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Zhou SM, Wang F, Yan SY, Zhu ZM, Gao XF, Zhao XL. Phylogenomics and plastome evolution of Indigofera (Fabaceae). FRONTIERS IN PLANT SCIENCE 2023; 14:1186598. [PMID: 37346129 PMCID: PMC10280451 DOI: 10.3389/fpls.2023.1186598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023]
Abstract
Introduction Indigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of Indigofera taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of Indigofera. Methods Here, we newly assembled 18 chloroplast genomes of Indigofera. We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae. Results and discussion The chloroplast genomes of Indigofera exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which trnK-rbcL, ndhF-trnL, and ycf1 were considered as candidate DNA barcodes for species identification of Indigofera. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on complete chloroplast genome and protein-coding genes (PCGs) generated a well-resolved phylogeny of Indigofera and allied species. Indigofera monophyly was strongly supported, and four monophyletic lineages (i.e., the Pantropical, East Asian, Tethyan, and Palaeotropical clades) were resolved within the genus. The species pairwise Ka/Ks ratios showed values lower than 1, and 13 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis using the branch-site model, eight of which were associated with photosynthesis. Positive selection of accD suggested that Indigofera species have experienced adaptive evolution to selection pressures imposed by their herbivores and pathogens. Our study provided insight into the structural variation of chloroplast genomes, phylogenetic relationships, and adaptive evolution in Indigofera. These results will facilitate future studies on species identification, interspecific and intraspecific delimitation, adaptive evolution, and the phylogenetic relationships of the genus Indigofera.
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Affiliation(s)
- Sheng-Mao Zhou
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Forestry, Southwest Forestry University, Kunming, China
| | - Fang Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Forestry, Southwest Forestry University, Kunming, China
| | - Si-Yuan Yan
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Forestry, Southwest Forestry University, Kunming, China
| | - Zhang-Ming Zhu
- School of Ecology and Environmental Science and Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, China
| | - Xin-Fen Gao
- Chinese Academy of Sciences (CAS) Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xue-Li Zhao
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Forestry, Southwest Forestry University, Kunming, China
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Zhang P, Yang B, Xu X, Zhang H, Feng X, Hao H, Du W, Zhu H, Li S, Yu W, Khan A, Umer S, Zhao X. Combination of CNP, MT and FLI during IVM Significantly Improved the Quality and Development Abilities of Bovine Oocytes and IVF-Derived Embryos. Antioxidants (Basel) 2023; 12:antiox12040897. [PMID: 37107273 PMCID: PMC10135536 DOI: 10.3390/antiox12040897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/04/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Oocyte maturation is a critical step in the completion of female gametogenesis in the ovary; thus, for subsequent fertilization and embryogenesis. Vitrification of embryo also has been shown to be closely associated with oocyte maturation. To improve the quality and developmental potential of bovine oocytes derived from in vitro maturation (IVM), Pre-IVM with C-type natriuretic peptide (CNP), melatonin (MT) and in combination, IGF1, FGF2, LIF (FLI) were supplemented in the IVM medium. In this current study, we cultured bovine oocytes in Pre-IVM with CNP for 6 h before transferring them to the IVM medium supplemented with MT and FLI. The developmental potential of bovine oocytes was then investigated by measuring the reactive oxygen species (ROS), the intracellular glutathione (GSH) and ATP levels, the transzonal projections (TZP), the mitochondrial membrane potential (ΔΨm), cacline-AM, and the expression of related genes (cumulus cells (CCs), oocytes, blastocysts). The results revealed that oocytes treated with a combination of CNP, MT, and FLI had dramatically improved the percentage of oocytes developed to blastocyst, ATP content, GSH levels, TZP intensity, the ΔΨm, cacline-AM fluorescence intensity, and considerably reduced ROS levels of oocytes. Furthermore, the survival rate and the hatched rate after vitrification of the CNP+MT+FLI group were significantly higher than those other groups. Thus, we speculated that CNP+MT+FLI increases the IVM of bovine oocytes. In conclusion, our findings deepen our understanding and provide new perspectives on targeting the combination of CNP, MT and FLI to enhance the quality and developmental potential of bovine oocytes.
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Affiliation(s)
- Peipei Zhang
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China
| | - Baigao Yang
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China
| | - Xi Xu
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China
| | - Hang Zhang
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China
| | - Xiaoyi Feng
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China
| | - Haisheng Hao
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China
| | - Weihua Du
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China
| | - Huabin Zhu
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China
| | - Shujing Li
- Shijiazhuang Tianquan Elite Dairy Ltd., Shijiazhuang 050200, China
| | - Wenli Yu
- Shijiazhuang Tianquan Elite Dairy Ltd., Shijiazhuang 050200, China
| | - Adnan Khan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Saqib Umer
- Department of Theriogenology, University of Agriculture, Faisalabad 38000, Punjab, Pakistan
| | - Xueming Zhao
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan Western Road, Haidian District, Beijing 100193, China
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Zhu M, He C, Zhou J, Li Y, Qian L, Zhang J, Qiao Y, Chang W, Lou H. Liverwort-Derived Metabolites Retard Endophyte Growth and Inspire Antifungal Application. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4863-4875. [PMID: 36919252 DOI: 10.1021/acs.jafc.2c08866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Liverwort secondary metabolites play an important role in the peaceful relationship between liverwort endophytic fungi and the host. This study identified potential antifungal agents based on interactions between host plants and endophytic fungi. Two endophytic fungi strains and 25 metabolites, including nine new compounds, were isolated from the Chinese liverwort Herbertus herpocladioides. Endophytic fungi were identified using internal transcribed spacer and whole-genome sequencing, and the compound structures were determined using comprehensive spectroscopic analysis coupled with electronic circular dichroism calculations. Among these compounds, compounds 10-13 exhibited potent antifungal activities. Compound 10, the most potent antifungal agent, disrupted fungal mitochondrial respiration by inhibiting the activity of mitochondrial complexes I and IV and resulted in the intracellular ATP content of endophytic fungi being significantly reduced. The in vivo results show that compound 10 protected fruits and animals from infection by phytopathogen Alternaria citriarbusti and human pathogen Candida albicans, respectively.
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Affiliation(s)
- Mingzhu Zhu
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Chen He
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Jinchuan Zhou
- School of Pharmacy, Linyi University, Linyi 276000, China
| | - Yi Li
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Lilin Qian
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Jiaozhen Zhang
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Yanan Qiao
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Wenqiang Chang
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Hongxiang Lou
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
- Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Qilu Hospital, Jinan, Shandong 250012, China
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Qin HH, Cai J, Liu CK, Zhou RX, Price M, Zhou SD, He XJ. The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution. BMC PLANT BIOLOGY 2023; 23:9. [PMID: 36604614 PMCID: PMC9814190 DOI: 10.1186/s12870-022-04027-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The Ferula genus encompasses 180-185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, but its infrageneric relationships are still confusing. In addition, its genetic basis of its adaptive evolution remains poorly understood. Plastid genomes with more variable sites have the potential to reconstruct robust phylogeny in plants and investigate the adaptive evolution of plants. Although chloroplast genomes have been reported within the Ferula genus, few studies have been conducted using chloroplast genomes, especially for endemic species in China. RESULTS Comprehensively comparative analyses of 22 newly sequenced and assembled plastomes indicated that these plastomes had highly conserved genome structure, gene number, codon usage, and repeats type and distribution, but varied in plastomes size, GC content, and the SC/IR boundaries. Thirteen mutation hotspot regions were detected and they would serve as the promising DNA barcodes candidates for species identification in Ferula and related genera. Phylogenomic analyses with high supports and resolutions showed that Talassia transiliensis and Soranthus meyeri were nested in the Ferula genus, and thus they should be transferred into the Ferula genus. Our phylogenies also indicated the monophyly of subgenera Sinoferula and subgenera Narthex in Ferula genus. Twelve genes with significant posterior probabilities for codon sites were identified in the positively selective analysis, and their function may relate to the photosystem II, ATP subunit, and NADH dehydrogenase. Most of them might play an important role to help Ferula species adapt to high-temperatures, strong-light, and drought habitats. CONCLUSION Plastome data is powerful and efficient to improve the support and resolution of the complicated Ferula phylogeny. Twelve genes with significant posterior probabilities for codon sites were helpful for Ferula to adapt to the harsh environment. Overall, our study supplies a new perspective for comprehending the phylogeny and evolution of Ferula.
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Affiliation(s)
- Huan-Huan Qin
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jing Cai
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chang-Kun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Ren-Xiu Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Megan Price
- Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Xie DF, Xie C, Ren T, Song BN, Zhou SD, He XJ. Plastid phylogenomic insights into relationships, divergence, and evolution of Apiales. PLANTA 2022; 256:117. [PMID: 36376499 DOI: 10.1007/s00425-022-04031-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/06/2022] [Indexed: 06/16/2023]
Abstract
Members of Apiales are monophyletic and radiated in the Late Cretaceous. Fruit morphologies are critical for Apiales evolution and negative selection and mutation pressure play important roles in environmental adaptation. Apiales include many foods, spices, medicinal, and ornamental plants, but the phylogenetic relationships, origin and divergence, and adaptive evolution remain poorly understood. Here, we reconstructed Apiales phylogeny based on 72 plastid genes from 280 species plastid genomes representing six of seven families of this order. Highly supported phylogenetic relationships were detected, which revealed that each family of Apiales is monophyletic and confirmed that Pennanticeae is a member of Apiales. Genera Centella and Dickinsia are members of Apiaceae, and the genus Hydrocotyle previously classified into Apiaceae is confirmed to belong to Araliaceae. Besides, coalescent phylogenetic analysis and gene trees cluster revealed ten genes that can be used for distinguishing species among families of Apiales. Molecular dating suggested that the Apiales originated during the mid-Cretaceous (109.51 Ma), with the families' radiation occurring in the Late Cretaceous. Apiaceae species exhibit higher differentiation compared to other families. Ancestral trait reconstruction suggested that fruit morphological evolution may be related to shifts in plant types (herbaceous or woody), which in turn is related to the distribution areas and species numbers. Codon bias and positive selection analyses suggest that negative selection and mutation pressure may play important roles in environmental adaptation of Apiales members. Our results improve the phylogenetic framework of Apiales and provide insights into the origin, divergence, and adaptive evolution of this order and its members.
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Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Chuan Xie
- Sichuan Academy of Forestry, Chengdu, 610081, Sichuan, People's Republic of China
| | - Ting Ren
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Bo-Ni Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.
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Yue J, Lu Q, Ni Y, Chen P, Liu C. Comparative analysis of the plastid and mitochondrial genomes of Artemisia giraldii Pamp. Sci Rep 2022; 12:13931. [PMID: 35978085 PMCID: PMC9385723 DOI: 10.1038/s41598-022-18387-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 08/10/2022] [Indexed: 12/30/2022] Open
Abstract
Artemisia giraldii Pamp. is an herbaceous plant distributed only in some areas in China. To understand the evolutionary relationship between plastid and mitochondria in A. giraldii, we sequenced and analysed the plastome and mitogenome of A. giraldii on the basis of Illumina and Nanopore DNA sequencing data. The mitogenome was 194,298 bp long, and the plastome was 151,072 bp long. The mitogenome encoded 56 genes, and the overall GC content was 45.66%. Phylogenetic analysis of the two organelle genomes revealed that A. giraldii is located in the same branching position. We found 13 pairs of homologous sequences between the plastome and mitogenome, and only one of them might have transferred from the plastid to the mitochondria. Gene selection pressure analysis in the mitogenome showed that ccmFc, nad1, nad6, atp9, atp1 and rps12 may undergo positive selection. According to the 18 available plastome sequences, we found 17 variant sites in two hypervariable regions that can be used in completely distinguishing 18 Artemisia species. The most interesting discovery was that the mitogenome of A. giraldii was only 43,226 bp larger than the plastome. To the best of our knowledge, this study represented one of the smallest differences between all sequenced mitogenomes and plastomes from vascular plants. The above results can provide a reference for future taxonomic and molecular evolution studies of Asteraceae species.
