soil and Water Science Department, University of Florida , Gainesville, Florida 32611, United States
| |
Collapse
|
13
|
O’Farrell AC, Evans R, Silvola JMU, Miller IS, Conroy E, Hector S, Cary M, Murray DW, Jarzabek MA, Maratha A, Alamanou M, Udupi GM, Shiels L, Pallaud C, Saraste A, Liljenbäck H, Jauhiainen M, Oikonen V, Ducret A, Cutler P, McAuliffe FM, Rousseau JA, Lecomte R, Gascon S, Arany Z, Ky B, Force T, Knuuti J, Gallagher WM, Roivainen A, Byrne AT. A Novel Positron Emission Tomography (PET) Approach to Monitor Cardiac Metabolic Pathway Remodeling in Response to Sunitinib Malate. PLoS One 2017; 12:e0169964. [PMID: 28129334 PMCID: PMC5271313 DOI: 10.1371/journal.pone.0169964] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 12/25/2016] [Indexed: 01/17/2023] Open
Abstract
Sunitinib is a tyrosine kinase inhibitor approved for the treatment of multiple solid tumors. However, cardiotoxicity is of increasing concern, with a need to develop rational mechanism driven approaches for the early detection of cardiac dysfunction. We sought to interrogate changes in cardiac energy substrate usage during sunitinib treatment, hypothesising that these changes could represent a strategy for the early detection of cardiotoxicity. Balb/CJ mice or Sprague-Dawley rats were treated orally for 4 weeks with 40 or 20 mg/kg/day sunitinib. Cardiac positron emission tomography (PET) was implemented to investigate alterations in myocardial glucose and oxidative metabolism. Following treatment, blood pressure increased, and left ventricular ejection fraction decreased. Cardiac [18F]-fluorodeoxyglucose (FDG)-PET revealed increased glucose uptake after 48 hours. [11C]Acetate-PET showed decreased myocardial perfusion following treatment. Electron microscopy revealed significant lipid accumulation in the myocardium. Proteomic analyses indicated that oxidative metabolism, fatty acid β-oxidation and mitochondrial dysfunction were among the top myocardial signalling pathways perturbed. Sunitinib treatment results in an increased reliance on glycolysis, increased myocardial lipid deposition and perturbed mitochondrial function, indicative of a fundamental energy crisis resulting in compromised myocardial energy metabolism and function. Our findings suggest that a cardiac PET strategy may represent a rational approach to non-invasively monitor metabolic pathway remodeling following sunitinib treatment.
Collapse
Affiliation(s)
- Alice C. O’Farrell
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Rhys Evans
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Johanna M. U. Silvola
- Turku PET Centre, Turku University Hospital and Åbo Akademi University, Turku, Finland
| | - Ian S. Miller
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Emer Conroy
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Suzanne Hector
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Roche Innovation Center Basel, F Hoffman La Roche, Basel, Switzerland
| | | | - David W. Murray
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Oncomark Ltd, Dublin, Ireland
| | - Monika A. Jarzabek
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Roche Innovation Center Basel, F Hoffman La Roche, Basel, Switzerland
| | | | | | | | - Liam Shiels
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Celine Pallaud
- Roche Innovation Center Basel, F Hoffman La Roche, Basel, Switzerland
| | - Antti Saraste
- Turku PET Centre, Turku University Hospital and Åbo Akademi University, Turku, Finland
- Heart Center, Turku University Hospital and Åbo Akademi University, Turku, Finland
| | - Heidi Liljenbäck
- Turku PET Centre, Turku University Hospital and Åbo Akademi University, Turku, Finland
| | - Matti Jauhiainen
- Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Vesa Oikonen
- Turku PET Centre, Turku University Hospital and Åbo Akademi University, Turku, Finland
| | - Axel Ducret
- Roche Innovation Center Basel, F Hoffman La Roche, Basel, Switzerland
| | - Paul Cutler
- Roche Innovation Center Basel, F Hoffman La Roche, Basel, Switzerland
| | - Fionnuala M. McAuliffe
- UCD Obstetrics & Gynaecology, School of Medicine, University College, Dublin, National Maternity Hospital, Dublin, Ireland
| | | | | | | | - Zoltan Arany
- Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, United States of America
| | - Bonnie Ky
- Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, United States of America
| | - Thomas Force
- Vanderbilt University School of Medicine, Nashville, United States of America
| | - Juhani Knuuti
- Turku PET Centre, Turku University Hospital and Åbo Akademi University, Turku, Finland
| | - William M. Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
- Oncomark Ltd, Dublin, Ireland
| | - Anne Roivainen
- Turku PET Centre, Turku University Hospital and Åbo Akademi University, Turku, Finland
- Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Annette T. Byrne
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- * E-mail:
| |
Collapse
|
14
|
Dormán G, Nakamura H, Pulsipher A, Prestwich GD. The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore. Chem Rev 2016; 116:15284-15398. [PMID: 27983805 DOI: 10.1021/acs.chemrev.6b00342] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread applications of benzophenone (BP) photochemistry in biological chemistry, bioorganic chemistry, and material science have been prominent in both academic and industrial research. BP photophores have unique photochemical properties: upon n-π* excitation at 365 nm, a biradicaloid triplet state is formed reversibly, which can abstract a hydrogen atom from accessible C-H bonds; the radicals subsequently recombine, creating a stable covalent C-C bond. This light-directed covalent attachment process is exploited in many different ways: (i) binding/contact site mapping of ligand (or protein)-protein interactions; (ii) identification of molecular targets and interactome mapping; (iii) proteome profiling; (iv) bioconjugation and site-directed modification of biopolymers; (v) surface grafting and immobilization. BP photochemistry also has many practical advantages, including low reactivity toward water, stability in ambient light, and the convenient excitation at 365 nm. In addition, several BP-containing building blocks and reagents are commercially available. In this review, we explore the "forbidden" (transitions) and excitation-activated world of photoinduced covalent attachment of BP photophores by touring a colorful palette of recent examples. In this exploration, we will see the pros and cons of using BP photophores, and we hope that both novice and expert photolabelers will enjoy and be inspired by the breadth and depth of possibilities.
