Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome sequence of a chronic obstructive pulmonary disease Rattus norvegicus C57CE strain Zhong Chen, Dong-Dong Yang, Xin-Hong Zhang & Li Wei To cite this article: Zhong Chen, Dong-Dong Yang, Xin-Hong Zhang & Li Wei (2014): Complete mitochondrial genome sequence of a chronic obstructive pulmonary disease Rattus norvegicus C57CE strain, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.958694
Published online: 26 Sep 2014.
Submit your article to this journal
Article views: 11
View related articles
View Crossmark data
Citing articles: 1 View citing articles
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [NUS National University of Singapore]
Date: 05 November 2015, At: 13:26
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.958694
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome sequence of a chronic obstructive pulmonary disease Rattus norvegicus C57CE strain Zhong Chen1, Dong-Dong Yang2, Xin-Hong Zhang3, and Li Wei1
Downloaded by [NUS National University of Singapore] at 13:27 05 November 2015
1
Department of Thoracic Surgery and Thoracic Tumor Center, Henan Provincial People’s Hospital, Zhengzhou, P.R. China, 2Department of Cardiothoracic Surgery, Zhangqiu City People’s Hospital, Zhangqiu, P.R. China, and 3Department of Cardiology, people’s Hospital of Zhangqiu, Zhangqiu, P.R. China Abstract
Keywords
We sequenced a chronic obstructive pulmonary disease Rattus norvegicus C57CE strain mitochondrial genome for the first time (GenBank Accession No. KM114607). Its mitogenome was 16,307 bp and coding 13 protein–coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes. This genome will provide definite information for genetic perspective into this disease.
Chronic Obstructive Pulmonary Disease, mitochondrial genome, Rattus norvegicus History Received 10 August 2014 Accepted 23 August 2014 Published online 25 September 2014
Chronic obstructive pulmonary disease (COPD) is an increasingly important cause of morbidity and mortality. COPD is now the fifth leading cause of death worldwide (Pauwels & Rabe, 2004), and recent estimates suggest that the prevalence is as high as 9–10% of adults over age 40 (Halbert et al., 2006; Stang et al., 2000). In the developed world, cigarette smoking is by far the most important risk factor for COPD. Exposure to air pollution particles, occupational exposures to dusts and fumes (Harber et al., 2007), and, in the developing world, exposure to biomass fuels used for cooking is also believed to be etiological agents of COPD (Halbert et al., 2006). There are few animal models of COPD related to air pollution particles, dusts and fumes, and biomass fuels; most COPD models
have either used cigarette smoke or other approaches, including genetic modifications to rat, believed to reproduce some of the mechanisms behind cigarette smoke. The various animal species commonly used to model COPD differ significantly from each other and from humans in anatomy of the bronchial tree. Rats have less extensive airway branching than do humans (McBride, 1991). Rats do not normally have respiratory bronchioles; rather, a respiratory bronchiole-like type of metaplasia is induced by reaction to injury (Pinkerton et al., 1992). In this study, we reported complete mitochondrial genome sequence of a COPD disorder Rattus norvegicus C57CE strain (Johanson & Pierce, 1973). Sequence from the current study was deposited in GenBank (Accession No. KM114607). It included
Table 1. A list of genes encoded by this mitochondrial genome. Position Gene
From Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla
362 432 1388 1455 3025 3102 4058 4124 4198 4267 5309 5377
Base composition (%) To 429 1386 1454 3024 3099 4058 4126 4195 4266 5310 5375 5445
Size (bp)
A
C
G
T
67 955 67 1570 75 957 69 72 69 1044 67 69
35.8 36.8 38.8 37.7 33.3 31.9 40.6 25.0 27.5 36.4 37.3 27.6
25.4 22.7 19.4 21.0 21.3 27.9 13.0 9.7 24.6 26.4 20.9 10.1
17.9 18.0 11.9 17.7 16.0 12.6 14.5 29.2 18.9 8.9 16.4 23.2
20.9 22.5 29.9 23.6 29.4 27.6 31.9 36.1 29.0 28.3 25.4 39.1
Start codon
Stop codon
ATG
TAA
ATA
TAG
Strand H H H H H H H L H H H L (continued )