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Affiliation(s)
- Jingwen Yue
- grid.256111.00000 0004 1760 2876Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, No.15, Shangxiadian Road, Fuzhou, 350002 Fujian People’s Republic of China ,grid.506261.60000 0001 0706 7839Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193 People’s Republic of China
| | - Qianqi Lu
- grid.256111.00000 0004 1760 2876Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, No.15, Shangxiadian Road, Fuzhou, 350002 Fujian People’s Republic of China
| | - Yang Ni
- grid.506261.60000 0001 0706 7839Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193 People’s Republic of China
| | - Pinghua Chen
- grid.256111.00000 0004 1760 2876Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, No.15, Shangxiadian Road, Fuzhou, 350002 Fujian People’s Republic of China
| | - Chang Liu
- grid.506261.60000 0001 0706 7839Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193 People’s Republic of China
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Li C, Liu Y, Lin F, Zheng Y, Huang P. Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae). PeerJ 2022; 10:e13570. [PMID: 35795179 PMCID: PMC9252178 DOI: 10.7717/peerj.13570] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/20/2022] [Indexed: 01/17/2023] Open
Abstract
Dalbergia spp. are numerous and widely distributed in pantropical areas in Asia, Africa and America, and most of the species have important economic and ecological value as precious timber. In this study, we determined and characterized six complete chloroplast genomes of Dalbergia species (Dalbergia obtusifolia, D. hupeana, D. mimosoides, D. sissoo, D. hancei, D. balansae), which displayed the typical quadripartite structure of angiosperms. The sizes of the genomes ranged from 155,698 bp (D. hancei) to 156,419 bp (D. obtusifolia). The complete chloroplast genomes of Dalbergia include 37 tRNA genes, eight rRNA genes and 84 protein-coding genes. We analysed the sequence diversity of Dalberigia chloroplast genomes coupled with previous reports. The results showed 12 noncoding regions (rps16-accD, trnR-UCU-trnG-UCC, ndhE-ndhG, trnG-UCC-psbZ, rps8-rpl14, trnP-UGG-psaJ, ndhH-rps15, trnQ-UUG-rps16, trnS-GCU-psbI, rps12-clpP, psbA-trnK-UUU, trnK-UUU-intron), and four coding regions (rps16, ycf1, rps15 and ndhF) showed many nucleotide variations that could be used as potential molecular markers. Based on a site-specific model, we analysed the selective pressure of chloroplast genes in Dalbergia species. Twenty-two genes with positively selected sites were detected, involving the photosynthetic system (ndhC, adhD, ndhF, petB, psaA, psaB, psbB, psbC, psbK and rbcL), self-replication category of genes (rpoA, rpoC2, rps3, rps12 and rps18) and others (accD, ccsA, cemA, clpP, matK, ycf1 and ycf2). Additionally, we identified potential RNA editing sites that were relatively conserved in the genus Dalbergia. Furthermore, the comparative analysis of cp genomes of Dalbergieae species indicated that the boundary of IRs/SSC was highly variable, which resulted in the size variation of cp genomes. Finally, phylogenetic analysis showed an inferred phylogenetic tree of Papilionoideae species with high bootstrap support and suggested that Amorpheae was the sister of the clade Dalbergieae. Moreover, three genera of the Pterocarpus clade showed a nested evolutionary relationship. These complete cp genomes provided valuable information for understanding the genetic variation and phylogenetic relationship of Dalbergia species with their relatives.
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Affiliation(s)
- Changhong Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yu Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Resource Plant Innovation and Utilization, Institute of Subtropical Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Wenzhou, Zhejiang, China
| | - Furong Lin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Comparative Plastome Analysis of Three Amaryllidaceae Subfamilies: Insights into Variation of Genome Characteristics, Phylogeny, and Adaptive Evolution. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3909596. [PMID: 35372568 PMCID: PMC8970886 DOI: 10.1155/2022/3909596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/19/2022] [Accepted: 02/05/2022] [Indexed: 11/17/2022]
Abstract
In the latest APG IV classification system, Amaryllidaceae is placed under the order of Asparagus and includes three subfamilies: Agapanthoideae, Allioideae, and Amaryllidoideae, which include many economically important crops. With the development of molecular phylogeny, research on the phylogenetic relationship of Amaryllidaceae has become more convenient. However, the current comparative analysis of Amaryllidaceae at the whole chloroplast genome level is still lacking. In this study, we sequenced 18 Allioideae plastomes and combined them with publicly available data (a total of 41 plastomes), including 21 Allioideae species, 1 Agapanthoideae species, 14 Amaryllidoideae species, and 5 Asparagaceae species. Comparative analyses were performed including basic characteristics of genome structure, codon usage, repeat elements, IR boundary, and genome divergence. Phylogenetic relationships were detected using single-copy genes (SCGs) and ribosomal internal transcribed spacer sequences (ITS), and the branch-site model was also employed to conduct the positive selection analysis. The results indicated that all Amaryllidaceae species showed a highly conserved typical tetrad structure. The GC content and five codon usage indexes in Allioideae species were lower than those in the other two subfamilies. Comparison analysis of Bayesian and ML phylogeny based on SCGs strongly supports the monophyly of three subfamilies and the sisterhood among them. Besides, positively selected genes (PSGs) were detected in each of the three subfamilies. Almost all genes with significant posterior probabilities for codon sites were associated with self-replication and photosynthesis. Our study investigated the three subfamilies of Amaryllidaceae at the whole chloroplast genome level and suggested the key role of selective pressure in the adaptation and evolution of Amaryllidaceae.
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Xu L, Chen X, Jiang H, Xu J, Wang L, Sun Y. NDUFC1 Is Upregulated in Gastric Cancer and Regulates Cell Proliferation, Apoptosis, Cycle and Migration. Front Oncol 2021; 11:709044. [PMID: 34966665 PMCID: PMC8710466 DOI: 10.3389/fonc.2021.709044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/04/2021] [Indexed: 01/13/2023] Open
Abstract
Gastric cancer is one of the most common primary tumors of the digestive system. NADH: ubiquinone oxidoreductase subunit C1 (NDUFC1), which is an accessory subunit of the NADH dehydrogenase (complex I), is responsible for the transportation of electrons from NADH to the respiratory chain essential for the oxidative phosphorylation. However, little is known about the roles of NDUFC1 in carcinogenesis. In this study, NDUFC1 protein level in NSCLC tissues was tested by immunohistochemistry (IHC) staining. NDUFC1 mRNA level in gastric cancer cell lines was determined by qRT-PCR. MGC-803 and SGC-7901 cells were transfected with shNDUFC1 lentivirus designed to silence NDUFC1. MTT assay, CCK8 assay, wound healing assay and transwell migration assay were conducted. Cell cycle and apoptosis were detected by flow cytometry. In vivo experiments were performed using nude mice. The results indicated that overexpressed NDUFC1 in gastric cancer was related to more serious tumor infiltrates, a higher risk of lymphatic metastasis, a higher proportion of positive lymph nodes, and a more advanced tumor stage. Compared with shCtrl groups, MGC-803 and SGC-7901 of shNDUFC1 groups had lower abilities of proliferation and migration, higher levels of apoptosis. NDUFC1 knockdown also inhibited SGC-7901 cell growth in vivo and suppressed Ki67 expression in xenograft tumors. More importantly, we found that NDUFC1 downregulation made the levels of P-Akt, P-mTOR, CCND1, CDK6, PIK3CA, Bcl-2, Survivin, and XIAP decreased, and that PI3K/AKT signaling pathway agonist SC79 rescued the inhibitory effects on cell proliferation and migration, reversed the promoted effects on cell apoptosis caused by NDUFC1 knockdown. More importantly, compared with NDUFC1 knockdown group, the expression of P-Akt, Bcl-2, Survivin, and XIAP was raised in shNDUFC1 + SC79 group. Thus, our suspicion was that NDUFC1 exacerbates NSCLC progression via PI3K/Akt pathway. Taken together, our study indicated that targeting NDUFC1 could open innovative perspectives for new multi-targeting approaches in the treatment of gastric cancer.
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Affiliation(s)
- Liang Xu
- Department of Organ Transplantation, The Second Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Xiuxiu Chen
- Surgery of Breast Nail, The Second Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Hongtao Jiang
- Department of Organ Transplantation, The Second Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Jian Xu
- Department of Organ Transplantation, The Second Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Lixia Wang
- Department of Organ Transplantation, The Second Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Yuemin Sun
- Department of Pancreatic & Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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10
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Zhang J, Song R, Wu S, Cai D, Wu Z, Liu Z, Hu D, Song B. Discovery of Pyrido[1,2- a]pyrimidinone Mesoionic Compounds Incorporating a Dithioacetal Moiety as Novel Potential Insecticidal Agents. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15136-15144. [PMID: 34878774 DOI: 10.1021/acs.jafc.1c05823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A series of novel mesoionic pyrido[1,2-a]pyrimidinone compounds incorporating a dithioacetal skeleton were designed and synthesized for use as insecticidal agents. The biological activity of the title compounds indicated good to excellent insecticidal activities against bean aphids (Aphis craccivora) and white-backed planthoppers (Sogatella furcifera). Compound 34 showed excellent insecticidal activity against bean aphids (A. craccivora) with an LC50 value of 2.80 μg/mL, exceeding the insecticidal activity of trifluoropyrimidine (LC50 = 4.20 μg/mL). Proteomics and molecular docking results indicated that compound 34 could act on nicotinic acetylcholine receptors. This study provides support for the application of mesoionic pyrido[1,2-a]pyrimidinone compounds containing dithioacetal as novel insecticidal agents.
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Affiliation(s)
- Jian Zhang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Runjiang Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Shang Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Di Cai
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Zengxue Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Zhengjun Liu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Deyu Hu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
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11
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Ma X, Zhang Q, La Y, Fu D, Jiang H, Bao P, Wu X, Chu M, Guo X, Yan P, Liang C. Differential Abundance of Brain Mitochondrial Proteins in Yak and Cattle: A Proteomics-Based Study. Front Vet Sci 2021; 8:663031. [PMID: 34532350 PMCID: PMC8438127 DOI: 10.3389/fvets.2021.663031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
The plateau adaptability and stress resistance of yaks are widely known based on their capacity to survive under severe habitat conditions. However, a few studies on brain mitochondria have characterized these adaptations at the protein level. We identified and quantified the brain mitochondrial proteins using isobaric tags for relative and absolute quantification (iTRAQ) and Proteomics. Western blotting was used to verify changes in the expression of target proteins. A total of 57 differentially abundant proteins (DAPs) were identified in the yak brain tissue. Gene Ontology (GO) analysis showed molecular functions of these DAPs including downregulated oxidoreductase activity but upregulated coenzyme binding. Significantly enriched biological processes were oxidation-reduction process (downregulated) and small molecule metabolic processes (upregulated). STRING protein interaction analysis indicated a complex interaction between dehydrogenase, transaminase, and ATP synthetase families. Reactome pathway analysis highlighted that the majority of DAPs participated in aerobic metabolic pathways such as metabolism, citric acid cycle, and respiratory electron transport. Immunoblotting confirmed that changes in FKBP4 and ATPAF2 expression were consistent with the results of mass spectrometry. We performed a high-throughput screening to identify DAPs in brain mitochondria between yak and cattle, which could explain the plateau adaptability of yaks.