Collapse
Affiliation(s)
- György Dormán
- Targetex llc , Dunakeszi H-2120, Hungary.,Faculty of Pharmacy, University of Szeged , Szeged H-6720, Hungary
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , Yokohama 226-8503, Japan
| | - Abigail Pulsipher
- GlycoMira Therapeutics, Inc. , Salt Lake City, Utah 84108, United States.,Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| | - Glenn D Prestwich
- Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| |
Collapse
|
15
|
Xu H, Ma J, Wu J, Chen L, Sun F, Qu C, Zheng D, Xu S. Gene expression profiling analysis of lung adenocarcinoma. Braz J Med Biol Res 2016; 49:S0100-879X2016000300601. [PMID: 26840709 PMCID: PMC4763816 DOI: 10.1590/1414-431x20154861] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 08/05/2015] [Indexed: 02/03/2023] Open
Abstract
The present study screened potential genes related to lung adenocarcinoma, with the
aim of further understanding disease pathogenesis. The GSE2514 dataset including 20
lung adenocarcinoma and 19 adjacent normal tissue samples from 10 patients with lung
adenocarcinoma aged 45-73 years was downloaded from Gene Expression Omnibus.
Differentially expressed genes (DEGs) between the two groups were screened using the
t-test. Potential gene functions were predicted using functional
and pathway enrichment analysis, and protein-protein interaction (PPI) networks
obtained from the STRING database were constructed with Cytoscape. Module analysis of
PPI networks was performed through MCODE in Cytoscape. In total, 535 upregulated and
465 downregulated DEGs were identified. These included ATP5D,
UQCRC2, UQCR11 and genes encoding nicotinamide
adenine dinucleotide (NADH), which are mainly associated with mitochondrial ATP
synthesis coupled electron transport, and which were enriched in the oxidative
phosphorylation pathway. Other DEGs were associated with DNA replication
(PRIM1, MCM3, and RNASEH2A),
cell surface receptor-linked signal transduction and the enzyme-linked receptor
protein signaling pathway (MAPK1, STAT3,
RAF1, and JAK1), and regulation of the
cytoskeleton and phosphatidylinositol signaling system (PIP5K1B,
PIP5K1C, and PIP4K2B). Our findings suggest that
DEGs encoding subunits of NADH, PRIM1, MCM3, MAPK1, STAT3, RAF1, and JAK1 might be
associated with the development of lung adenocarcinoma.
Collapse
Affiliation(s)
- H Xu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - J Ma
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - J Wu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - L Chen
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - F Sun
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - C Qu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - D Zheng
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - S Xu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| |
Collapse
|
16
|
Narayanan M, Leung SA, Inaba Y, Elguindy MM, Nakamaru-Ogiso E. Semiquinone intermediates are involved in the energy coupling mechanism of E. coli complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:681-9. [PMID: 25868873 DOI: 10.1016/j.bbabio.2015.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 03/14/2015] [Accepted: 04/05/2015] [Indexed: 11/28/2022]
Abstract
Complex I (NADH:quinone oxidoreductase) is central to cellular aerobic energy metabolism, and its deficiency is involved in many human mitochondrial diseases. Complex I translocates protons across the membrane using electron transfer energy. Semiquinone (SQ) intermediates appearing during catalysis are suggested to be key for the coupling mechanism in complex I. However, the existence of SQ has remained controversial due to the extreme difficulty in detecting unstable and low intensity SQ signals. Here, for the first time with Escherichia coli complex I reconstituted in proteoliposomes, we successfully resolved and characterized three distinct SQ species by EPR. These species include: fast-relaxing SQ (SQNf) with P1/2 (half-saturation power level)>50mW and a wider linewidth (12.8 G); slow-relaxing SQ (SQNs) with P1/2=2-3mW and a 10G linewidth; and very slow-relaxing SQ (SQNvs) with P1/2= ~0.1mW and a 7.5G linewidth. The SQNf signals completely disappeared in the presence of the uncoupler gramicidin D or squamotacin, a potent E. coli complex I inhibitor. The pH dependency of the SQNf signals correlated with the proton-pumping activities of complex I. The SQNs signals were insensitive to gramicidin D, but sensitive to squamotacin. The SQNvs signals were insensitive to both gramicidin D and squamotacin. Our deuterium exchange experiments suggested that SQNf is neutral, while SQNs and SQNvs are anion radicals. The SQNs signals were lost in the ΔNuoL mutant missing transporter module subunits NuoL and NuoM. The roles and relationships of the SQ intermediates in the coupling mechanism are discussed.