Correspondence: Zhong Chen, Department of Thoracic Surgery and Thoracic Tumor Center, Henan Provincial People’s Hospital, Zhengzhou 450003, P.R. China. E-mail: [email protected]
2
Z. Chen et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Position Gene
Downloaded by [NUS National University of Singapore] at 13:27 05 November 2015
Asn
tRNA OL tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu CytB tRNAThr tRNAPro
Base composition (%)
From
To
Size (bp)
A
C
G
T
5447 5520 5552 5619 5688 7230 7306 7375 8065 8130 8291 8971 9755 9824 10,171 10,240 10,530 11,908 11,978 12,039 12,110 13,914 14,442 14,515 15,658 15,727
5519 5550 5618 5686 7232 7298 7373 8058 8127 8330 8971 9774 9823 10,180 10,239 10,536 11,907 11,977 12,037 12,109 13,930 14,441 14,510 15,654 15,727 15,789
73 31 67 68 1545 69 68 684 63 201 681 804 69 357 69 297 1378 70 60 71 1821 528 69 1140 70 66
23.3 35.5 25.4 33.8 28.8 26.1 36.8 34.2 34.9 39.8 33.6 26.5 31.9 30.3 40.6 32.3 32.3 41.4 31.7 38.0 32.7 22.2 29.0 31.2 34.3 24.2
16.4 29.0 20.9 16.2 25.3 14.5 13.2 23.8 17.5 23.9 27.4 28.7 18.8 29.4 10.1 24.6 28.2 15.7 18.3 14.1 29.3 8.7 11.6 30.2 21.4 13.7
31.5 25.8 25.4 20.6 16.3 27.5 17.6 14.6 17.5 7.9 11.1 14.8 16.0 12.9 10.1 11.5 10.9 8.6 16.7 18.3 10.5 28.2 20.3 13.4 17.1 28.8
28.8 9.7 28.3 29.4 29.6 31.9 32.4 27.4 30.1 28.4 27.9 30.0 33.3 27.4 39.2 31.6 28.6 34.3 33.3 29.6 27.5 40.9 39.1 25.2 27.2 33.3
13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region (Table 1), which showed a similar genome structure and gene content with previous reported R. norvegicus mitochondrial genomes. In this genome, most protein-coding genes employed ATG as the start codon besides ND2, ND3 and ND5 initiating with ATA. The overall composition of the mitogenome was estimated to be 34% for A, 27% for T, 26% for C and 13% for G with an A-T (61%)-rich feature. ND6 gene was encoded on the L strand, while the others were encoded on the H strand. These genes had four types of stop codon, including TAG for ND2, TAA for eight genes, AGA for CytB, and an incomplete termination codon T– – for COX3, ND3 and ND4. This sequence was largely similar to the Rattus norvegicus strain BN mitochondrion in gene order and contents except some single nucleotide polymorphisms (SNPs) that 112 SNPs in mtDNA were observed between these two strains.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Start codon
Stop codon
ATG
TAA
ATG
TAA
ATG ATG ATG
TAA TAA TAG
ATA
TAG
ATG ATG
TAA T– –
ATA ATG
TAA TAA
ATG
AGA
Strand L L L L H L H H H H H H H H H H H H H H H L L H H L
References Halbert RJ, Natoli JL, Gano A, Badamqarav E, Buist AS, Mannino DM. (2006). Global burden of COPD: Systematic review and meta-analysis. Eur Respir J 28:523–32. Harber P, Tashkin DP, Simmons M, Crawford L, Hnizdo E, Connett J, Lung Health Study Group. (2007). Effect of occupational exposures on decline of lung function in early chronic obstructive pulmonary disease. Am J Respir Crit Care Med 176:994–1000. Johanson WG, Pierce AK. (1973). Lung structure and function with age in normal rats and rats with papain emphysema. J Clin Invest 52:2921–7. McBride JT. (1991). Architecture of the tracheobronchial tree. In: Parent RA, editor. Comparative biology of the normal lung. Boca Raton: CRC. p 49–62. Pauwels RA, Rabe KF. (2004). Burden and clinical features of chronic obstructive pulmonary disease. Lancet 364:613–20. Pinkerton KE, Dodge DE, Cederdahl-Demmier J, Wong VJ, Peake J, Haselton CJ, Mellick PW, et al. (1992). Differentiated bronchiolar epithelium in alveolar ducts of rats exposed to ozone for 20 months. Am J Pathol 142:947–56. Stang P, Lydick E, Silberman C, Kempel A, Keating ET. (2000). The prevalence of COPD: Using smoking rates to estimate disease frequency in the general population. Chest 117:354S–9S.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome sequence of a chronic obstructive pulmonary disease Rattus norvegicus C57CE strain Zhong Chen, Dong-Dong Yang, Xin-Hong Zhang & Li Wei To cite this article: Zhong Chen, Dong-Dong Yang, Xin-Hong Zhang & Li Wei (2014): Complete mitochondrial genome sequence of a chronic obstructive pulmonary disease Rattus norvegicus C57CE strain, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.958694
Published online: 26 Sep 2014.
