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A 69 kb Deletion in chr19q13.42 including PRPF31 Gene in a Chinese Family Affected with Autosomal Dominant Retinitis Pigmentosa. J Clin Med 2022; 11:jcm11226682. [PMID: 36431159 PMCID: PMC9695658 DOI: 10.3390/jcm11226682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/20/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
We aimed to identify the genetic cause of autosomal dominant retinitis pigmentosa (adRP) and characterize the underlying molecular mechanisms of incomplete penetrance in a Chinese family affected with adRP. All enrolled family members underwent ophthalmic examinations. Whole-genome sequencing (WGS), multiplex ligation-dependent probe amplification (MLPA), linkage analysis and haplotype construction were performed in all participants. RNA-seq was performed to analyze the regulating mechanism of incomplete penetrance among affected patients, mutation carriers and healthy controls. In the studied family, 14 individuals carried a novel heterozygous large deletion of 69 kilobase (kb) in 19q13.42 encompassing exon 1 of the PRPF31 gene and five upstream genes: TFPT, OSCAR, NDUFA3, TARM1, and VSTM1. Three family members were sequenced and diagnosed as non-penetrant carriers (NPCs). RNA-seq showed significant differential expression of genes in deletion between mutation carriers and healthy control. The RP11 pedigree in this study was the largest pedigree compared to other reported RP11 pedigrees with large deletions. Early onset in all affected members in this pedigree was considered to be a special phenotype and was firstly reported in a RP11 family for the first time. Differential expression of PRPF31 between affected and unaffected subjects indicates a haploinsufficiency to cause the disease in the family. The other genes with significant differential expression might play a cooperative effect on the penetrance of RP11.
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Wu MX, Zou Y, Yu YH, Chen BX, Zheng QW, Ye ZW, Wei T, Ye SQ, Guo LQ, Lin JF. Comparative transcriptome and proteome provide new insights into the regulatory mechanisms of the postharvest deterioration of Pleurotus tuoliensis fruitbodies during storage. Food Res Int 2021; 147:110540. [PMID: 34399517 DOI: 10.1016/j.foodres.2021.110540] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/05/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
The Pleurotus tuoliensis (Pt), a precious edible mushroom with high economic value, is widely popular for its rich nutrition and meaty texture. However, rapid postharvest deterioration depreciates the commercial value of Pt and severely restricts its marketing. By RNA-Seq transcriptomic and TMT-MS MS proteomic, we study the regulatory mechanisms of the postharvest storage of Pt fruitbodies at 25 ℃ for 0, 38, and 76 h (these three-time points recorded as groups A, B, and C, respectively). 2,008 DEGs (Differentially expressed genes) were identified, and all DEGs shared 265 factors with all DEPs (Differentially expressed proteins). Jointly, the DEGs and DEPs of two-omics showed that the category of the metabolic process contained the most DEGs and DEPs in the biological process by GO (Gene Ontology) classification. The top 17 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways with the highest sum of DEG and DEP numbers in groups B/A (38 h vs. 0 h) and C/A (76 h vs. 0 h) and pathways closely related to energy metabolism were selected for analysis and discussion. Actively expression of CAZymes (Carbohydrate active enzymes), represented by laccase, chitinase, and β-glucanase, directly leads to the softening of fruitbodies. The transcription factor Rlm1 of 1,3-β-glucan synthase attracted attention with a significant down-regulation of gene levels in the C/A group. Laccase also contributes, together with phenylalanine ammonia-lyase (PAL), to the discoloration reaction in the first 76 h of the fruitbodies. Significant expression of several crucial enzymes for EMP (Glycolysis), Fatty acid degradation, and Valine, leucine and isoleucine degradation at the gene or protein level supply substantial amounts of acetyl-CoA to the TCA cycle. Citrate synthase (CS), isocitrate dehydrogenase (ICDH), and three mitochondrial respiratory complexes intensify respiration and produce high levels of ROS (Reactive oxygen species) by significant up-regulation. In the ROS scavenging system, only Mn-SOD was significantly up-regulated at the gene level and was probably interacted with Hsp60 (Heat shock protein 60), which was significantly up-regulated at the protein level, to play a dominant role in antioxidation. Three types of stresses - cell wall stress, starvation, and oxidative stress - were suffered by Pt fruitbodies postharvest, resulting in cell cycle arrest and gene expression disorder.