Collapse
Affiliation(s)
- Madhavan Narayanan
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Steven A Leung
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Yuta Inaba
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Mahmoud M Elguindy
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Eiko Nakamaru-Ogiso
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
| |
Collapse
|
17
|
Liu H, Sultan MARF, Liu XL, Zhang J, Yu F, Zhao HX. Physiological and comparative proteomic analysis reveals different drought responses in roots and leaves of drought-tolerant wild wheat (Triticum boeoticum). PLoS One 2015; 10:e0121852. [PMID: 25859656 PMCID: PMC4393031 DOI: 10.1371/journal.pone.0121852] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/16/2015] [Indexed: 11/18/2022] Open
Abstract
To determine the proteomic-level responses of drought tolerant wild wheat (Triticum boeoticum), physiological and comparative proteomic analyses were conducted using the roots and the leaves of control and short term drought-stressed plants. Drought stress was imposed by transferring hydroponically grown seedlings at the 3-leaf stage into 1/2 Hoagland solution containing 20% PEG-6000 for 48 h. Root and leaf samples were separately collected at 0 (control), 24, and 48 h of drought treatment for analysis. Physiological analysis indicated that abscisic acid (ABA) level was greatly increased in the drought-treated plants, but the increase was greater and more rapid in the leaves than in the roots. The net photosynthetic rate of the wild wheat leaves was significantly decreased under short-term drought stress. The deleterious effects of drought on the studied traits mainly targeted photosynthesis. Comparative proteomic analysis identified 98 and 85 differently changed protein spots (DEPs) (corresponding to 87 and 80 unique proteins, respectively) in the leaves and the roots, respectively, with only 6 mutual unique proteins in the both organs. An impressive 86% of the DEPs were implicated in detoxification and defense, carbon metabolism, amino acid and nitrogen metabolism, proteins metabolism, chaperones, transcription and translation, photosynthesis, nucleotide metabolism, and signal transduction. Further analysis revealed some mutual and tissue-specific responses to short-term drought in the leaves and the roots. The differences of drought-response between the roots and the leaves mainly included that signal sensing and transduction-associated proteins were greatly up-regulated in the roots. Photosynthesis and carbon fixation ability were decreased in the leaves. Glycolysis was down-regulated but PPP pathway enhanced in the roots, resulting in occurrence of complex changes in energy metabolism and establishment of a new homeostasis. Protein metabolism was down-regulated in the roots, but enhanced in the leaves. These results will contribute to the existing knowledge on the complexity of root and leaf protein changes that occur in response to drought, and also provide a framework for further functional studies on the identified proteins.
Collapse
Affiliation(s)
- Hui Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | | | - Xiang li Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jin Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fei Yu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hui xian Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| |
Collapse
|
18
|
Sinha PK, Castro-Guerrero N, Patki G, Sato M, Torres-Bacete J, Sinha S, Miyoshi H, Matsuno-Yagi A, Yagi T. Conserved amino acid residues of the NuoD segment important for structure and function of Escherichia coli NDH-1 (complex I). Biochemistry 2015; 54:753-64. [PMID: 25545070 PMCID: PMC4310626 DOI: 10.1021/bi501403t] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
The NuoD segment (homologue of mitochondrial
49 kDa subunit) of
the proton-translocating NADH:quinone oxidoreductase (complex I/NDH-1)
from Escherichia coli is in the hydrophilic domain
and bears many highly conserved amino acid residues. The three-dimensional
structural model of NDH-1 suggests that the NuoD segment, together
with the neighboring subunits, constitutes a putative quinone binding
cavity. We used the homologous DNA recombination technique to clarify
the role of selected key amino acid residues of the NuoD segment.
Among them, residues Tyr273 and His224 were considered candidates
for having important interactions with the quinone headgroup. Mutant
Y273F retained partial activity but lost sensitivity to capsaicin-40.
Mutant H224R scarcely affected the activity, suggesting that this
residue may not be essential. His224 is located in a loop near the
N-terminus of the NuoD segment (Gly217–Phe227) which is considered
to form part of the quinone binding cavity. In contrast to the His224
mutation, mutants G217V, P218A, and G225V almost completely lost the
activity. One region of this loop is positioned close to a cytosolic
loop of the NuoA subunit in the membrane domain, and together they
seem to be important in keeping the quinone binding cavity intact.
The structural role of the longest helix in the NuoD segment located
behind the quinone binding cavity was also investigated. Possible
roles of other highly conserved residues of the NuoD segment are discussed.