Submit your article to this journal
Article views: 11
View related articles
View Crossmark data
Citing articles: 1 View citing articles
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [NUS National University of Singapore]
Date: 05 November 2015, At: 13:26
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.958694
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome sequence of a chronic obstructive pulmonary disease Rattus norvegicus C57CE strain Zhong Chen1, Dong-Dong Yang2, Xin-Hong Zhang3, and Li Wei1
Downloaded by [NUS National University of Singapore] at 13:27 05 November 2015
1
Department of Thoracic Surgery and Thoracic Tumor Center, Henan Provincial People’s Hospital, Zhengzhou, P.R. China, 2Department of Cardiothoracic Surgery, Zhangqiu City People’s Hospital, Zhangqiu, P.R. China, and 3Department of Cardiology, people’s Hospital of Zhangqiu, Zhangqiu, P.R. China Abstract
Keywords
We sequenced a chronic obstructive pulmonary disease Rattus norvegicus C57CE strain mitochondrial genome for the first time (GenBank Accession No. KM114607). Its mitogenome was 16,307 bp and coding 13 protein–coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes. This genome will provide definite information for genetic perspective into this disease.
Chronic Obstructive Pulmonary Disease, mitochondrial genome, Rattus norvegicus History Received 10 August 2014 Accepted 23 August 2014 Published online 25 September 2014
Chronic obstructive pulmonary disease (COPD) is an increasingly important cause of morbidity and mortality. COPD is now the fifth leading cause of death worldwide (Pauwels & Rabe, 2004), and recent estimates suggest that the prevalence is as high as 9–10% of adults over age 40 (Halbert et al., 2006; Stang et al., 2000). In the developed world, cigarette smoking is by far the most important risk factor for COPD. Exposure to air pollution particles, occupational exposures to dusts and fumes (Harber et al., 2007), and, in the developing world, exposure to biomass fuels used for cooking is also believed to be etiological agents of COPD (Halbert et al., 2006). There are few animal models of COPD related to air pollution particles, dusts and fumes, and biomass fuels; most COPD models
have either used cigarette smoke or other approaches, including genetic modifications to rat, believed to reproduce some of the mechanisms behind cigarette smoke. The various animal species commonly used to model COPD differ significantly from each other and from humans in anatomy of the bronchial tree. Rats have less extensive airway branching than do humans (McBride, 1991). Rats do not normally have respiratory bronchioles; rather, a respiratory bronchiole-like type of metaplasia is induced by reaction to injury (Pinkerton et al., 1992). In this study, we reported complete mitochondrial genome sequence of a COPD disorder Rattus norvegicus C57CE strain (Johanson & Pierce, 1973). Sequence from the current study was deposited in GenBank (Accession No. KM114607). It included
Table 1. A list of genes encoded by this mitochondrial genome. Position Gene
From Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla
362 432 1388 1455 3025 3102 4058 4124 4198 4267 5309 5377
Base composition (%) To 429 1386 1454 3024 3099 4058 4126 4195 4266 5310 5375 5445
Size (bp)
A
C
G
T
67 955 67 1570 75 957 69 72 69 1044 67 69
35.8 36.8 38.8 37.7 33.3 31.9 40.6 25.0 27.5 36.4 37.3 27.6
25.4 22.7 19.4 21.0 21.3 27.9 13.0 9.7 24.6 26.4 20.9 10.1
17.9 18.0 11.9 17.7 16.0 12.6 14.5 29.2 18.9 8.9 16.4 23.2
20.9 22.5 29.9 23.6 29.4 27.6 31.9 36.1 29.0 28.3 25.4 39.1
Start codon
Stop codon
ATG
TAA
ATA
TAG
Strand H H H H H H H L H H H L (continued )