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Affiliation(s)
- Mu-Xiu Wu
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Yuan Zou
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Ying-Hao Yu
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Bai-Xiong Chen
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Qian-Wang Zheng
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Zhi-Wei Ye
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Tao Wei
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Si-Qiang Ye
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Li-Qiong Guo
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China.
| | - Jun-Fang Lin
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China.
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Zhang Q, Zhang B, Luo Y. Cardiac transcriptome study of the effect of heat stress in yellow-feather broilers. ITALIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1080/1828051x.2019.1610338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Quan Zhang
- Department of Animal Science, Agricultural College, Guangdong Ocean University, Zhanjiang, China
| | - BoHai Zhang
- Department of Animal Science, Agricultural College, Guangdong Ocean University, Zhanjiang, China
| | - YiKang Luo
- Department of Animal Science, Agricultural College, Guangdong Ocean University, Zhanjiang, China
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Xiao R, Zhou H, Chen CM, Cheng H, Li H, Xie J, Zhao H, Han Q, Diao X. Transcriptional responses of Acropora hyacinthus embryo under the benzo(a)pyrene stress by deep sequencing. CHEMOSPHERE 2018; 206:387-397. [PMID: 29754063 DOI: 10.1016/j.chemosphere.2018.04.149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
Coral embryos are a critical and sensitive period for the early growth and development of coral. Benzo(a)pyrene (BaP) is widely distributed in the ocean and has strong toxicity, but there is little information on the toxic effects to coral embryos exposed to this widespread environmental contaminant. Thus, in this study, we utilized the Illumina Hiseq™ 4000 platform to explore the gene response of Acropora hyacinthus embryos under the BaP stress. A total of 130,042 Unigenes were obtained and analyzed, and approximately 37.67% of those matched with sequences from four different species. In total, 2606 Unigenes were up-regulated, and 3872 Unigenes were down-regulated. After Gene Ontology (GO) annotation, the results show that the "cellular process" and "metabolic process" were leading in the category of biological processes, which the "binding" and "catalytic activity" were the most abundant subcategories in molecular function. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the most differentially expressed genes (DEGs) were enriched, as well as down-regulated in the pathways of oxidative phosphorylation, metabolism of xenobiotics, immune-related genes, apoptosis and human disease genes. At the same time, 388,197 of Single-nucleotide Polymorphisms (SNPs) and 6164 of Simple Sequence Repeats (SSRs) were obtained, which can be served as the richer and more valuable SSRs molecular markers in the future. The results of this study can help to better understand the toxicological mechanism of coral embryo exposed to BaP, and it is also essential for the protection and restoration of coral reef ecosystem in the future.
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Affiliation(s)
- Rong Xiao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Hailong Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Chien-Min Chen
- Department of Environmental Resources Management, Chia Nan University of Pharmacy & Science, Tainan, Taiwan, China
| | - Huamin Cheng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Hongwu Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; College of Ocean, Hainan University, Haikou 570228, China
| | - Jia Xie
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; College of Ocean, Hainan University, Haikou 570228, China
| | - Hongwei Zhao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Qian Han
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Xiaoping Diao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; Ministry of Education Key Laboratory of Tropical Island Ecology, Hainan Normal University, Haikou, 571158, China.
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5
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The miR-29 transcriptome in endocrine-sensitive and resistant breast cancer cells. Sci Rep 2017; 7:5205. [PMID: 28701793 PMCID: PMC5507892 DOI: 10.1038/s41598-017-05727-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/01/2017] [Indexed: 01/08/2023] Open
Abstract
Aberrant microRNA expression contributes to breast cancer progression and endocrine resistance. We reported that although tamoxifen stimulated miR-29b-1/a transcription in tamoxifen (TAM)-resistant breast cancer cells, ectopic expression of miR-29b-1/a did not drive TAM-resistance in MCF-7 breast cancer cells. However, miR-29b-1/a overexpression significantly repressed TAM-resistant LCC9 cell proliferation, suggesting that miR-29b-1/a is not mediating TAM resistance but acts as a tumor suppressor in TAM-resistant cells. The target genes mediating this tumor suppressor activity were unknown. Here, we identify miR-29b-1 and miR-29a target transcripts in both MCF-7 and LCC9 cells. We find that miR-29b-1 and miR-29a regulate common and unique transcripts in each cell line. The cell-specific and common downregulated genes were characterized using the MetaCore Gene Ontology (GO) enrichment analysis algorithm. LCC9-sepecific miR-29b-1/a-regulated GO processes include oxidative phosphorylation, ATP metabolism, and apoptosis. Extracellular flux analysis of cells transfected with anti- or pre- miR-29a confirmed that miR-29a inhibits mitochondrial bioenergetics in LCC9 cells. qPCR,luciferase reporter assays, and western blot also verified the ATP synthase subunit genes ATP5G1 and ATPIF1 as bone fide miR29b-1/a targets. Our results suggest that miR-29 repression of TAM-resistant breast cancer cell proliferation is mediated in part through repression of genes important in mitochondrial bioenergetics.