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Affiliation(s)
- Xiaoming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Qiang Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China.,State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Yongfu La
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Donghai Fu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Hiu Jiang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China.,State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Pengjia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Chunnian Liang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
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12
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Overbey EG, Ng TT, Catini P, Griggs LM, Stewart P, Tkalcic S, Hawkins RD, Drechsler Y. Transcriptomes of an Array of Chicken Ovary, Intestinal, and Immune Cells and Tissues. Front Genet 2021; 12:664424. [PMID: 34276773 PMCID: PMC8278112 DOI: 10.3389/fgene.2021.664424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/27/2021] [Indexed: 12/16/2022] Open
Abstract
While the chicken (Gallus gallus) is the most consumed agricultural animal worldwide, the chicken transcriptome remains understudied. We have characterized the transcriptome of 10 cell and tissue types from the chicken using RNA-seq, spanning intestinal tissues (ileum, jejunum, proximal cecum), immune cells (B cells, bursa, macrophages, monocytes, spleen T cells, thymus), and reproductive tissue (ovary). We detected 17,872 genes and 24,812 transcripts across all cell and tissue types, representing 73% and 63% of the current gene annotation, respectively. Further quantification of RNA transcript biotypes revealed protein-coding and lncRNAs specific to an individual cell/tissue type. Each cell/tissue type also has an average of around 1.2 isoforms per gene, however, they all have at least one gene with at least 11 isoforms. Differential expression analysis revealed a large number of differentially expressed genes between tissues of the same category (immune and intestinal). Many of these differentially expressed genes in immune cells were involved in cellular processes relating to differentiation and cell metabolism as well as basic functions of immune cells such as cell adhesion and signal transduction. The differential expressed genes of the different segments of the chicken intestine (jejunum, ileum, proximal cecum) correlated to the metabolic processes in nutrient digestion and absorption. These data should provide a valuable resource in understanding the chicken genome.
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Affiliation(s)
- Eliah G Overbey
- Department of Genome Sciences, Interdepartmental Astrobiology Program, University of Washington, Seattle, WA, United States
| | - Theros T Ng
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Pietro Catini
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Lisa M Griggs
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Paul Stewart
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Suzana Tkalcic
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - R David Hawkins
- Department of Genome Sciences, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Yvonne Drechsler
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
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13
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Liu X, Chen G, He J, Wan G, Shen D, Xia A, Chen F. Transcriptomic analysis reveals the inhibition of reproduction in rice brown planthopper, Nilaparvata lugens, after silencing the gene of MagR (IscA1). INSECT MOLECULAR BIOLOGY 2021; 30:253-263. [PMID: 33410574 DOI: 10.1111/imb.12692] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/18/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
MagR (IscA1) is a member of the iron-sulphur cluster assembly proteins, which plays vital roles in many physiological processes, such as energy metabolism, electron transfer, iron homeostasis, heme biosynthesis and physiologically magnetic response. Its deletion leads to the loss of mitochondrial DNA, inactivation of iron-sulphur proteins and abnormal embryonic development in organisms. However, the physiological roles of MagR in insects are unclear. This study characterized the effects and molecular regulatory mechanism of MagR gene silencing on the reproduction of brachypterous female adults of Nilaparvata lugens. After silencing the MagR gene using RNAi approach, the duration of reproductive period was shortened and the fecundity and hatchability reduced significantly. A total of 479 differentially expressed genes (DEGs) were identified for female adults after 2 days of dsRNA injection through RNA-sequencing technology, including 352 significantly upregulated DEGs and 127 significantly downregulated DEGs, among which 44 DEGs were considered the key genes involved in the effects of NlMagR silencing on the reproduction, revealing the regulatory mechanism of MagR at RNA transcription level and providing a new strategy for the control of N. lugens.
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Affiliation(s)
- X Liu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - G Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - J He
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - G Wan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - D Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - A Xia
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - F Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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14
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Liu Y, Luo C, Li T, Zhang W, Zong Z, Liu X, Deng H. Reduced Nicotinamide Mononucleotide (NMNH) Potently Enhances NAD + and Suppresses Glycolysis, the TCA Cycle, and Cell Growth. J Proteome Res 2021; 20:2596-2606. [PMID: 33793246 DOI: 10.1021/acs.jproteome.0c01037] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Decreased cellular NAD+ levels are causally linked to aging and aging-associated diseases. NAD+ precursors in oxidized form such as nicotinamide mononucleotide (NMN) and nicotinamide riboside (NR) have gained much attention and been well studied for their ability to restore NAD+ levels in model organisms. Less is known about whether NAD+ precursors in reduced form can also efficiently increase the tissue and cellular NAD+ levels and have different effects on cellular processes than NMN or NR. In the present study, we developed a chemical method to produce dihydronicotinamide mononucleotide (NMNH), which is the reduced form of NMN. We demonstrated that NMNH was a better NAD+ enhancer than NMN both in vitro and in vivo, mediated by nicotinamide mononucleotide adenylyltransferase (NMNAT). Additionally, NMNH increased the reduced NAD (NADH) levels in cells and in mouse livers. Metabolomic analysis revealed that NMNH inhibited glycolysis and the TCA cycle. In vitro experiments demonstrated that NMNH induced cell cycle arrest and suppressed cell growth. Nevertheless, NMNH treatment did not cause an observable difference in mouse weight. Taken together, our work demonstrates that NMNH is a potent NAD+ enhancer and suppresses glycolysis, the TCA cycle, and cell growth.
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Affiliation(s)
- Yan Liu
- Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.,MOE Key Laboratory of Bioinformatics, Centre for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chengting Luo
- Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.,MOE Key Laboratory of Bioinformatics, Centre for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ting Li
- MOE Key Laboratory of Bioinformatics, Centre for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenhao Zhang
- Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhaoyun Zong
- MOE Key Laboratory of Bioinformatics, Centre for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohui Liu
- MOE Key Laboratory of Bioinformatics, Centre for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,National Center for Protein Science, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, Centre for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,National Center for Protein Science, Tsinghua University, Beijing 100084, China
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15
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Xin JW, Chai ZX, Zhang CF, Zhang Q, Zhu Y, Cao HW, Ji CY, Chen XY, Jiang H, Zhong JC, Ji QM. Signature of high altitude adaptation in the gluteus proteome of the yak. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:362-372. [PMID: 32779369 DOI: 10.1002/jez.b.22995] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/23/2022]
Abstract
Yak is the unique Bovidae species in the Qinghai-Tibetan Plateau. A previous proteomic study has compared the yak muscle tissue to one cattle strain using the isobaric tags for relative and absolute quantification approach. In this study, to further investigate the molecular mechanisms underlying yak adaptation, the proteomic profiles of gluteus were compared between yak and one moderate-altitude cattle strain (Tibetan cattle) and two low-altitude cattle strains (Holstein and Sanjiang cattle) using a label-free quantitative method. The comparisons identified 20, 364, 143 upregulated proteins and 4, 6, 37 downregulated proteins in yak, compared with Tibetan, Holstein, and Sanjiang cattle, respectively. Protein-protein interaction analysis indicated that these differentially expressed proteins were mainly related to "oxidative phosphorylation" and "electron transport chain." Further analysis revealed that NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4, cytochrome C oxidase subunit 6A2, mitochondrial and cytochrome c oxidase subunit NDUFA4 were all increased in the yak, suggesting that yak might increase mitochondrial capacity to sustain metabolic rates under high altitude conditions, which might be a long-term adaptive mechanism underlying adaptation to high altitude environments. Yak increased the level of thioredoxin reductase 2 to protect themselves from oxidative damages. Moreover, the increased expression levels of phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform and caveolin-1 in yak suggested that yaks promoted glucose uptake for adaptation to high altitude. These results provided more information to better understand the molecular mechanisms underlying yak adaption.
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Affiliation(s)
- Jin-Wei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, P. R. China.,Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, P. R. China
| | - Zhi-Xin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, P. R. China
| | - Cheng-Fu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, P. R. China.,Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, P. R. China
| | - Qiang Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, P. R. China.,Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, P. R. China
| | - Yong Zhu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, P. R. China.,Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, P. R. China
| | - Han-Wen Cao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, P. R. China.,Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, P. R. China
| | - Cidan Yang Ji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, P. R. China.,Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, P. R. China
| | - Xiao-Ying Chen
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, P. R. China.,Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, P. R. China
| | - Hui Jiang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, P. R. China.,Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, P. R. China
| | - Jin-Cheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, P. R. China
| | - Qiu-Mei Ji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, P. R. China.,Institute of Animal Science and Veterinary Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, P. R. China
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16
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Yu L, Zhang Y, Li M, Wang C, Lin X, Li L, Shi X, Guo C, Lin S. Comparative metatranscriptomic profiling and microRNA sequencing to reveal active metabolic pathways associated with a dinoflagellate bloom. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 699:134323. [PMID: 31522044 DOI: 10.1016/j.scitotenv.2019.134323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/05/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Harmful algal blooms (HABs) have increased as a result of global climate and environmental changes, exerting increasing impacts on the aquatic ecosystem, coastal economy, and human health. Despite great research efforts, our understanding on the drivers of HABs is still limited in part because HAB species' physiology is difficult to probe in situ. Here, we used molecular ecological analyses to characterize a dinoflagellate bloom at Xiamen Harbor, China. Prorocentrum donghaiense was identified as the culprit, which nutrient bioassays showed were not nutrient-limited. Metatranscriptome profiling revealed that P. donghaiense highly expressed genes related to N- and P-nutrient uptake, phagotrophy, energy metabolism (photosynthesis, oxidative phophorylation, and rhodopsin) and carbohydrate metabolism (glycolysis/gluconeogenesis, TCA cycle and pentose phosphate) during the bloom. Many genes in P. donghaiense were up-regulated at night, including phagotrophy and environmental communication genes, and showed active expression in mitosis. Eight microbial defense genes were up-regulated in the bloom compared with previously analyzed laboratory cultures. Furthermore, 76 P. donghaiense microRNA were identified from the bloom, and their target genes exhibited marked differences in amino acid metabolism between the bloom and cultures and the potential of up-regulated antibiotic and cell communication capabilities. These findings, consistent with and complementary to recent reports, reveal major metabolic processes in P. donghaiense potentially important for bloom formation and provide a gene repertoire for developing bloom markers in future research.
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Affiliation(s)
- Liying Yu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yaqun Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Meizhen Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Cong Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xinguo Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; College of Biological Science and Engineering, Fuzhou University, Fujian 350116, China
| | - Chentao Guo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
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17
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Mao GH, Huang XH, Geng XJ, Li Q, Zhang Y, Dou Q. Correlation between sperm mitochondrial ND5 and ND6 gene variations and total fertilisation failure. Arch Med Sci 2020; 16:692-698. [PMID: 32399119 PMCID: PMC7212212 DOI: 10.5114/aoms.2020.94658] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 08/10/2017] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION The purpose of this study was to investigate the correlation between sperm mitochondrial NADH dehydrogenase subunit 5 (ND5) and NADH dehydrogenase subunit 6 (ND6) gene variations and total fertilisation failure (TFF). MATERIAL AND METHODS A total of 232 sperm samples at the fresh in vitro fertilisation (IVF) cycle or the half-intracytoplasmic sperm injection (ICSI) cycle were collected for this retrospective controlled study on Han Chinese people between July 2011 and April 2014. Of the 232 total samples, 45 were from the IVF-TFF group and 187 were from couples with normal fertilisation (fertilisation rate > 50%). The mitochondrial ND5 and ND6 gene variations and sperm haplotypes were confirmed using nested PCR and DNA sequencing. RESULTS Ten homozygous variations were newly discovered, namely C12417T, T12441A, C12543A, C13650A, C13765A, T13769C, C13775T, A13776G, C13785A and C13845T. The gene variation rates of six sites, C12417T, C13650A, C13765A, T13769C, C13785A and C13845T, in the TFF group were significantly higher than those in the control group (p < 0.05). There were 231 heterozygous variations discovered; however, only nine heterozygous sites (12441, 12561, 12735, 13164, 13743, 13812, 13928, 14172 and 14368) had significantly higher gene variation rates than those in the control group (p < 0.05). In addition, the results showed that haplogroup C did not affect TFF (p > 0.05), and the fertilisation failure rates of haplogroup R and haplogroup D4a were both higher than those in the control group (p < 0.05). CONCLUSIONS Our results suggested that the ND5 and ND6 gene variations are correlated with TFF. Furthermore, this study indicated that haplogroup R and haplogroup D4a might be risk factors for TFF.