Collapse
Affiliation(s)
- Prem Kumar Sinha
- Deparment of Molecular and Experimental Medicine, and ‡Department of Cell and Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, MEM256, La Jolla, California 92037, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Edwardson DW, Narendrula R, Chewchuk S, Mispel-Beyer K, Mapletoft JPJ, Parissenti AM. Role of Drug Metabolism in the Cytotoxicity and Clinical Efficacy of Anthracyclines. Curr Drug Metab 2015; 16:412-26. [PMID: 26321196 PMCID: PMC5398089 DOI: 10.2174/1389200216888150915112039] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 07/31/2015] [Accepted: 08/10/2015] [Indexed: 01/19/2023]
Abstract
Many clinical studies involving anti-tumor agents neglect to consider how these agents are metabolized within the host and whether the creation of specific metabolites alters drug therapeutic properties or toxic side effects. However, this is not the case for the anthracycline class of chemotherapy drugs. This review describes the various enzymes involved in the one electron (semi-quinone) or two electron (hydroxylation) reduction of anthracyclines, or in their reductive deglycosidation into deoxyaglycones. The effects of these reductions on drug antitumor efficacy and toxic side effects are also discussed. Current evidence suggests that the one electron reduction of anthracyclines augments both their tumor toxicity and their toxicity towards the host, in particular their cardiotoxicity. In contrast, the two electron reduction (hydroxylation) of anthracyclines strongly reduces their ability to kill tumor cells, while augmenting cardiotoxicity through their accumulation within cardiomyocytes and their direct effects on excitation/contraction coupling within the myocytes. The reductive deglycosidation of anthracyclines appears to inactivate the drug and only occurs under rare, anaerobic conditions. This knowledge has resulted in the identification of important new approaches to improve the therapeutic index of anthracyclines, in particular by inhibiting their cardiotoxicity. The true utility of these approaches in the management of cancer patients undergoing anthracycline-based chemotherapy remains unclear, although one such agent (the iron chelator dexrazoxane) has recently been approved for clinical use.
Collapse
Affiliation(s)
| | | | | | | | | | - Amadeo M Parissenti
- Dept. of Chemistry and Biochemistry, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON P3E 2C6, Canada.
| |
Collapse
|
20
|
Xie L, Wang X, Peng M, Meng F, Zhou Y, Chen L, Liu L, Gao Y, Guo Y. Isolation and detection of differential genes in hot pepper (Capsicum annuum L.) after space flight using AFLP markers. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.07.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
21
|
Burkova EE, Dmitrenok PS, Sedykh SE, Buneva VN, Soboleva SE, Nevinsky GA. Extremely stable soluble high molecular mass multi-protein complex with DNase activity in human placental tissue. PLoS One 2014; 9:e111234. [PMID: 25426722 PMCID: PMC4245193 DOI: 10.1371/journal.pone.0111234] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 09/26/2014] [Indexed: 01/06/2023] Open
Abstract
Human placenta is an organ which protects, feeds, and regulates the grooving of the embryo. Therefore, identification and characterization of placental components including proteins and their multi-protein complexes is an important step to understanding the placenta function. We have obtained and analyzed for the first time an extremely stable multi-protein complex (SPC, ∼1000 kDa) from the soluble fraction of three human placentas. By gel filtration on Sepharose-4B, the SPC was well separated from other proteins of the placenta extract. Light scattering measurements and gel filtration showed that the SPC is stable in the presence of NaCl, MgCl2, acetonitrile, guanidinium chloride, and Triton in high concentrations, but dissociates efficiently in the presence of 8 M urea, 50 mM EDTA, and 0.5 M NaCl. Such a stable complex is unlikely to be a casual associate of different proteins. According to SDS-PAGE and MALDI mass spectrometry data, this complex contains many major glycosylated proteins with low and moderate molecular masses (MMs) 4–14 kDa and several moderately abundant (79.3, 68.5, 52.8, and 27.2 kDa) as well as minor proteins with higher MMs. The SPC treatment with dithiothreitol led to a disappearance of some protein bands and revealed proteins with lower MMs. The SPCs from three placentas efficiently hydrolyzed plasmid supercoiled DNA with comparable rates and possess at least two DNA-binding sites with different affinities for a 12-mer oligonucleotide. Progress in study of placental protein complexes can promote understanding of their biological functions.
Collapse
Affiliation(s)
- Evgeniya E. Burkova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Pavel S. Dmitrenok
- Pacific Institute of Bioorganic Chemistry, Far East Division, Russian Academy of Sciences, Vladivostok, Russia
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Valentina N. Buneva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Svetlana E. Soboleva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Georgy A. Nevinsky
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- * E-mail:
| |
Collapse
|
22
|
Friedrich T. On the mechanism of respiratory complex I. J Bioenerg Biomembr 2014; 46:255-68. [PMID: 25022766 DOI: 10.1007/s10863-014-9566-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 07/03/2014] [Indexed: 02/08/2023]
Abstract
The energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, couples the transfer of electrons from NADH to ubiquinone with the translocation of protons across the membrane. Electron microscopy and X-ray crystallography revealed the two-part structure of the enzyme complex. A peripheral arm extending into the aqueous phase catalyzes the electron transfer reaction. Accordingly, this arm contains the redox-active cofactors, namely one flavin mononucleotide (FMN) and up to ten iron-sulfur (Fe/S) clusters. A membrane arm embedded in the lipid bilayer catalyzes proton translocation by a yet unknown mechanism. The binding site of the substrate (ubi) quinone is located at the interface of the two arms. The oxidation of one NADH is coupled with the translocation of four protons across the membrane. In this review, the binding of the substrates, the intramolecular electron transfer, the role of individual Fe/S clusters and the mechanism of proton translocation are discussed in the light of recent data obtained from our laboratory.