Correspondence: Zhong Chen, Department of Thoracic Surgery and Thoracic Tumor Center, Henan Provincial People’s Hospital, Zhengzhou 450003, P.R. China. E-mail: [email protected]
2
Z. Chen et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Position Gene
Downloaded by [NUS National University of Singapore] at 13:27 05 November 2015
Asn
tRNA OL tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu CytB tRNAThr tRNAPro
Base composition (%)
From
To
Size (bp)
A
C
G
T
5447 5520 5552 5619 5688 7230 7306 7375 8065 8130 8291 8971 9755 9824 10,171 10,240 10,530 11,908 11,978 12,039 12,110 13,914 14,442 14,515 15,658 15,727
5519 5550 5618 5686 7232 7298 7373 8058 8127 8330 8971 9774 9823 10,180 10,239 10,536 11,907 11,977 12,037 12,109 13,930 14,441 14,510 15,654 15,727 15,789
73 31 67 68 1545 69 68 684 63 201 681 804 69 357 69 297 1378 70 60 71 1821 528 69 1140 70 66
23.3 35.5 25.4 33.8 28.8 26.1 36.8 34.2 34.9 39.8 33.6 26.5 31.9 30.3 40.6 32.3 32.3 41.4 31.7 38.0 32.7 22.2 29.0 31.2 34.3 24.2
16.4 29.0 20.9 16.2 25.3 14.5 13.2 23.8 17.5 23.9 27.4 28.7 18.8 29.4 10.1 24.6 28.2 15.7 18.3 14.1 29.3 8.7 11.6 30.2 21.4 13.7
31.5 25.8 25.4 20.6 16.3 27.5 17.6 14.6 17.5 7.9 11.1 14.8 16.0 12.9 10.1 11.5 10.9 8.6 16.7 18.3 10.5 28.2 20.3 13.4 17.1 28.8
28.8 9.7 28.3 29.4 29.6 31.9 32.4 27.4 30.1 28.4 27.9 30.0 33.3 27.4 39.2 31.6 28.6 34.3 33.3 29.6 27.5 40.9 39.1 25.2 27.2 33.3
13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region (Table 1), which showed a similar genome structure and gene content with previous reported R. norvegicus mitochondrial genomes. In this genome, most protein-coding genes employed ATG as the start codon besides ND2, ND3 and ND5 initiating with ATA. The overall composition of the mitogenome was estimated to be 34% for A, 27% for T, 26% for C and 13% for G with an A-T (61%)-rich feature. ND6 gene was encoded on the L strand, while the others were encoded on the H strand. These genes had four types of stop codon, including TAG for ND2, TAA for eight genes, AGA for CytB, and an incomplete termination codon T– – for COX3, ND3 and ND4. This sequence was largely similar to the Rattus norvegicus strain BN mitochondrion in gene order and contents except some single nucleotide polymorphisms (SNPs) that 112 SNPs in mtDNA were observed between these two strains.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Start codon
Stop codon
ATG
TAA
ATG
TAA
ATG ATG ATG
TAA TAA TAG
ATA
TAG
ATG ATG
TAA T– –
ATA ATG
TAA TAA
ATG
AGA
Strand L L L L H L H H H H H H H H H H H H H H H L L H H L
References Halbert RJ, Natoli JL, Gano A, Badamqarav E, Buist AS, Mannino DM. (2006). Global burden of COPD: Systematic review and meta-analysis. Eur Respir J 28:523–32. Harber P, Tashkin DP, Simmons M, Crawford L, Hnizdo E, Connett J, Lung Health Study Group. (2007). Effect of occupational exposures on decline of lung function in early chronic obstructive pulmonary disease. Am J Respir Crit Care Med 176:994–1000. Johanson WG, Pierce AK. (1973). Lung structure and function with age in normal rats and rats with papain emphysema. J Clin Invest 52:2921–7. McBride JT. (1991). Architecture of the tracheobronchial tree. In: Parent RA, editor. Comparative biology of the normal lung. Boca Raton: CRC. p 49–62. Pauwels RA, Rabe KF. (2004). Burden and clinical features of chronic obstructive pulmonary disease. Lancet 364:613–20. Pinkerton KE, Dodge DE, Cederdahl-Demmier J, Wong VJ, Peake J, Haselton CJ, Mellick PW, et al. (1992). Differentiated bronchiolar epithelium in alveolar ducts of rats exposed to ozone for 20 months. Am J Pathol 142:947–56. Stang P, Lydick E, Silberman C, Kempel A, Keating ET. (2000). The prevalence of COPD: Using smoking rates to estimate disease frequency in the general population. Chest 117:354S–9S.