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Affiliation(s)
- Gen-Hong Mao
- Reproductive Medical Center, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Xiao-Hui Huang
- Reproductive Medical Center, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Xu-Jing Geng
- Reproductive Medical Center, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Qian Li
- Reproductive Medical Center, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yu Zhang
- Reproductive Medical Center, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Qian Dou
- Reproductive Medical Center, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
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Mitochondrial Bioenergetics in Brain Following Ozone Exposure in Rats Maintained on Coconut, Fish and Olive Oil-Rich Diets. Int J Mol Sci 2019; 20:ijms20246303. [PMID: 31847143 PMCID: PMC6941048 DOI: 10.3390/ijms20246303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022] Open
Abstract
Dietary supplementation with omega-3 and omega-6 fatty acids offer cardioprotection against air pollution, but these protections have not been established in the brain. We tested whether diets rich in omega-3 or -6 fatty acids offered neuroprotective benefits, by measuring mitochondrial complex enzyme I, II and IV activities and oxidative stress measures in the frontal cortex, cerebellum, hypothalamus, and hippocampus of male rats that were fed either a normal diet, or a diet enriched with fish oil olive oil, or coconut oil followed by exposure to either filtered air or ozone (0.8 ppm) for 4 h/day for 2 days. Results show that mitochondrial complex I enzyme activity was significantly decreased in the cerebellum, hypothalamus and hippocampus by diets. Complex II enzyme activity was significantly lower in frontal cortex and cerebellum of rats maintained on all test diets. Complex IV enzyme activity was significantly lower in the frontal cortex, hypothalamus and hippocampus of animals maintained on fish oil. Ozone exposure decreased complex I and II activity in the cerebellum of rats maintained on the normal diet, an effect blocked by diet treatments. While diet and ozone have no apparent influence on endogenous reactive oxygen species production, they do affect antioxidant levels in the brain. Fish oil was the only diet that ozone exposure did not alter. Microglial morphology and GFAP immunoreactivity were assessed across diet groups; results indicated that fish oil consistently decreased reactive microglia in the hypothalamus and hippocampus. These results indicate that acute ozone exposure alters mitochondrial bioenergetics in brain and co-treatment with omega-6 and omega-3 fatty acids alleviate some adverse effects within the brain.
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Priyanka K, Singh S. Applications of conjugated systems, nanomedicines, peptides and herbal drugs as mitochondrial targeted delivery systems in the treatment of oxidative stress induced diabetes. J Drug Deliv Sci Technol 2019. [DOI: 10.1016/j.jddst.2019.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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20
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Expression of mitochondrial genes predicts survival in pediatric acute myeloid leukemia. Int J Hematol 2019; 110:205-212. [DOI: 10.1007/s12185-019-02666-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/10/2019] [Accepted: 05/14/2019] [Indexed: 12/24/2022]
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21
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Xie DF, Yu HX, Price M, Xie C, Deng YQ, Chen JP, Yu Y, Zhou SD, He XJ. Phylogeny of Chinese Allium Species in Section Daghestanica and Adaptive Evolution of Allium (Amaryllidaceae, Allioideae) Species Revealed by the Chloroplast Complete Genome. FRONTIERS IN PLANT SCIENCE 2019; 10:460. [PMID: 31114591 PMCID: PMC6503222 DOI: 10.3389/fpls.2019.00460] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 03/27/2019] [Indexed: 05/25/2023]
Abstract
The genus Allium (Amaryllidaceae, Allioideae) is one of the largest monocotyledonous genera and it includes many economically important crops that are cultivated for consumption or medicinal uses. Recent advances in molecular phylogenetics have revolutionized our understanding of Allium taxonomy and evolution. However, the phylogenetic relationships in some Allium sections (such as the Allium section Daghestanica) and the genetic bases of adaptative evolution, remain poorly understood. Here, we newly assembled six chloroplast genomes from Chinese endemic species in Allium section Daghestanica and by combining these genomes with another 35 allied species, we performed a series of analyses including genome structure, GC content, species pairwise Ka/Ks ratios, and the SSR component, nucleotide diversity and codon usage. Positively selected genes (PSGs) were detected in the Allium lineage using the branch-site model. Comparison analysis of Bayesian and ML phylogeny on CCG (complete chloroplast genome), SCG (single copy genes) and CDS (coding DNA sequences) produced a well-resolved phylogeny of Allioideae plastid lineages, which illustrated several novel relationships with the section Daghestanica. In addition, six species in section Daghestanica showed highly conserved structures. The GC content and the GC3s content in Allioideae species exhibited lower values than studied non-Allioideae species, along with elevated pairwise Ka/Ks ratios. The rps2 gene was lost in all examined Allioideae species, and 10 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis, seven of them are associated with photosynthesis. Our study uncovered a new species relationship in section Daghestanica and suggested that the selective pressure has played an important role in Allium adaptation and evolution, these results will facilitate our further understanding of evolution and adaptation of species in the genus Allium.
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Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Huan-Xi Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chuan Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yi-Qi Deng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jun-Pei Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Duan L, Chen Q, Duan S. Transcriptional Analysis of Chlorella Pyrenoidosa Exposed to Bisphenol A. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16081374. [PMID: 30995802 PMCID: PMC6518184 DOI: 10.3390/ijerph16081374] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/22/2022]
Abstract
Bisphenol A (BPA) is the raw material of 71% of polycarbonate-based resins and 27% of epoxy-based resins which are used for coating metal-based food and beverage cans. Meanwhile, it is taken into account as a typical environmental pollutant. Hormesis may occur in algae exposed to BPA. In this study, the effects of BPA on Chlorella pyrenoidosa were assessed based on growth inhibition and transcriptome analysis. We have focused on two exposure scenarios as follows: (1) exposure to a low stimulation concentration (0.1 mg.L−1, 19.35% promotion in cell density on the 3rd day); (2) exposure to a high inhibition concentration (10 mg.L−1, 64.71% inhibition in cell density on the 3rd day). Transcriptome analysis showed enrichment in nucleotide transport, single-organism transport, cellular respiration. Among them, adenosine triphosphate (ATP) synthase and Nicotinamide adenine dinucleotide (NADH) dehydrogenase were upregulated under 0.1 mg.L−1 BPA treatment. These changes enhanced the physiological and energy metabolic pathways of C. pyrenoidosa, thereby stimulating cell proliferation. At exposure to the high BPA, severe inhibited changes in the expression levels of several pathways were observed, which were related to tricarboxylic acid (TCA) cycle, glycolysis, fatty acid metabolism, oxidative phosphorylation, and photosynthesis. Therefore, BPA could negatively affect growth inhibition through the multiple energy metabolism processes. These results may result in a deeper insight into BPA-induced biphasic responses in algae, and provide vital information to assess the potential ecological risks of exposure to BPA in an aquatic ecosystem.
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Affiliation(s)
- Leyi Duan
- Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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23
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Valdez JM, Johnstone AFM, Richards JE, Schmid JE, Royland JE, Kodavanti PRS. Interaction of Diet and Ozone Exposure on Oxidative Stress Parameters within Specific Brain Regions of Male Brown Norway Rats. Int J Mol Sci 2018; 20:ijms20010011. [PMID: 30577502 PMCID: PMC6337237 DOI: 10.3390/ijms20010011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/29/2018] [Accepted: 12/18/2018] [Indexed: 12/18/2022] Open
Abstract
Oxidative stress (OS) contributes to the neurological and cardio/pulmonary effects caused by adverse metabolic states and air pollutants such as ozone (O3). This study explores the interactive effects of O3 and diet (high-fructose (FRUC) or high–fat (FAT)) on OS in different rat brain regions. In acute exposure, there was a decrease in markers of reactive oxygen species (ROS) production in some brain regions by diet and not by O3. Total antioxidant substances (TAS) were increased in the cerebellum (CER) and frontal cortex (FC) and decreased in the striatum (STR) by both diets irrespective of O3 exposure. Protein carbonyls (PC) and total aconitase decreased in some brain regions irrespective of exposure. Following subacute exposure, an increase in markers of ROS was observed in both diet groups. TAS was increased in the FC (FAT only) and there was a clear O3 effect where TAS was increased in the FC and STR. Diet increased PC formation within the CER in the FAT group, while the hippocampus showed a decrease in PC after O3 exposure in controls. In general, these results indicate that diet/O3 did not have a global effect on brain OS parameters, but showed some brain region- and OS parameter-specific effects by diets.
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Affiliation(s)
- Joseph M Valdez
- Neurotoxicology Branch, Toxicity Assessment Division, NHEERL/ORD, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Andrew F M Johnstone
- Neurotoxicology Branch, Toxicity Assessment Division, NHEERL/ORD, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Judy E Richards
- Environmental Public Health Division, NHEERL/ORD, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Judith E Schmid
- Neurotoxicology Branch, Toxicity Assessment Division, NHEERL/ORD, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Joyce E Royland
- Integrated Systems Toxicology Division, NHEERL/ORD, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| | - Prasada Rao S Kodavanti
- Neurotoxicology Branch, Toxicity Assessment Division, NHEERL/ORD, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
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24
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Ohnishi T, Ohnishi ST, Salerno JC. Five decades of research on mitochondrial NADH-quinone oxidoreductase (complex I). Biol Chem 2018; 399:1249-1264. [DOI: 10.1515/hsz-2018-0164] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/16/2018] [Indexed: 02/06/2023]
Abstract
Abstract
NADH-quinone oxidoreductase (complex I) is the largest and most complicated enzyme complex of the mitochondrial respiratory chain. It is the entry site into the respiratory chain for most of the reducing equivalents generated during metabolism, coupling electron transfer from NADH to quinone to proton translocation, which in turn drives ATP synthesis. Dysfunction of complex I is associated with neurodegenerative diseases such as Parkinson’s and Alzheimer’s, and it is proposed to be involved in aging. Complex I has one non-covalently bound FMN, eight to 10 iron-sulfur clusters, and protein-associated quinone molecules as electron transport components. Electron paramagnetic resonance (EPR) has previously been the most informative technique, especially in membrane in situ analysis. The structure of complex 1 has now been resolved from a number of species, but the mechanisms by which electron transfer is coupled to transmembrane proton pumping remains unresolved. Ubiquinone-10, the terminal electron acceptor of complex I, is detectable by EPR in its one electron reduced, semiquinone (SQ) state. In the aerobic steady state of respiration the semi-ubiquinone anion has been observed and studied in detail. Two distinct protein-associated fast and slow relaxing, SQ signals have been resolved which were designated SQNf and SQNs. This review covers a five decade personal journey through the field leading to a focus on the unresolved questions of the role of the SQ radicals and their possible part in proton pumping.