Collapse
Affiliation(s)
- Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, 79104, Freiburg, Germany,
| |
Collapse
|
23
|
Narayanan M, Gabrieli DJ, Leung SA, Elguindy MM, Glaser CA, Saju N, Sinha SC, Nakamaru-Ogiso E. Semiquinone and cluster N6 signals in His-tagged proton-translocating NADH:ubiquinone oxidoreductase (complex I) from Escherichia coli. J Biol Chem 2013; 288:14310-14319. [PMID: 23543743 DOI: 10.1074/jbc.m113.467803] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
NADH:ubiquinone oxidoreductase (complex I) pumps protons across the membrane using downhill redox energy. The Escherichia coli complex I consists of 13 different subunits named NuoA-N coded by the nuo operon. Due to the low abundance of the protein and some difficulty with the genetic manipulation of its large ~15-kb operon, purification of E. coli complex I has been technically challenging. Here, we generated a new strain in which a polyhistidine sequence was inserted upstream of nuoE in the operon. This allowed us to prepare large amounts of highly pure and active complex I by efficient affinity purification. The purified complex I contained 0.94 ± 0.1 mol of FMN, 29.0 ± 0.37 mol of iron, and 1.99 ± 0.07 mol of ubiquinone/1 mol of complex I. The extinction coefficient of isolated complex I was 495 mM(-1) cm(-1) at 274 nm and 50.3 mM(-1) cm(-1) at 410 nm. NADH:ferricyanide activity was 219 ± 9.7 μmol/min/mg by using HEPES-Bis-Tris propane, pH 7.5. Detailed EPR analyses revealed two additional iron-sulfur cluster signals, N6a and N6b, in addition to previously assigned signals. Furthermore, we found small but significant semiquinone signal(s), which have been reported only for bovine complex I. The line width was ~12 G, indicating its neutral semiquinone form. More than 90% of the semiquinone signal originated from the single entity with P½ (half-saturation power level) = 1.85 milliwatts. The semiquinone signal(s) decreased by 60% when with asimicin, a potent complex I inhibitor. The functional role of semiquinone and the EPR assignment of clusters N6a/N6b are discussed.
Collapse
Affiliation(s)
- Madhavan Narayanan
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - David J Gabrieli
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Steven A Leung
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Mahmoud M Elguindy
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Carl A Glaser
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Nitha Saju
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Subhash C Sinha
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Eiko Nakamaru-Ogiso
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104.
| |
Collapse
|
24
|
Identification of differential expression genes in leaves of rice (Oryza sativa L.) in response to heat stress by cDNA-AFLP analysis. BIOMED RESEARCH INTERNATIONAL 2013; 2013:576189. [PMID: 23509744 PMCID: PMC3590577 DOI: 10.1155/2013/576189] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 12/14/2012] [Accepted: 01/07/2013] [Indexed: 11/17/2022]
Abstract
High temperature impedes the growth and productivity of various crop species. To date, rice (Oryza sativa L.) has not been exploited to understand the molecular basis of its abnormally high level of temperature tolerance. To identify transcripts induced by heat stress, twenty-day-old rice seedlings of different rice cultivars suffering from heat stress were treated at different times, and differential gene expression analyses in leaves were performed by cDNA-AFLP and further verified by real-time RT-PCR. In aggregate, more than three thousand different fragments were indentified, and 49 fragments were selected for the sequence and differential expressed genes were classified functionally into different groups. 6 of 49 fragments were measured by real-time RT-PCR. In addition, the variations of three different polyamine contents in response to heat stress through high-performance liquid chromatography (HPLC) analysis were also performed. The results and their direct and indirect relationships to heat stress tolerance mechanism were discussed.
Collapse
|
25
|
Wilm A, Aw PPK, Bertrand D, Yeo GHT, Ong SH, Wong CH, Khor CC, Petric R, Hibberd ML, Nagarajan N. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res 2012; 40:11189-201. [PMID: 23066108 PMCID: PMC3526318 DOI: 10.1093/nar/gks918] [Citation(s) in RCA: 877] [Impact Index Per Article: 73.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The study of cell-population heterogeneity in a range of biological systems, from viruses to bacterial isolates to tumor samples, has been transformed by recent advances in sequencing throughput. While the high-coverage afforded can be used, in principle, to identify very rare variants in a population, existing ad hoc approaches frequently fail to distinguish true variants from sequencing errors. We report a method (LoFreq) that models sequencing run-specific error rates to accurately call variants occurring in <0.05% of a population. Using simulated and real datasets (viral, bacterial and human), we show that LoFreq has near-perfect specificity, with significantly improved sensitivity compared with existing methods and can efficiently analyze deep Illumina sequencing datasets without resorting to approximations or heuristics. We also present experimental validation for LoFreq on two different platforms (Fluidigm and Sequenom) and its application to call rare somatic variants from exome sequencing datasets for gastric cancer. Source code and executables for LoFreq are freely available at http://sourceforge.net/projects/lofreq/.
Collapse
Affiliation(s)
- Andreas Wilm
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore
| | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Verkhovskaya M, Bloch DA. Energy-converting respiratory Complex I: on the way to the molecular mechanism of the proton pump. Int J Biochem Cell Biol 2012; 45:491-511. [PMID: 22982742 DOI: 10.1016/j.biocel.2012.08.024] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 08/27/2012] [Accepted: 08/28/2012] [Indexed: 12/16/2022]
Abstract
In respiring organisms the major energy transduction flux employs the transmembrane electrochemical proton gradient as a physical link between exergonic redox reactions and endergonic ADP phosphorylation. Establishing the gradient involves electrogenic, transmembrane H(+) translocation by the membrane-embedded respiratory complexes. Among others, Complex I (NADH:ubiquinone oxidoreductase) is the most structurally complex and functionally enigmatic respiratory enzyme; its molecular mechanism is as yet unknown. Here we highlight recent progress and discuss the catalytic events during Complex I turnover in relation to their role in energy conversion and to the enzyme structure.