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Identification and prediction of alternative transcription start sites that generate rod photoreceptor-specific transcripts from ubiquitously expressed genes. PLoS One 2017. [PMID: 28640837 PMCID: PMC5480877 DOI: 10.1371/journal.pone.0179230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Transcriptome complexity is substantially increased by the use of multiple transcription start sites for a given gene. By utilizing a rod photoreceptor-specific chromatin signature, and the RefSeq database of established transcription start sites, we have identified essentially all known rod photoreceptor genes as well as a group of novel genes that have a high probability of being expressed in rod photoreceptors. Approximately half of these novel rod genes are transcribed into multiple mRNA and/or protein isoforms through alternative transcriptional start sites (ATSS), only one of which has a rod-specific epigenetic signature and gives rise to a rod transcript. This suggests that, during retina development, some genes use ATSS to regulate cell type and temporal specificity, effectively generating a rod transcript from otherwise ubiquitously expressed genes. Biological confirmation of the relationship between epigenetic signatures and gene expression, as well as comparison of our genome-wide chromatin signature maps with available data sets for retina, namely a ChIP-on-Chip study of Polymerase-II (Pol-II) binding sites, ChIP-Seq studies for NRL- and CRX- binding sites and DHS (University of Washington data, available on UCSC mouse Genome Browser as a part of ENCODE project) fully support our hypothesis and together accurately identify and predict an array of new rod transcripts. The same approach was used to identify a number of TSS that are not currently in RefSeq. Biological conformation of the use of some of these TSS suggests that this method will be valuable for exploring the range of transcriptional complexity in many tissues. Comparison of mouse and human genome-wide data indicates that most of these alternate TSS appear to be present in both species, indicating that our approach can be useful for identification of regulatory regions that might play a role in human retinal disease.
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Hanazono Y, Takeda K, Miki K. Characterization of the Nqo5 subunit of bacterial complex I in the isolated state. FEBS Open Bio 2016; 6:687-95. [PMID: 27398308 PMCID: PMC4932448 DOI: 10.1002/2211-5463.12070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 04/12/2016] [Accepted: 04/14/2016] [Indexed: 11/09/2022] Open
Abstract
The subunits that comprise bacterial complex I (NADH:ubiquinone oxidoreductase) are also found in more complicated mitochondrial enzymes in eukaryotic organisms. Although the Nqo5 subunit is one of these conserved components and important for the formation of complex, it has been little studied. Here, we report structure analyses of isolated Nqo5 from Thermus thermophilus. Biochemical studies indicated that the C-terminal region following the 30-Kd subunit motif is disordered in the isolated state, while the remaining portion is already folded. Crystallographic studies of a trypsin-resistant fragment revealed detailed structural differences in the folded domain between the isolated and complexed states.