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Affiliation(s)
- Tomoko Ohnishi
- Department of Biochemistry and Biophysics , Perelman School of Medicine at University of Pennsylvania , Philadelphia, PA 19104 , USA
| | | | - John C. Salerno
- Cell and Molecular Biology Department , Kennesaw State University , Kennesaw, GA 30144 , USA
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25
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Identification and characterization two isoforms of NADH:ubiquinone oxidoreductase from the hyperthermophilic eubacterium Aquifex aeolicus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:366-373. [DOI: 10.1016/j.bbabio.2018.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 02/18/2018] [Accepted: 02/24/2018] [Indexed: 12/20/2022]
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26
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Kang JW, Kim SS, Kang DH. Inactivation dynamics of 222 nm krypton-chlorine excilamp irradiation on Gram-positive and Gram-negative foodborne pathogenic bacteria. Food Res Int 2018; 109:325-333. [PMID: 29803456 DOI: 10.1016/j.foodres.2018.04.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/02/2018] [Accepted: 04/12/2018] [Indexed: 11/29/2022]
Abstract
The object of this study was to elucidate the bactericidal mechanism of a 222 nm Krypton Chlorine (KrCl) excilamp compared with that of a 254 nm Low Pressure mercury (LP Hg) lamp. The KrCl excilamp had higher bactericidal capacity against Gram-positive pathogenic bacteria (Staphylococcus aureus and L. monocytogenes) and Gram-negative pathogenic bacteria (S. Typhimurium and E. coli O157:H7) than did the LP Hg lamp when cell suspensions in PBS were irradiated with each type of UV lamp. It was found out that the KrCl excilamp induced cell membrane damage as a form of depolarization. From the study of respiratory chain dehydrogenase activity and the lipid peroxidation assay, it was revealed that cell membrane damage was attributed to inactivation of enzymes related to generation of membrane potential and occurrence of lipid peroxidation. Direct absorption of UV radiation which led to photoreaction through formation of an excited state was one of the causes inducing cell damage. Additionally, generation of ROS and thus occurrence of secondary damage can be another cause. The LP Hg lamp only induced damage to DNA but not to other components such as lipids or proteins. This difference was derived from differences of UV radiation absorption by cellular materials.
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Affiliation(s)
- Jun-Won Kang
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Institutes of Green Bio Science & Technology, Seoul National University, Pyeongchang-gun, Gangwon-do 25354, Republic of Korea
| | - Sang-Soon Kim
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Institutes of Green Bio Science & Technology, Seoul National University, Pyeongchang-gun, Gangwon-do 25354, Republic of Korea
| | - Dong-Hyun Kang
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Institutes of Green Bio Science & Technology, Seoul National University, Pyeongchang-gun, Gangwon-do 25354, Republic of Korea.
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27
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Martínez de Castro DL, García-Gómez BI, Gómez I, Bravo A, Soberón M. Identification of Bacillus thuringiensis Cry1AbMod binding-proteins from Spodoptera frugiperda. Peptides 2017; 98:99-105. [PMID: 28958733 DOI: 10.1016/j.peptides.2017.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/06/2017] [Accepted: 09/22/2017] [Indexed: 12/12/2022]
Abstract
Bacillus thuringiensis Cry toxins are currently used for pest control in transgenic crops but evolution of resistance by the insect pests threatens the use of this technology. The Cry1AbMod toxin was engineered to lack the alpha helix-1 of the parental Cry1Ab toxin and was shown to counter resistance to Cry1Ab and Cry1Ac toxins in different insect species including the fall armyworm Spodoptera frugiperda. In addition, Cry1AbMod showed enhanced toxicity to Cry1Ab-susceptible S. frugiperda populations. To gain insights into the mechanisms of this Cry1AbMod-enhanced toxicity, we isolated the Cry1AbMod toxin binding proteins from S. frugiperda brush border membrane vesicles (BBMV), which were identified by pull-down assay and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The LC-MS/MS results indicated that Cry1AbMod toxin could bind to four classes of aminopeptidase (N1, N3, N4 y N5) and actin, with the highest amino acid sequence coverage acquired for APN 1 and APN4. In addition to these proteins, we found other proteins not previously described as Cry toxin binding proteins. This is the first report that suggests the interaction between Cry1AbMod and APN in S. frugiperda.
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Affiliation(s)
- Diana L Martínez de Castro
- Instituto de Biotecnología, Universidad Nacional Autónoma de México. Apdo. Postal 510-3, Cuernavaca, 62250 Morelos, Mexico
| | - Blanca I García-Gómez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México. Apdo. Postal 510-3, Cuernavaca, 62250 Morelos, Mexico
| | - Isabel Gómez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México. Apdo. Postal 510-3, Cuernavaca, 62250 Morelos, Mexico
| | - Alejandra Bravo
- Instituto de Biotecnología, Universidad Nacional Autónoma de México. Apdo. Postal 510-3, Cuernavaca, 62250 Morelos, Mexico
| | - Mario Soberón
- Instituto de Biotecnología, Universidad Nacional Autónoma de México. Apdo. Postal 510-3, Cuernavaca, 62250 Morelos, Mexico.
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Shen C, Li M, Zhang P, Guo Y, Zhang H, Zheng B, Teng H, Zhou T, Guo X, Huo R. A Comparative Proteome Profile of Female Mouse Gonads Suggests a Tight Link between the Electron Transport Chain and Meiosis Initiation. Mol Cell Proteomics 2017; 17:31-42. [PMID: 29158290 DOI: 10.1074/mcp.m117.066993] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 08/24/2017] [Indexed: 01/23/2023] Open
Abstract
Generation of haploid gametes by meiosis is a unique property of germ cells and is critical for sexual reproduction. Leaving mitosis and entering meiosis is a key step in germ cell development. Several inducers or intrinsic genes are known to be important for meiotic initiation, but the regulation of meiotic initiation, especially at the protein level, is still not well understood. We constructed a comparative proteome profile of female mouse fetal gonads at specific time points (11.5, 12.5, and 13.5 days post coitum), spanning a critical window for initiation of meiosis in female germ cells. We identified 3666 proteins, of which 473 were differentially expressed. Further bioinformatics analysis showed that these differentially expressed proteins were enriched in the mitochondria, especially in the electron transport chain and, notably, 9 proteins in electron transport chain Complex I were differentially expressed. We disrupted the mitochondrial electron transport chain function by adding the complex I inhibitor, rotenone to 11.5 days post coitum female gonads cultured in vitro. This treatment resulted in a decreased proportion of meiotic germ cells, as assessed by staining for histone γH2AX. Rotenone treatment also caused decreased ATP levels, increased reactive oxygen species levels and failure of the germ cells to undergo premeiotic DNA replication. These effects were partially rescued by adding Coenzyme Q10. Taken together, our results suggested that a functional electron transport chain is important for meiosis initiation. Our characterization of the quantitative proteome of female gonads provides an inventory of proteins, useful for understanding the mechanisms of meiosis initiation and female fertility.
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Affiliation(s)
- Cong Shen
- From the ‡State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, P.R. China.,§Center for Reproduction and Genetics, Suzhou Municipal Hospital, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou 215002, P.R. China
| | - Mingrui Li
- From the ‡State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, P.R. China
| | - Pan Zhang
- From the ‡State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, P.R. China
| | - Yueshuai Guo
- From the ‡State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, P.R. China
| | - Hao Zhang
- From the ‡State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, P.R. China
| | - Bo Zheng
- From the ‡State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, P.R. China.,§Center for Reproduction and Genetics, Suzhou Municipal Hospital, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou 215002, P.R. China
| | - Hui Teng
- From the ‡State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, P.R. China
| | - Tao Zhou
- From the ‡State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, P.R. China
| | - Xuejiang Guo
- From the ‡State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, P.R. China;
| | - Ran Huo
- From the ‡State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, P.R. China;
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Sedlak E, Musatov A. Inner mechanism of protection of mitochondrial electron-transfer proteins against oxidative damage. Focus on hydrogen peroxide decomposition. Biochimie 2017; 142:152-157. [DOI: 10.1016/j.biochi.2017.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/06/2017] [Indexed: 11/25/2022]
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30
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Laskowski D, Båge R, Humblot P, Andersson G, Sirard MA, Sjunnesson Y. Insulin during in vitro oocyte maturation has an impact on development, mitochondria, and cytoskeleton in bovine day 8 blastocysts. Theriogenology 2017; 101:15-25. [DOI: 10.1016/j.theriogenology.2017.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 05/30/2017] [Accepted: 06/04/2017] [Indexed: 01/07/2023]
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31
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Senkler J, Senkler M, Braun HP. Structure and function of complex I in animals and plants - a comparative view. PHYSIOLOGIA PLANTARUM 2017; 161:6-15. [PMID: 28261805 DOI: 10.1111/ppl.12561] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 06/06/2023]
Abstract
The mitochondrial NADH dehydrogenase complex (complex I) has a molecular mass of about 1000 kDa and includes 40-50 subunits in animals, fungi and plants. It is composed of a membrane arm and a peripheral arm and has a conserved L-like shape in all species investigated. However, in plants and possibly some protists it has a second peripheral domain which is attached to the membrane arm on its matrix exposed side at a central position. The extra domain includes proteins resembling prokaryotic gamma-type carbonic anhydrases. We here present a detailed comparison of complex I from mammals and flowering plants. Forty homologous subunits are present in complex I of both groups of species. In addition, five subunits are present in mammalian complex I, which are absent in plants, and eight to nine subunits are present in plant complex I which do not occur in mammals. Based on the atomic structure of mammalian complex I and biochemical insights into complex I architecture from plants we mapped the species-specific subunits. Interestingly, four of the five animal-specific and five of the eight to nine plant-specific subunits are localized at the inner surface of the membrane arm of complex I in close proximity. We propose that the inner surface of the membrane arm represents a workbench for attaching proteins to complex I, which are not directly related to respiratory electron transport, like nucleoside kinases, acyl-carrier proteins or carbonic anhydrases. We speculate that further enzyme activities might be bound to this micro-location in other groups of organisms.
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Affiliation(s)
- Jennifer Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, 30419, Germany
| | - Michael Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, 30419, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, 30419, Germany
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Yuan CC, Kazmierczak K, Liang J, Kanashiro-Takeuchi R, Irving TC, Gomes AV, Wang Y, Burghardt TP, Szczesna-Cordary D. Hypercontractile mutant of ventricular myosin essential light chain leads to disruption of sarcomeric structure and function and results in restrictive cardiomyopathy in mice. Cardiovasc Res 2017; 113:1124-1136. [PMID: 28371863 PMCID: PMC5852631 DOI: 10.1093/cvr/cvx060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 02/02/2017] [Accepted: 03/22/2017] [Indexed: 01/13/2023] Open
Abstract
AIMS The E143K (Glu → Lys) mutation in the myosin essential light chain has been associated with restrictive cardiomyopathy (RCM) in humans, but the mechanisms that underlie the development of defective cardiac function are unknown. Using transgenic E143K-RCM mice, we sought to determine the molecular and cellular triggers of E143K-induced heart remodelling. METHODS AND RESULTS The E143K-induced abnormalities in cardiac function and morphology observed by echocardiography and invasive haemodynamics were paralleled by augmented active and passive tension measured in skinned papillary muscle fibres compared with wild-type (WT)-generated force. In vitro, E143K-myosin had increased duty ratio and binding affinity to actin compared with WT-myosin, increased actin-activated ATPase activity and slower rates of ATP-dependent dissociation of the acto-myosin complex, indicating an E143K-induced myosin hypercontractility. E143K was also observed to reduce the level of myosin regulatory light chain phosphorylation while that of troponin-I remained unchanged. Small-angle X-ray diffraction data showed a decrease in the filament lattice spacing (d1,0) with no changes in the equatorial reflections intensity ratios (I1,1/I1,0) in E143K vs. WT skinned papillary muscles. The hearts of mutant-mice demonstrated ultrastructural defects and fibrosis that progressively worsened in senescent animals and these changes were hypothesized to contribute to diastolic disturbance and to mild systolic dysfunction. Gene expression profiles of E143K-hearts supported the histopathology results and showed an upregulation of stress-response and collagen genes. Finally, proteomic analysis evidenced RCM-dependent metabolic adaptations and higher energy demands in E143K vs. WT hearts. CONCLUSIONS As a result of the E143K-induced myosin hypercontractility, the hearts of RCM mice model exhibited cardiac dysfunction, stiff ventricles and physiological, morphologic, and metabolic remodelling consistent with the development of RCM. Future efforts should be directed toward normalization of myosin motor function and the use of myosin-specific therapeutics to avert the hypercontractile state of E143K-myosin and prevent pathological cardiac remodelling.