Collapse
Affiliation(s)
- Marina Verkhovskaya
- Helsinki Bioenergetics Group, Institute of Biotechnology, PO Box 65 (Viikinkaari 1) FIN-00014 University of Helsinki, Finland.
| | | |
Collapse
|
27
|
Yao Z, Jones AWE, Fassone E, Sweeney MG, Lebiedzinska M, Suski JM, Wieckowski MR, Tajeddine N, Hargreaves IP, Yasukawa T, Tufo G, Brenner C, Kroemer G, Rahman S, Szabadkai G. PGC-1β mediates adaptive chemoresistance associated with mitochondrial DNA mutations. Oncogene 2012; 32:2592-600. [PMID: 22777349 DOI: 10.1038/onc.2012.259] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Primary mitochondrial dysfunction commonly leads to failure in cellular adaptation to stress. Paradoxically, however, nonsynonymous mutations of mitochondrial DNA (mtDNA) are frequently found in cancer cells and may have a causal role in the development of resistance to genotoxic stress induced by common chemotherapeutic agents, such as cis-diammine-dichloroplatinum(II) (cisplatin, CDDP). Little is known about how these mutations arise and the associated mechanisms leading to chemoresistance. Here, we show that the development of adaptive chemoresistance in the A549 non-small-cell lung cancer cell line to CDDP is associated with the hetero- to homoplasmic shift of a nonsynonymous mutation in MT-ND2, encoding the mitochondrial Complex-I subunit ND2. The mutation resulted in a 50% reduction of the NADH:ubiquinone oxidoreductase activity of the complex, which was compensated by increased biogenesis of respiratory chain complexes. The compensatory mitochondrial biogenesis was most likely mediated by the nuclear co-activators peroxisome proliferator-activated receptor gamma co-activator-1α (PGC-1α) and PGC-1β, both of which were significantly upregulated in the CDDP-resistant cells. Importantly, both transient and stable silencing of PGC-1β re-established the sensitivity of these cells to CDDP-induced apoptosis. Remarkably, the PGC-1β-mediated CDDP resistance was independent of the mitochondrial effects of the co-activator. Altogether, our results suggest that partial respiratory chain defects because of mtDNA mutations can lead to compensatory upregulation of nuclear transcriptional co-regulators, in turn mediating resistance to genotoxic stress.
Collapse
Affiliation(s)
- Z Yao
- Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
EPR detection of two protein-associated ubiquinone components (SQ(Nf) and SQ(Ns)) in the membrane in situ and in proteoliposomes of isolated bovine heart complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1803-9. [PMID: 22503829 DOI: 10.1016/j.bbabio.2012.03.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 03/26/2012] [Accepted: 03/29/2012] [Indexed: 02/01/2023]
Abstract
The success of Sazanov's group in determining the X-ray structure of the whole bacterial complex I is a great contribution to the progress of complex I research. In this mini-review of 35years' history of my laboratory and collaborators, we characterized the function of protein-associated semiquinone molecules in the proton-pumping mechanism in complex I (NADH-quinone oxidoreductase). We have constructed most of the frame work of our hypothesis, utilizing EPR techniques before the X-ray structures of complex I were reported by Sazanov's and Brandt's groups. One of the semiquinones (SQ(Nf)) is extremely sensitive to a proton motive force imposed on the energy-transducing membrane, while the other (SQ(Ns)) is insensitive. Their sensitivity to rotenone inhibition also differs. These differences were exploited using tightly coupled bovine heart submitochondrial particles with a high respiratory control ratio (>8). We determined the distance between SQ(Nf) and iron-sulfur cluster N2 on the basis of their direct spin-spin interaction. We are extending this line of work using reconstituted bovine heart complex I proteoliposomes which shows a respiratory control ratio >5. Two frontier research groups support our view point based on their mutagenesis studies. High frequency (33.9GHz; Q-band) EPR experiments appear to favor our two-semiquinone model. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
Collapse
|
29
|
Roy SS, Patra M, Basu T, Dasgupta R, Bagchi A. Evolutionary analysis of prokaryotic heat-shock transcription regulatory protein σ³². Gene 2012; 495:49-55. [PMID: 22240312 DOI: 10.1016/j.gene.2011.12.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 12/22/2011] [Indexed: 10/14/2022]
Abstract
Heat-stress to any living cell is known to trigger a universal defense response, called heat-shock response, with rapid induction of tens of different heat-shock proteins. Bacterial heat-shock genes are transcribed by the σ(32)-bound RNA polymerase instead of the normal σ(70)-bound RNA polymerase. In this study, the diversity in sequence, variation in secondary structure and function amongst the different functional regions of the proteobacterial σ(32) family of proteins, and their phylogenetic relationships have been analyzed. Bacterial σ(32) proteins can be subdivided into different functional regions which are referred to as regions 2, 3, and 4. There is a great deal of sequence conservation among the functional regions of proteobacterial σ(32) family of proteins though some mutations are also present in these regions. Region 2 is the most conserved one, while region 4 has comparatively more variable sequences. In the present work, we tried to explore the effects of mutations in these regions. Our study suggests that the sequence diversities due to natural mutations in the different regions of proteobacterial σ(32) family lead to different functions. So far, this study is the first bioinformatic approach towards the understanding of the mechanistic details of σ(32) family of proteins using the protein sequence information only. This study therefore may help in elucidating the hitherto unknown molecular mechanism of the functionalities of σ(32)family of proteins.