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Affiliation(s)
- Yuya Hanazono
- Department of Chemistry Graduate School of Science Kyoto University Sakyo-ku Kyoto Japan
| | - Kazuki Takeda
- Department of Chemistry Graduate School of Science Kyoto University Sakyo-ku Kyoto Japan; RIKEN SPring-8 Center at Harima Institute Sayo Hyogo Japan
| | - Kunio Miki
- Department of Chemistry Graduate School of Science Kyoto University Sakyo-ku Kyoto Japan; RIKEN SPring-8 Center at Harima Institute Sayo Hyogo Japan
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Reduced Expression of NDUFS3 and Its Clinical Significance in Serous Ovarian Cancer. Int J Gynecol Cancer 2013; 23:622-9. [DOI: 10.1097/igc.0b013e318287a90d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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9
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Tuppen HAL, Hogan VE, He L, Blakely EL, Worgan L, Al-Dosary M, Saretzki G, Alston CL, Morris AA, Clarke M, Jones S, Devlin AM, Mansour S, Chrzanowska-Lightowlers ZMA, Thorburn DR, McFarland R, Taylor RW. The p.M292T NDUFS2 mutation causes complex I-deficient Leigh syndrome in multiple families. ACTA ACUST UNITED AC 2010; 133:2952-63. [PMID: 20819849 PMCID: PMC2947428 DOI: 10.1093/brain/awq232] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Isolated complex I deficiency is the most frequently observed oxidative phosphorylation defect in children with mitochondrial disease, leading to a diverse range of clinical presentations, including Leigh syndrome. For most patients the genetic cause of the biochemical defect remains unknown due to incomplete understanding of the complex I assembly process. Nonetheless, a plethora of pathogenic mutations have been described to date in the seven mitochondrial-encoded subunits of complex I as well as in 12 of the nuclear-encoded subunits and in six assembly factors. Whilst several mitochondrial DNA mutations are recurrent, the majority of these mutations are reported in single families. We have sequenced core structural and functional nuclear-encoded subunits of complex I in a cohort of 34 paediatric patients with isolated complex I deficiency, identifying pathogenic mutations in 6 patients. These included a novel homozygous NDUFS1 mutation in an Asian child with Leigh syndrome, a previously identified NDUFS8 mutation (c.236C>T, p.P79L) in a second Asian child with Leigh-like syndrome and six novel, compound heterozygous NDUFS2 mutations in four white Caucasian patients with Leigh or Leigh-like syndrome. Three of these children harboured an identical NDUFS2 mutation (c.875T>C, p.M292T), which was also identified in conjunction with a novel NDUFS2 splice site mutation (c.866+4A>G) in a fourth Caucasian child who presented to a different diagnostic centre, with microsatellite and single nucleotide polymorphism analyses indicating that this was due to an ancient common founder event. Our results confirm that NDUFS2 is a mutational hotspot in Caucasian children with isolated complex I deficiency and recommend the routine diagnostic investigation of this gene in patients with Leigh or Leigh-like phenotypes.
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Affiliation(s)
- Helen A L Tuppen
- Mitochondrial Research Group, Institute for Ageing and Health, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, UK
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Kisby GE, Olivas A, Standley M, Lu X, Pattee P, O’Malley J, Li X, Muniz J, Nagalla SR. Genotoxicants target distinct molecular networks in neonatal neurons. ENVIRONMENTAL HEALTH PERSPECTIVES 2006; 114:1703-12. [PMID: 17107856 PMCID: PMC1665395 DOI: 10.1289/ehp.9073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
BACKGROUND Exposure of the brain to environmental agents during critical periods of neuronal development is considered a key factor underlying many neurologic disorders. OBJECTIVES In this study we examined the influence of genotoxicants on cerebellar function during early development by measuring global gene expression changes. METHODS We measured global gene expression in immature cerebellar neurons (i.e., granule cells) after treatment with two distinct alkylating agents, methylazoxymethanol (MAM) and nitrogen mustard (HN2). Granule cell cultures were treated for 24 hr with MAM (10-1,000 microM) or HN2 (0.1-20 microM) and examined for cell viability, DNA damage, and markers of apoptosis. RESULTS Neuronal viability was significantly reduced (p < 0.01) at concentrations > 500 microM for MAM and > 1.0 microM for HN2; this correlated with an increase in both DNA damage and markers of apoptosis. Neuronal cultures treated with sublethal concentrations of MAM (100 microM) or HN2 (1.0 microM) were then examined for gene expression using large-scale mouse cDNA microarrays (27,648). Gene expression results revealed that a) global gene expression was predominantly up-regulated by both genotoxicants; b) the number of down-regulated genes was approximately 3-fold greater for HN2 than for MAM; and c) distinct classes of molecules were influenced by MAM (i.e, neuronal differentiation, the stress and immune response, and signal transduction) and HN2 (i.e, protein synthesis and apoptosis). CONCLUSIONS These studies demonstrate that individual genotoxicants induce distinct gene expression signatures. Further study of these molecular networks may explain the variable response of the developing brain to different types of environmental genotoxicants.