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MESH Headings
- Actins/metabolism
- Adenosine Triphosphate/metabolism
- Animals
- Cardiomyopathy, Restrictive/genetics
- Cardiomyopathy, Restrictive/metabolism
- Cardiomyopathy, Restrictive/pathology
- Cardiomyopathy, Restrictive/physiopathology
- Collagen/metabolism
- Disease Models, Animal
- Energy Metabolism
- Female
- Fibrosis
- Genetic Predisposition to Disease
- Humans
- Male
- Mice, Transgenic
- Mutation
- Myocardial Contraction/genetics
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Myocytes, Cardiac/ultrastructure
- Myosin Light Chains/genetics
- Myosin Light Chains/metabolism
- Phenotype
- Phosphorylation
- Sarcomeres/metabolism
- Sarcomeres/pathology
- Sarcomeres/ultrastructure
- Ventricular Function, Left/genetics
- Ventricular Myosins/genetics
- Ventricular Myosins/metabolism
- Ventricular Remodeling/genetics
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Affiliation(s)
- Chen-Ching Yuan
- Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Katarzyna Kazmierczak
- Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jingsheng Liang
- Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | | | | | - Aldrin V. Gomes
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA 95616, USA
| | - Yihua Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, Rochester, MN 55905, USA
| | - Thomas P. Burghardt
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, Rochester, MN 55905, USA
| | - Danuta Szczesna-Cordary
- Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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33
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Liu L, Xu QM, Chen T, Cheng JS, Yuan YJ. Artificial consortium that produces riboflavin regulates distribution of acetoin and 2,3-butanediol by Paenibacillus polymyxa CJX518. Eng Life Sci 2017; 17:1039-1049. [PMID: 32624854 DOI: 10.1002/elsc.201600239] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 05/23/2017] [Accepted: 05/29/2017] [Indexed: 11/09/2022] Open
Abstract
The introduction of an NADH/NAD+ regeneration system can regulate the distribution between acetoin and 2,3-butanediol. NADH regeneration can also enhance butanol production in coculture fermentation. In this work, a novel artificial consortium of Paenibacillus polymyxa CJX518 and recombinant Escherichia coli LS02T that produces riboflavin (VB2) was used to regulate the NADH/NAD+ ratio and, consequently, the distribution of acetoin and 2,3-butanediol by P. polymyxa. Compared with a pure culture of P. polymyxa, the level of acetoin was increased 76.7% in the P. polymyxa and recombinant E. coli coculture. Meanwhile, the maximum production and yield of acetoin in an artificial consortium with fed-batch fermentation were 57.2 g/L and 0.4 g/g glucose, respectively. Additionally, the VB2 production of recombinant E. coli could maintain a relatively low NADH/NAD+ ratio by changing NADH dehydrogenase activity. It was also found that 2,3-butanediol dehydrogenase activity was enhanced and improved acetoin production by the addition of exogenous VB2 or by being in the artificial consortium that produces VB2. These results illustrate that the coculture of P. polymyxa and recombinant E. coli has enormous potential to improve acetoin production. It was also a novel strategy to regulate the NADH/NAD+ ratio to improve the acetoin production of P. polymyxa.
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Affiliation(s)
- Lei Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China.,SynBio Research Platform Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China
| | - Qiu-Man Xu
- College of Life Science Tianjin Normal University Tianjin People's Republic of China
| | - Tao Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China.,SynBio Research Platform Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China
| | - Jing-Sheng Cheng
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China.,SynBio Research Platform Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China.,SynBio Research Platform Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin) School of Chemical Engineering and Technology Tianjin University Tianjin People's Republic of China
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Zhou T, Qin L, Zhu X, Shen W, Zou J, Wang Z, Wei Y. The D-lactate dehydrogenase MoDLD1 is essential for growth and infection-related development in Magnaporthe oryzae. Environ Microbiol 2017; 19:3938-3958. [PMID: 28654182 DOI: 10.1111/1462-2920.13794] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 04/28/2017] [Accepted: 05/04/2017] [Indexed: 12/28/2022]
Abstract
Rice blast disease caused by Magnaporthe oryzae is initiated by the attachment of conidia to plant surfaces. Germ tubes emerging from conidia develop melanized appressoria to physically penetrate the host surface. Previous studies revealed that appressorium development requires the breakdown of storage lipids and glycogen that occur in peroxisomes and the cytosol respectively, culminating in production of pyruvate. However, the downstream product(s) entering the mitochondria for further oxidation is unclear. In this study, we aimed to investigate the molecular basis underlying the metabolic flux towards the mitochondria associated with the infectious-related development in M. oryzae. We showed that D-lactate is a key intermediate metabolite of the mobilization of lipids and glycogen, and its oxidative conversion to pyruvate is catalysed by a mitochondrial D-lactate dehydrogenase MoDLD1. Deletion of MoDLD1 caused defects in conidiogenesis and appressorium formation, and subsequently the loss of fungal pathogenicity. Further analyses demonstrated that MoDLD1 activity is involved in the maintenance of redox homeostasis during conidial germination. Thus, MoDLD1 is a critical modulator that channels metabolite flow to the mitochondrion coupling cellular redox state, and contributes to development and virulence of M. oryzae.
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Affiliation(s)
- Tengsheng Zhou
- Department of Biology, College of Arts and Science, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
| | - Li Qin
- Department of Biology, College of Arts and Science, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
| | - Xiaohan Zhu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenyun Shen
- National Research Council of Canada, Plant Biotechnology Institute, Saskatoon SK, S7N 0W9, Canada
| | - Jitao Zou
- National Research Council of Canada, Plant Biotechnology Institute, Saskatoon SK, S7N 0W9, Canada
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yangdou Wei
- Department of Biology, College of Arts and Science, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
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35
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Zhang B, Zhang Y, Wang X, Zhang H, Lin Q. The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment. Ecol Evol 2017; 7:4951-4962. [PMID: 28690821 PMCID: PMC5496520 DOI: 10.1002/ece3.3067] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/13/2017] [Accepted: 04/24/2017] [Indexed: 01/14/2023] Open
Abstract
The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep‐sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein‐coding genes and two ribosomal RNAs. However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon‐like noncanonical open reading frames (ORFs), and a control region‐like (CR‐like) element. All of the mitochondrial genes were coded by the same strand (the H‐strand). The genetic order and orientation were identical to those of most sequenced actiniarians. Phylogenetic analyses showed that this species was closely related to Bolocera tuediae. Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp. were positively selected sites. By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes. This study may provide some clues regarding the adaptation of Bolocera sp. to the deep‐sea environment.
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Affiliation(s)
- Bo Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yan‐Hong Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hui‐Xian Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
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36
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Antolak A, Bodzoń-Kułakowska A, Cetnarska E, Pietruszka M, Marszałek-Grabska M, Kotlińska J, Suder P. Proteomic Data in Morphine Addiction Versus Real Protein Activity: Metabolic Enzymes. J Cell Biochem 2017; 118:4323-4330. [PMID: 28430368 DOI: 10.1002/jcb.26085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 04/20/2017] [Indexed: 01/01/2023]
Abstract
Drug dependence is an escalating problem worldwide and many efforts are being made to understand the molecular basis of addiction. The morphine model is widely used in these investigations. To date, at least 29 studies exploring the influence of morphine on mammals' proteomes have been published. Among various proteins indicated as up- or down-regulated, the expression changes of enzymes engaged in energy metabolism pathways have often been confirmed. To verify whether proteomics-indicated alterations in enzyme levels reflect changes in their activity, four enzymes: PK, MDH, Complex I, and Complex V were investigated in morphine addiction and abstinence models. After analyses of the rat brain mitochondria fraction in the model of morphine dependence, we found that one of the investigated enzymes (pyruvate kinase) showed statistically significant differences observed between morphine, control, and abstinence groups. J. Cell. Biochem. 118: 4323-4330, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Anna Antolak
- Faculty of Materials Science and Technology, Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Cracow, Poland
| | - Anna Bodzoń-Kułakowska
- Faculty of Materials Science and Technology, Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Cracow, Poland
| | - Ewa Cetnarska
- Faculty of Materials Science and Technology, Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Cracow, Poland
| | - Monika Pietruszka
- Faculty of Materials Science and Technology, Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Cracow, Poland
| | - Marta Marszałek-Grabska
- Faculty of Pharmacy, Departament of Pharmacology and Pharmacodynamics, Medical University of Lublin, Lublin, Poland
| | - Jolanta Kotlińska
- Faculty of Materials Science and Technology, Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Cracow, Poland
| | - Piotr Suder
- Faculty of Materials Science and Technology, Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Cracow, Poland
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37
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Yang JA, Stires H, Belden WJ, Roepke TA. The Arcuate Estrogen-Regulated Transcriptome: Estrogen Response Element-Dependent and -Independent Signaling of ERα in Female Mice. Endocrinology 2017; 158:612-626. [PMID: 28359086 PMCID: PMC5460777 DOI: 10.1210/en.2016-1663] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 12/29/2016] [Indexed: 01/14/2023]
Abstract
To influence energy homeostasis and reproduction, 17β-estradiol (E2) controls the arcuate nucleus (ARC) through multiple receptor-mediated mechanisms, but primarily via estrogen receptor (ER) α, which signals through both estrogen response element (ERE)-dependent and -independent mechanisms. To determine ERα-mediated, ERE-dependent, and ERE-independent E2 signaling in the ARC, we examined the differential regulation of the mouse arcuate transcriptome by E2 using three mice genotypes: (1) wild-type, (2) ERα knock-in/knockout (ERE-independent mechanisms), and (3) total ERα knockout (ERα-independent mechanisms). Females were ovariectomized and injected with oil or E2, and RNA sequencing on the ARC was used to identify E2-regulated genes in each genotype. Our results show that E2 regulates numerous genes involved in cell signaling, cytoskeleton structure, inflammation, neurotransmission, neuropeptide production, and transcription. Furthermore, ERE-independent signaling regulates ARC genes expressed in kisspeptin neurons and transcription factors that control the hypothalamic/pituitary/gonadal axis. Interestingly, a few genes involved in mitochondrial oxidative respiration were regulated by E2 through ERα-independent signaling. A comparison within oil- and E2-treated females across the three genotypes suggests that genes involved in cell growth and proliferation, extracellular matrices, neuropeptides, receptors, and transcription are differentially expressed across the genotypes. Comparing with previously published chromatin immunoprecipitation sequencing analysis, we found that ERE-independent regulation in the ARC is mainly mediated by tethering of ERα, which is consistent with previous findings. We conclude that the mouse arcuate estrogen-regulated transcriptome is regulated by multiple receptor-mediated mechanisms to modulate the central control of energy homeostasis and reproduction, including novel E2-responsive pathways.