Collapse
Affiliation(s)
- Sourav Singha Roy
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, West Bengal, India
| | | | | | | | | |
Collapse
|
30
|
Shiraishi Y, Murai M, Sakiyama N, Ifuku K, Miyoshi H. Fenpyroximate Binds to the Interface between PSST and 49 kDa Subunits in Mitochondrial NADH-Ubiquinone Oxidoreductase. Biochemistry 2012; 51:1953-63. [DOI: 10.1021/bi300047h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yusuke Shiraishi
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
| | - Masatoshi Murai
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
| | - Naoto Sakiyama
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
| | - Kentaro Ifuku
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
| | - Hideto Miyoshi
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
| |
Collapse
|
31
|
Abstract
Mitochondrial dysfunction often leads to cell death and disease. We can now draw correlations between the dysfunction of one of the most important mitochondrial enzymes, NADH:ubiquinone reductase or complex I, and its structural organization thanks to the recent advances in the X-ray structure of its bacterial homologs. The new structural information on bacterial complex I provide essential clues to finally understand how complex I may work. However, the same information remains difficult to interpret for many scientists working on mitochondrial complex I from different angles, especially in the field of cell death. Here, we present a novel way of interpreting the bacterial structural information in accessible terms. On the basis of the analogy to semi-automatic shotguns, we propose a novel functional model that incorporates recent structural information with previous evidence derived from studies on mitochondrial diseases, as well as functional bioenergetics.
Collapse
|
32
|
Murai M, Mashimo Y, Hirst J, Miyoshi H. Exploring interactions between the 49 kDa and ND1 subunits in mitochondrial NADH-ubiquinone oxidoreductase (complex I) by photoaffinity labeling. Biochemistry 2011; 50:6901-8. [PMID: 21721533 DOI: 10.1021/bi200883c] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quinazolines are strong inhibitors of NADH-ubiquinone oxidoreductase (complex I) from bovine heart mitochondria. Using a photoreactive quinazoline, [(125)I]AzQ, and bovine heart submitochondrial particles (SMPs), we demonstrated previously that [(125)I]AzQ binds at the interface of the 49 kDa and ND1 subunits in complex I; it labeled a site in the N-terminal (Asp41-Arg63) region of the 49 kDa subunit, suggesting that this region contacts the ND1 subunit [Murai, M., et al. (2009) Biochemistry 48, 688-698]. The labeled region of ND1 could not be identified because it is highly hydrophobic, and the SMPs did not yield sufficient amounts of labeled protein. Here, we describe how photoaffinity labeling of isolated complex I by [(125)I]AzQ yielded sufficient material for identification of the labeled region of the ND1 subunit. The inhibition of the isolated enzyme by AzQ is comparable to that of SMPs. Our results reveal that the labeled site in ND1 is between Asp199 and Lys262, mostly likely in the third matrix loop that connects the fifth and sixth transmembrane helices. Thus, our results reveal new information about the interface between the hydrophilic and hydrophobic domains of complex I, a region that is thought to be important for ubiquinone reduction and energy transduction.
Collapse
Affiliation(s)
- Masatoshi Murai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | | | | | | |
Collapse
|
33
|
Steimle S, Bajzath C, Dörner K, Schulte M, Bothe V, Friedrich T. Role of Subunit NuoL for Proton Translocation by Respiratory Complex I. Biochemistry 2011; 50:3386-93. [DOI: 10.1021/bi200264q] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Stefan Steimle
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg, Germany
| | - Csaba Bajzath
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg, Germany
| | - Katerina Dörner
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg, Germany
| | - Marius Schulte
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg, Germany
| | - Vinzenz Bothe
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg, Germany
| |
Collapse
|
34
|
Michel J, DeLeon-Rangel J, Zhu S, Van Ree K, Vik SB. Mutagenesis of the L, M, and N subunits of Complex I from Escherichia coli indicates a common role in function. PLoS One 2011; 6:e17420. [PMID: 21387012 PMCID: PMC3046159 DOI: 10.1371/journal.pone.0017420] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 01/24/2011] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The membrane arm of Complex I (NADH:ubiquinone oxidoreductase) contains three large, and closely related subunits, which are called L, M, and N in E. coli. These subunits are homologous to components of multi-subunit Na(+)/H(+) antiporters, and so are implicated in proton translocation. METHODOLOGY/PRINCIPAL FINDINGS Nineteen site-specific mutations were constructed at two corresponding positions in each of the three subunits. Two positions were selected in each subunit: L_K169, M_K173, N_K158 and L_Q236, M_H241, N_H224. Membrane vesicles were prepared from all of the resulting mutant strains, and were assayed for deamino-NADH oxidase activity, proton translocation, ferricyanide reductase activity, and sensitivity to capsaicin. Corresponding mutations in the three subunits were found to have very similar effects on all activities measured. In addition, the effect of adding exogenous decylubiquinone on these activities was tested. 50 µM decylubiquinone stimulated both deamino-NADH oxidase activity and proton translocation by wild type membrane vesicles, but was inhibitory towards the same activities by membrane vesicles bearing the lysine substitution at the L236/M241/N224 positions. CONCLUSIONS/SIGNIFICANCE The results show a close correlation with reduced activity among the corresponding mutations, and provide evidence that the L, M, and N subunits have a common role in Complex I.