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Affiliation(s)
- Glen E. Kisby
- Center for Research on Occupational and Environmental Toxicology (CROET), Oregon Health & Science University, Portland, Oregon
| | - Antoinette Olivas
- Center for Research on Occupational and Environmental Toxicology (CROET), Oregon Health & Science University, Portland, Oregon
| | - Melissa Standley
- Department of Pediatrics, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Xinfang Lu
- Department of Pediatrics, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Patrick Pattee
- Department of Pediatrics, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Jean O’Malley
- Department of Pediatrics, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Xiaorong Li
- Center for Research on Occupational and Environmental Toxicology (CROET), Oregon Health & Science University, Portland, Oregon
| | - Juan Muniz
- Center for Research on Occupational and Environmental Toxicology (CROET), Oregon Health & Science University, Portland, Oregon
| | - Srinavasa R. Nagalla
- Department of Pediatrics, School of Medicine, Oregon Health & Science University, Portland, Oregon
- Address correspondence to S. Nagalla, Department of Pediatrics, School of Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239 USA. Telephone: (503) 494-1928. Fax: (503) 494-4821. E-mail:
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11
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Kubo N, Arimura SI, Tsutsumi N, Kadowaki KI, Hirai M. Isolation and characterization of the pea cytochrome c oxidase Vb gene. Genome 2006; 49:1481-9. [PMID: 17426763 DOI: 10.1139/g06-105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Three copies of the gene that encodes cytochrome c oxidase subunit Vb were isolated from the pea (PscoxVb-1, PscoxVb-2, and PscoxVb-3). Northern Blot and reverse transcriptase-PCR analyses suggest that all 3 genes are transcribed in the pea. Each pea coxVb gene has an N-terminal extended sequence that can encode a mitochondrial targeting signal, called a presequence. The localization of green fluorescent proteins fused with the presequence strongly suggests the targeting of pea COXVb proteins to mitochondria. Each pea coxVb gene has 5 intron sites within the coding region. These are similar to Arabidopsis and rice, although the intron lengths vary greatly. A phylogenetic analysis of coxVb suggests the occurrence of gene duplication events during angiosperm evolution. In particular, 2 duplication events might have occurred in legumes, grasses, and Solanaceae. A comparison of amino acid sequences in COXVb or its counterpart shows the conservation of several amino acids within a zinc finger motif. Interestingly, a homology search analysis showed that bacterial protein COG4391 and a mitochondrial complex I 13 kDa subunit also have similar amino acid compositions around this motif. Such similarity might reflect evolutionary relationships among the 3 proteins.
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Affiliation(s)
- Nakao Kubo
- Graduate School of Agriculture, Kyoto Prefectural University, Kyoto Prefectural Institute of Agricultural Biotechnology, 74 Oji, Kitainayazuma, Seika, Soraku, Kyoto 619-0244, Japan.
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12
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Fong CJ, Burgoon LD, Zacharewski TR. Comparative microarray analysis of basal gene expression in mouse Hepa-1c1c7 wild-type and mutant cell lines. Toxicol Sci 2005; 86:342-53. [PMID: 15888666 DOI: 10.1093/toxsci/kfi194] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Hepa-1c1c7 wild-type and benzo[a]pyrene-resistant derived mutant cell lines have been used to elucidate pathways and mechanisms involving the aryl hydrocarbon receptor (AhR). However, there has been little focus on other biological processes which may differ between the isolated lines. In this study, mouse cDNA microarrays representing 4858 genes were used to examine differences in basal gene expression between mouse Hepa-1c1c7 wild-type and c1 (truncated Cyp1a1 protein), c4 (AhR nuclear translocator, ARNT, deficient), and c12 (low AhR levels) mutant cell lines. Surprisingly, c1 mutants exhibited the greatest number of gene expression changes compared to wild-type cells, followed by c4 and c12 lines, respectively. Differences in basal gene expression were consistent with cell line specific variations in morphology, mitochondrial activity, and proliferation rate. MTT and direct cell count assays indicate both c4 and c12 mutants exhibit increased proliferative activity when compared to wild-type cells, while the c1 mutants exhibited decreased activity. This study further characterizes Hepa-1c1c7 wild-type and mutant cells and identifies significant differences in biological processes that should be considered when conducting comparative mechanistic studies with these lines.