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Affiliation(s)
- Jennifer A Yang
- Department of Animal Sciences and Program in Endocrinology and Animal Biosciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Hillary Stires
- Department of Animal Sciences and Program in Endocrinology and Animal Biosciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - William J Belden
- Department of Animal Sciences and Program in Endocrinology and Animal Biosciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Troy A Roepke
- Department of Animal Sciences and Program in Endocrinology and Animal Biosciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
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38
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Casaletti L, Lima PS, Oliveira LN, Borges CL, Báo SN, Bailão AM, Soares CMA. Analysis of Paracoccidioides lutzii mitochondria: a proteomic approach. Yeast 2017; 34:179-188. [PMID: 27886402 DOI: 10.1002/yea.3225] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 11/16/2016] [Accepted: 11/20/2016] [Indexed: 01/21/2023] Open
Abstract
The genus Paracoccidioides is composed of thermal dimorphic fungi, causative agents of paracoccidioidomycosis, one of the most frequent systemic mycoses in Latin America. Mitochondria have sophisticated machinery for ATP production, which involves metabolic pathways such as citric acid and glyoxylate cycles, electron transport chain and oxidative phosphorylation. In addition, this organelle performs a variety of functions in the cell, working as an exceptional metabolic signalling centre that contributes to cellular stress responses, as autophagy and apoptosis in eukaryotic organisms. The aim of this work was to perform a descriptive proteomic analysis of mitochondria in Paracoccidioides lutzii yeast cells. After mitochondria fractionation, samples enriched in mitochondrial proteins were digested with trypsin and analysed using a NanoUPLC-MSE system (Waters Corporation, Manchester, UK). Ours results revealed that the established protocol for purification of mitochondria was very effective for P. lutzii, and 298 proteins were identified as primarily mitochondrial, in our analysis. To our knowledge, this is the first compilation of mitochondrial proteins from P. lutzii, to date. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- L Casaletti
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil.,Escola de Engenharia, Pontifícia Universidade Católica de Goiás, 74605-010, Goiânia, Goiás, Brazil
| | - P S Lima
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil
| | - L N Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil.,Programa de Pós-graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, 70910-900, Brasília, Distrito Federal, Brazil
| | - C L Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil
| | - S N Báo
- Laboratório de Microscopia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, 70910-900, Brasília, Distrito Federal, Brazil
| | - A M Bailão
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil
| | - C M A Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICBII, Campus II, Universidade Federal de Goiás, 74001-970, Goiânia, Goiás, Brazil
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39
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Liu Q, Lan Y, Wen C, Zhao H, Wang J, Wang Y. Transcriptome Sequencing Analyses between the Cytoplasmic Male Sterile Line and Its Maintainer Line in Welsh Onion (Allium fistulosum L.). Int J Mol Sci 2016; 17:ijms17071058. [PMID: 27376286 PMCID: PMC4964434 DOI: 10.3390/ijms17071058] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 11/28/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is important for exploiting heterosis in crop plants and also serves as a model for investigating nuclear–cytoplasmic interaction. The molecular mechanism of cytoplasmic male sterility and fertility restoration was investigated in several important economic crops but remains poorly understood in the Welsh onion. Therefore, we compared the differences between the CMS line 64-2 and its maintainer line 64-1 using transcriptome sequencing with the aim of determining critical genes and pathways associated with male sterility. This study combined two years of RNA-seq data; there were 1504 unigenes (in May 2013) and 2928 unigenes (in May 2014) that were differentially expressed between the CMS and cytoplasmic male maintainer Welsh onion varieties. Known CMS-related genes were found in the set of differentially expressed genes and checked by qPCR. These genes included F-type ATPase, NADH dehydrogenase, cytochrome c oxidase, etc. Overall, this study demonstrated that the CMS regulatory genes and pathways may be associated with the mitochondria and nucleus in the Welsh onion. We believe that this transcriptome dataset will accelerate the research on CMS gene clones and other functional genomics research on A. fistulosum L.
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Affiliation(s)
- Qianchun Liu
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China.
| | - Yanping Lan
- Institute of Agricultural Integrated Development, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Changlong Wen
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China.
| | - Hong Zhao
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China.
| | - Jian Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China.
| | - Yongqin Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China.
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40
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Fromm S, Senkler J, Zabaleta E, Peterhänsel C, Braun HP. The carbonic anhydrase domain of plant mitochondrial complex I. PHYSIOLOGIA PLANTARUM 2016; 157:289-296. [PMID: 26829901 DOI: 10.1111/ppl.12424] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/06/2015] [Accepted: 12/15/2015] [Indexed: 06/05/2023]
Abstract
The mitochondrial NADH dehydrogenase complex (complex I) consists of several functional domains which independently arose during evolution. In higher plants, it contains an additional domain which includes proteins resembling gamma-type carbonic anhydrases. The Arabidopsis genome codes for five complex I-integrated gamma-type carbonic anhydrases (γCA1, γCA2, γCA3, γCAL1, γCAL2), but only three copies of this group of proteins form an individual extra domain. Biochemical analyses revealed that the domain is composed of one copy of either γCAL1 or γCAL2 plus two copies of the γCA1/γCA2 proteins. Thus, the carbonic anhydrase domain can have six distinct subunit configurations. Single and double mutants with respect to the γCA/γCAL proteins were employed to genetically dissect the function of the domain. New insights into complex I biology in plants will be reviewed and discussed.
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Affiliation(s)
- Steffanie Fromm
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, 30419, Germany
- Institut für Botanik, Leibniz Universität Hannover, Hannover, 30419, Germany
| | - Jennifer Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, 30419, Germany
| | - Eduardo Zabaleta
- Instituto de Investigaciones Biológicas IIB, CONICET, National University of Mar del Plata, Mar del Plata, 7600, Argentina
| | | | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, 30419, Germany
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41
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Pinske C, Sargent F. Exploring the directionality of Escherichia coli formate hydrogenlyase: a membrane-bound enzyme capable of fixing carbon dioxide to organic acid. Microbiologyopen 2016; 5:721-737. [PMID: 27139710 PMCID: PMC5061711 DOI: 10.1002/mbo3.365] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/14/2016] [Accepted: 03/23/2016] [Indexed: 12/31/2022] Open
Abstract
During mixed‐acid fermentation Escherichia coli produces formate, which is initially excreted out the cell. Accumulation of formate, and dropping extracellular pH, leads to biosynthesis of the formate hydrogenlyase (FHL) complex. FHL consists of membrane and soluble domains anchored within the inner membrane. The soluble domain comprises a [NiFe] hydrogenase and a formate dehydrogenase that link formate oxidation directly to proton reduction with the release of CO2 and H2. Thus, the function of FHL is to oxidize excess formate at low pH. FHL subunits share identity with subunits of the respiratory Complex I. In particular, the FHL membrane domain contains subunits (HycC and HycD) that are homologs of NuoL/M/N and NuoH, respectively, which have been implicated in proton translocation. In this work, strain engineering and new assays demonstrate unequivocally the nonphysiological reverse activity of FHL in vivo and in vitro. Harnessing FHL to reduce CO2 to formate is biotechnologically important. Moreover, assays for both possible FHL reactions provide opportunities to explore the bioenergetics using biochemical and genetic approaches. Comprehensive mutagenesis of hycC did not identify any single amino acid residues essential for FHL operation. However, the HycD E199, E201, and E203 residues were found to be critically important for FHL function.
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Affiliation(s)
- Constanze Pinske
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, Scotland, DD1 5EH, United Kingdom
| | - Frank Sargent
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, Scotland, DD1 5EH, United Kingdom.
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Candas D, Qin L, Fan M, Li JJ. Experimental Approaches to Study Mitochondrial Localization and Function of a Nuclear Cell Cycle Kinase, Cdk1. J Vis Exp 2016:53417. [PMID: 26967001 DOI: 10.3791/53417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Although mitochondria possess their own transcriptional machinery, merely 1% of mitochondrial proteins are synthesized inside the organelle. The nuclear-encoded proteins are transported into mitochondria guided by their mitochondria targeting sequences (MTS); however, a majority of mitochondrial localized proteins lack an identifiable MTS. Nevertheless, the fact that MTS can instruct proteins to go into the mitochondria provides a valuable tool for studying mitochondrial functions of normally nuclear and/or cytoplasmic proteins. We have recently identified the cell cycle kinase CyclinB1/Cdk1 complex in the mitochondria. To specifically study the mitochondrial functions of this complex, mitochondrial overexpression and knock-down of this complex without interfering with its nuclear or cytoplasmic functions were essential. By tagging CyclinB1/Cdk1 with MTS, we were able to achieve mitochondrial overexpression of this complex to study its mitochondrial targets as well as functions. Via tagging dominant-negative Cdk1 with MTS, inhibition of Cdk1 activity was accomplished particularly in the mitochondria. Potential mitochondrial targets of CyclinB1/Cdk1 complex were identified using a gel-based proteomics approach. Unlike traditional 2D gel analysis, we employed 2-dimensional difference gel electrophoresis (2D-DIGE) technology followed by phosphoprotein staining to fluorescently label differentially phosphorylated proteins in mitochondrial Cdk1 expressing cells. Identification of phosphoprotein spots that were altered in wild type versus dominant negative Cdk1 bearing mitochondria revealed the identity of mitochondrial targets of Cdk1. Finally, to determine the effect of CyclinB1/Cdk1 mitochondrial localization in cell cycle progression, a cell proliferation assay using a synthetic thymidine analogue EdU (5-ethynyl-2'-deoxyuridine) was used to monitor the cells as they go through the cell cycle and replicate their DNA. Altogether, we demonstrated a variety of approaches available to study mitochondrial localization and activity of a cell cycle kinase. These are advanced, yet easy to follow methods that will be beneficial to many cell biology researchers.
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Affiliation(s)
- Demet Candas
- Radiation Oncology, University of California, Davis;
| | - Lili Qin
- Radiation Oncology, University of California, Davis
| | - Ming Fan
- Radiation Oncology, University of California, Davis
| | - Jian-Jian Li
- Radiation Oncology, University of California, Davis
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Friedrich T, Dekovic DK, Burschel S. Assembly of the Escherichia coli NADH:ubiquinone oxidoreductase (respiratory complex I). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:214-23. [PMID: 26682761 DOI: 10.1016/j.bbabio.2015.12.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 12/03/2015] [Accepted: 12/07/2015] [Indexed: 12/13/2022]
Abstract
Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, couples the electron transfer from NADH to ubiquinone with the translocation of four protons across the membrane. The Escherichia coli complex I is made up of 13 different subunits encoded by the so-called nuo-genes. The electron transfer is catalyzed by nine cofactors, a flavin mononucleotide and eight iron-sulfur (Fe/S)-clusters. The individual subunits and the cofactors have to be assembled together in a coordinated way to guarantee the biogenesis of the active holoenzyme. Only little is known about the assembly of the bacterial complex compared to the mitochondrial one. Due to the presence of so many Fe/S-clusters the assembly of complex I is intimately connected with the systems responsible for the biogenesis of these clusters. In addition, a few other proteins have been reported to be required for an effective assembly of the complex in other bacteria. The proposed role of known bacterial assembly factors is discussed and the information from other bacterial species is used in this review to draw an as complete as possible model of bacterial complex I assembly. In addition, the supramolecular organization of the complex in E. coli is briefly described. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Prof. Conrad Mullineaux.