Collapse
Affiliation(s)
- Jose Michel
- Department of Biological Sciences, Southern Methodist University, Dallas,
Texas, United States of America
| | - Jessica DeLeon-Rangel
- Department of Biological Sciences, Southern Methodist University, Dallas,
Texas, United States of America
| | - Shaotong Zhu
- Department of Biological Sciences, Southern Methodist University, Dallas,
Texas, United States of America
| | - Kalie Van Ree
- Department of Biological Sciences, Southern Methodist University, Dallas,
Texas, United States of America
| | - Steven B. Vik
- Department of Biological Sciences, Southern Methodist University, Dallas,
Texas, United States of America
- * E-mail:
| |
Collapse
|
35
|
|
36
|
Kojima N, Morioka T, Urabe D, Yano M, Suga Y, Maezaki N, Ohashi-Kobayashi A, Fujimoto Y, Maeda M, Yamori T, Yoshimitsu T, Tanaka T. Convergent synthesis of fluorescence-labeled probes of Annonaceous acetogenins and visualization of their cell distribution. Bioorg Med Chem 2010; 18:8630-41. [DOI: 10.1016/j.bmc.2010.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/01/2010] [Accepted: 10/02/2010] [Indexed: 10/18/2022]
|
37
|
Ohnishi T, Nakamaru-Ogiso E, Ohnishi ST. A new hypothesis on the simultaneous direct and indirect proton pump mechanisms in NADH-quinone oxidoreductase (complex I). FEBS Lett 2010; 584:4131-7. [PMID: 20816962 DOI: 10.1016/j.febslet.2010.08.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 08/21/2010] [Accepted: 08/29/2010] [Indexed: 02/07/2023]
Abstract
Recently, Sazanov's group reported the X-ray structure of whole complex I [Nature, 465, 441 (2010)], which presented a strong clue for a "piston-like" structure as a key element in an "indirect" proton pump. We have studied the NuoL subunit which has a high sequence similarity to Na(+)/H(+) antiporters, as do the NuoM and N subunits. We constructed 27 site-directed NuoL mutants. Our data suggest that the H(+)/e(-) stoichiometry seems to have decreased from (4H(+)/2e(-)) in the wild-type to approximately (3H(+)/2e(-)) in NuoL mutants. We propose a revised hypothesis that each of the "direct" and the "indirect" proton pumps transports 2H(+) per 2e(-).
Collapse
Affiliation(s)
- Tomoko Ohnishi
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6059, USA.
| | | | | |
Collapse
|
38
|
Nakamaru-Ogiso E, Kao MC, Chen H, Sinha SC, Yagi T, Ohnishi T. The membrane subunit NuoL(ND5) is involved in the indirect proton pumping mechanism of Escherichia coli complex I. J Biol Chem 2010; 285:39070-8. [PMID: 20826797 DOI: 10.1074/jbc.m110.157826] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Complex I pumps protons across the membrane by using downhill redox energy. Here, to investigate the proton pumping mechanism by complex I, we focused on the largest transmembrane subunit NuoL (Escherichia coli ND5 homolog). NuoL/ND5 is believed to have H(+) translocation site(s), because of a high sequence similarity to multi-subunit Na(+)/H(+) antiporters. We mutated thirteen highly conserved residues between NuoL/ND5 and MrpA of Na(+)/H(+) antiporters in the chromosomal nuoL gene. The dNADH oxidase activities in mutant membranes were mostly at the control level or modestly reduced, except mutants of Glu-144, Lys-229, and Lys-399. In contrast, the peripheral dNADH-K(3)Fe(CN)(6) reductase activities basically remained unchanged in all the NuoL mutants, suggesting that the peripheral arm of complex I was not affected by point mutations in NuoL. The proton pumping efficiency (the ratio of H(+)/e(-)), however, was decreased in most NuoL mutants by 30-50%, while the IC(50) values for asimicin (a potent complex I inhibitor) remained unchanged. This suggests that the H(+)/e(-) stoichiometry has changed from 4H(+)/2e(-) to 3H(+) or 2H(+)/2e(-) without affecting the direct coupling site. Furthermore, 50 μm of 5-(N-ethyl-N-isopropyl)-amiloride (EIPA), a specific inhibitor for Na(+)/H(+) antiporters, caused a 38 ± 5% decrease in the initial H(+) pump activity in the wild type, while no change was observed in D178N, D303A, and D400A mutants where the H(+) pumping efficiency had already been significantly decreased. The electron transfer activities were basically unaffected by EIPA in both control and mutants. Taken together, our data strongly indicate that the NuoL subunit is involved in the indirect coupling mechanism.
Collapse
Affiliation(s)
- Eiko Nakamaru-Ogiso
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | | | | | | | | | | |
Collapse
|
39
|
|