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Affiliation(s)
- C J Fong
- Department of Biochemistry and Molecular Biology, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824, USA
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Loeffen J, Elpeleg O, Smeitink J, Smeets R, Stöckler-Ipsiroglu S, Mandel H, Sengers R, Trijbels F, van den Heuvel L. Mutations in the complex I NDUFS2 gene of patients with cardiomyopathy and encephalomyopathy. Ann Neurol 2001; 49:195-201. [PMID: 11220739 DOI: 10.1002/1531-8249(20010201)49:2<195::aid-ana39>3.0.co;2-m] [Citation(s) in RCA: 149] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human complex I is built up and regulated by genes encoded by the mitochondrial DNA (mtDNA) as well as the nuclear DNA (nDNA). In recent years, attention mainly focused on the relation between complex I deficiency and mtDNA mutations. However, a high percentage of consanguinity and an autosomal-recessive mode of inheritance observed within our patient group as well as the absence of common mtDNA mutations make a nuclear genetic cause likely. The NDUFS2 protein is part of complex I of many pro- and eukaryotes. The nuclear gene coding for this protein is therefore an important candidate for mutational detection studies in enzymatic complex I deficient patients. Screening of patient NDUFS2 cDNA by reverse transcriptase-polymerase chain reaction (RT-PCR) in combination with direct DNA sequencing revealed three missense mutations resulting in the substitution of conserved amino acids in three families.
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Affiliation(s)
- J Loeffen
- Nijmegen Center for Mitochondrial Disorders, Department of Pediatrics, The Netherlands
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14
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Triepels R, Smeitink J, Loeffen J, Smeets R, Buskens C, Trijbels F, van den Heuvel L. The human nuclear-encoded acyl carrier subunit (NDUFAB1) of the mitochondrial complex I in human pathology. J Inherit Metab Dis 1999; 22:163-73. [PMID: 10234612 DOI: 10.1023/a:1005402020569] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We present the cDNA sequence of the human mitochondrial acyl carrier protein NDUFAB1, a nuclear-encoded subunit of complex I of the mitochondrial respiratory chain. We obtained the NDUFAB1 cDNA using the cDNA sequence of the bovine mitochondrial acyl carrier protein. The human cDNA contains two putative translation initiation codons. The human NDUFAB1 protein contains a phosphopantetheine attachment site (DLGLDSLDQVEIIMAM), unique for acyl carrier proteins, and an EF-hand calcium binding domain (DIDAEKLMCPQEI). Transcripts of this gene are found in a wide range of human tissues. The highests expression levels were observed, in descending order, in adult heart, skeletal muscle and fetal heart. We subjected NDUFAB1 fibroblast cDNA of 20 patients with an isolated enzymatic complex I deficiency to mutational detection. No mutations in the NDUFAB1 open reading frame were observed. Future studies will answer whether mutations in the NDUFAB1 promoter or transcription elements are responsible for the observed complex I deficiency.
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Affiliation(s)
- R Triepels
- Nijmegen Center for Mitochondrial Disorders, University Children's Hospital, Department of Pediatrics, The Netherlands
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Loeffen JL, Triepels RH, van den Heuvel LP, Schuelke M, Buskens CA, Smeets RJ, Trijbels JM, Smeitink JA. cDNA of eight nuclear encoded subunits of NADH:ubiquinone oxidoreductase: human complex I cDNA characterization completed. Biochem Biophys Res Commun 1998; 253:415-22. [PMID: 9878551 DOI: 10.1006/bbrc.1998.9786] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits of which 34 are encoded by nDNA. Here we report the cDNA sequences of the hitherto uncharacterized 8 nuclear encoded subunits, all located within the hydrophobic protein (HP) fraction of complex I. Now all currently known 41 proteins of human NADH:ubiquinone oxidoreductase have been characterized and reported in literature, which enables more complete mutational analysis studies of isolated complex I-deficient patients.
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Affiliation(s)
- J L Loeffen
- University Hospital Nijmegen, Nijmegen Center for Mitochondrial Disorders, The Netherlands
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