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Affiliation(s)
- Thorsten Friedrich
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, 79104 Freiburg i. Br., Germany; Spemann Graduate School of Biology and Medicine, Albertstr. 19A, 79104 Freiburg i. Br., Germany.
| | - Doris Kreuzer Dekovic
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, 79104 Freiburg i. Br., Germany; Spemann Graduate School of Biology and Medicine, Albertstr. 19A, 79104 Freiburg i. Br., Germany
| | - Sabrina Burschel
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, 79104 Freiburg i. Br., Germany
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Zhang J, Zhu L, Huang X, Xu P, Chen Z, Huang Q, Zhang X. Mitochondrial DNA Haplogroup R Confers a Genetic Risk Factor for Intrauterine Adhesion in Han Women Population. Gynecol Obstet Invest 2015; 81:238-43. [PMID: 26465877 DOI: 10.1159/000439531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/12/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND To determine whether a specific mitochondrial DNA (mtDNA) haplogroup is implicated in the pathogenesis of intrauterine adhesion (IUA). METHODS Peripheral blood samples were collected from 486 women with (case group, n = 154) and without IUA (control group, n = 332) at the Women's Hospital, Zhejiang University School of Medicine. Genomic DNA was extracted from the blood, and the mtDNA haplogroups of Han women M, N and R were determined by sequencing hypervariable mtDNA segments and testing diagnostic polymorphisms in the mtDNA coding region. RESULTS Women with mtDNA haplogroup R had an independently increased genetic risk factor for IUA with an OR 1.77 (95% CI 1.16-2.70, p = 0.009) compared with women without. Moreover, repeated intrauterine surgery within 1 month and number of intrauterine operations were both significantly associated with IUA (p < 0.001). CONCLUSIONS These results suggest that mtDNA haplogroup R, one of the main mtDNA haplogroups in Han population, is a strong independent genetic risk factor for women with IUA.
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Affiliation(s)
- Jing Zhang
- Department of Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Kodavanti PRS, Royland JE, Moore-Smith DA, Besas J, Richards JE, Beasley TE, Evansky P, Bushnell PJ. Acute and subchronic toxicity of inhaled toluene in male Long-Evans rats: Oxidative stress markers in brain. Neurotoxicology 2015; 51:10-9. [PMID: 26343380 DOI: 10.1016/j.neuro.2015.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/31/2015] [Accepted: 09/01/2015] [Indexed: 10/23/2022]
Abstract
The effects of exposure to volatile organic compounds (VOCs), which are of concern to the EPA, are poorly understood, in part because of insufficient characterization of how human exposure duration impacts VOC effects. Two inhalation studies with multiple endpoints, one acute and one subchronic, were conducted to seek effects of the VOC, toluene, in rats and to compare the effects between acute and subchronic exposures. Adult male Long-Evans rats were exposed to toluene vapor (n=6 per group) at a concentration of 0 or 1019 ± 14 ppm for 6h in the acute study and at 0 ± 0, 10 ± 1.4, 97 ± 7, or 995 ± 43 ppm for 6h/d, 5d/week for 13 weeks in the subchronic study. For the acute study, brains were dissected on ice within 30 min of the end of exposure, while for the subchronic study, brains were dissected 18 h after the last exposure. Frontal cortex, hippocampus, cerebellum, and striatum were assayed for a variety of oxidative stress (OS) parameters including total aconitase (TA), protein carbonyls, glutathione peroxidase (GPX), glutathione reductase (GRD), glutathione transferase (GST), γ-glutamylcysteine synthetase (GCS), superoxide dismutase (SOD), total antioxidants (TAS), NADPH quinone oxidoreductase-1 (NQO1), and NADH ubiquinone reductase (UBIQ-RD) activities using commercially available kits. Following acute exposure, UBIQ-RD, GCS and GRD were increased significantly only in the cerebellum, while TAS was increased in frontal cortex. On the other hand, subchronic exposure affected several OS markers including increases in NQO1 and UBIQ-RD. The effect of subchronic toluene exposure on SOD and TAS was greater in the striatum than in the other brain regions. TA activity (involved in maintaining iron homeostasis and an indicator of DNA damage) was inhibited in striatum and cerebellum, increased in hippocampus, and unchanged in frontal cortex. Protein carbonyls increased significantly in both the frontal cortex and cerebellum. In general, the results showed that acute exposure to toluene affected OS parameters to a lesser extent than did subchronic exposure. These results suggest that toluene exposure induces OS in the brain and this may be a component of an adverse outcome pathway for some of the neurotoxic effects reported following toluene exposure.
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Affiliation(s)
- Prasada Rao S Kodavanti
- Neurotoxicology Branch, NHEERL, ORD, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA.
| | - Joyce E Royland
- Genetic and Cellular Toxicology Branch, NHEERL, ORD, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Debra A Moore-Smith
- Neurotoxicology Branch, NHEERL, ORD, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Jonathan Besas
- Neurotoxicology Branch, NHEERL, ORD, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Judy E Richards
- Cardiopulmonary and Immunotoxicology Branch, NHEERL, ORD, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Tracey E Beasley
- Neurotoxicology Branch, NHEERL, ORD, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Paul Evansky
- Inhalation Toxicology Facility, NHEERL, ORD, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Philip J Bushnell
- Neurotoxicology Branch, NHEERL, ORD, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
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Kohlstädt M, Dörner K, Labatzke R, Koç C, Heilscher R, Schiltz E, Einsle O, Hellwig P, Friedrich T. Heterologous production, isolation, characterization and crystallization of a soluble fragment of the NADH:ubiquinone oxidoreductase (complex I) from Aquifex aeolicus. Biochemistry 2015; 47:13036-45. [PMID: 19006332 DOI: 10.1021/bi801307n] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The proton-pumping NADH:ubiquinone oxidoreductase (complex I) is the first enzyme complex of the respiratory chains in many bacteria and most eukaryotes. It is the least understood of all, due to its enormous size and unique energy conversion mechanism. The bacterial complex is in general made up of 14 different subunits named NuoA-N. Subunits NuoE, -F, and -G comprise the electron input part of the complex. We have cloned these genes from the hyperthermophilic bacterium Aquifex aeolicus and expressed them heterologously in Escherichia coli. A soluble subcomplex made up of NuoE and NuoF and containing the NADH binding site, the primary electron acceptor flavin mononucleotide (FMN), the binuclear iron-sulfur cluster N1a, and the tetranuclear iron-sulfur cluster N3 was isolated by chromatographic methods. The proteins were identified by N-terminal sequencing and mass spectrometry; the cofactors were characterized by UV/vis and EPR spectroscopy. Subunit NuoG was not produced in this strain. The preparation was thermostable and exhibited maximum NADH/ferricyanide oxidoreductase activity at 85 degrees C. Analytical size-exclusion chromatography and dynamic light scattering revealed the homogeneity of the preparation. First attempts to crystallize the preparation led to crystals diffracting more than 2 A.
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Affiliation(s)
- Markus Kohlstädt
- Institut fur Organische Chemie and Biochemie, Albert-Ludwigs-Universitat, Albertstrasse 21, 79104 Freiburg, Germany, and Institut de Chimie UMR 7177, Laboratoire de spectroscopie vib. et electrochimie des biomolecules, CNRS, Universite Louis Pasteur, 4, rue Blaise Pascal, 67070 Strasbourg, France
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Lou YH, Wang JS, Dong G, Guo PP, Wei DD, Xie SS, Yang MH, Kong LY. The acute hepatotoxicity of tacrine explained by 1H NMR based metabolomic profiling. Toxicol Res (Camb) 2015. [DOI: 10.1039/c5tx00096c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
NMR based metabolomics approach was applied to study the mechanism of tacrine-induced acute hepatotoxicity and had found significant disturbances.
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Affiliation(s)
- Yan-Hong Lou
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing
- People's Republic of China
| | - Jun-Song Wang
- Center for Molecular Metabolism
- Nanjing University of Science and Technology
- Nanjing
- People's Republic of China
| | - Ge Dong
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing
- People's Republic of China
| | - Ping-Ping Guo
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing
- People's Republic of China
| | - Dan-Dan Wei
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing
- People's Republic of China
| | - Sai-Sai Xie
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing
- People's Republic of China
| | - Ming-Hua Yang
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing
- People's Republic of China
| | - Ling-Yi Kong
- State Key Laboratory of Natural Medicines
- Department of Natural Medicinal Chemistry
- China Pharmaceutical University
- Nanjing
- People's Republic of China
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Wei L, Wang Q, Wu H, Ji C, Zhao J. Proteomic and metabolomic responses of Pacific oyster Crassostrea gigas to elevated pCO2 exposure. J Proteomics 2015; 112:83-94. [DOI: 10.1016/j.jprot.2014.08.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/25/2014] [Accepted: 08/11/2014] [Indexed: 01/11/2023]
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49
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Masoudzadeh N, Alidoust L, Samie N, Hajfarajollah H, Sharafi H, Modiri S, Zahiri HS, Vali H, Noghabi KA. Distinctive protein expression patterns of the strain Brevundimonas sp. ZF12 isolated from the aqueous zone containing high levels of radiation to cadmium-induced stress. J Biotechnol 2014; 186:49-57. [PMID: 24997353 DOI: 10.1016/j.jbiotec.2014.05.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/16/2014] [Accepted: 05/21/2014] [Indexed: 11/18/2022]
Abstract
In the current study, different protein expression profiles in a strain Brevundimonas sp. ZF12, isolated from the aqueous zone containing high levels of radiation, were characterized following exposure to cadmium (II) using a proteomic strategy. In order to gain a deeper understanding of the cellular events that allow this strain to survive and undergo cadmium adaptation and sorption, the strain was tested under three experimental conditions of 5, 10 and 30 ppm cadmium (II) ions stress. Two-dimensional polyacrylamide gel electrophoresis and mass spectrometry were used to identify the differentially expressed proteins under cadmium (II) stress. 20 differentially expressed spots were successfully identified by MS/MS analysis. These proteins are involved in DNA repair and protection, amino acid metabolism, nucleotide metabolism, energy homeostasis, oxidative stress response, redox homeostasis, protein folding and heat-shock response. The results obviously indicate that the ZF12 strain tends to endure the cadmium (II) stress conditions by modification in many aspects of its cellular physiology and metabolism.
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Affiliation(s)
- Nasrin Masoudzadeh
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Leila Alidoust
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Nima Samie
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Hamidreza Hajfarajollah
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Hakimeh Sharafi
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Sima Modiri
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Hossein Shahbani Zahiri
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Hojatollah Vali
- Facility for Electron Microscopy Research, McGill University, 3640 Street, Montreal, Canada
| | - Kambiz Akbari Noghabi
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran.
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Zhou T, Shen X, Irwin DM, Shen Y, Zhang Y. Mitogenomic analyses propose positive selection in mitochondrial genes for high-altitude adaptation in galliform birds. Mitochondrion 2014; 18:70-5. [PMID: 25110061 DOI: 10.1016/j.mito.2014.07.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 07/28/2014] [Accepted: 07/31/2014] [Indexed: 02/05/2023]
Abstract
Galliform birds inhabit very diverse habitats, including plateaus that are above 3000 m in altitude. At high altitude, lower temperature and hypoxia are two important factors influencing survival. Mitochondria, as the ultimate oxygen transductor, play an important role in aerobic respiration through oxidative phosphorylation (OXPHOS). We analyzed the mitochondrial genomes of six high-altitude phasianidae birds and sixteen low-altitude relatives in an attempt to determine the role of mitochondrial genes in high-altitude adaptation. We reconstructed the phylogenetic relationships of these phasianidae birds and relatives and found at least four lineages that independently occupied this high-altitude habitat. Selective analyses revealed significant evidence for positive selection in the genes ND2, ND4, and ATP6 in three of the high-altitude lineages. This result strongly suggests that adaptive evolution of mitochondrial genes played a critical role during the independent acclimatization to high altitude by galliform birds.
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Affiliation(s)
- Taicheng Zhou
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xuejuan Shen
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou 515041, China
| | - David M Irwin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Yongyi Shen
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou 515041, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| | - Yaping Zhang
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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