Reconstruction of Acetogenesis Pathway Using Short-Read Sequencing of Clostridium aceticum Genome.
Identifieur interne : 001595 ( Main/Exploration ); précédent : 001594; suivant : 001596Reconstruction of Acetogenesis Pathway Using Short-Read Sequencing of Clostridium aceticum Genome.
Auteurs : Sooin Lee ; Yoseb Song ; Donghui Choe ; Suhyung Cho ; Seok Jong Yu ; Yongseong Cho ; Sun Chang Kim ; Byung-Kwan ChoSource :
- Journal of nanoscience and nanotechnology [ 1533-4880 ] ; 2015.
Descripteurs français
- KwdFr :
- ADN bactérien (analyse), ADN bactérien (génétique), Alignement de séquences, Analyse de séquence d'ADN (), Clostridium (génétique), Clostridium (métabolisme), Données de séquences moléculaires, Génome bactérien (génétique), Protéines bactériennes (génétique), Protéines bactériennes (métabolisme), Séquence d'acides aminés, Séquençage nucléotidique à haut débit (), Voies et réseaux métaboliques (génétique).
- MESH :
- analyse : ADN bactérien.
- génétique : ADN bactérien, Clostridium, Génome bactérien, Protéines bactériennes, Voies et réseaux métaboliques.
- métabolisme : Clostridium, Protéines bactériennes.
- Alignement de séquences, Analyse de séquence d'ADN, Données de séquences moléculaires, Séquence d'acides aminés, Séquençage nucléotidique à haut débit.
English descriptors
- KwdEn :
- Amino Acid Sequence, Bacterial Proteins (genetics), Bacterial Proteins (metabolism), Clostridium (genetics), Clostridium (metabolism), DNA, Bacterial (analysis), DNA, Bacterial (genetics), Genome, Bacterial (genetics), High-Throughput Nucleotide Sequencing (methods), Metabolic Networks and Pathways (genetics), Molecular Sequence Data, Sequence Alignment, Sequence Analysis, DNA (methods).
- MESH :
- chemical , analysis : DNA, Bacterial.
- chemical , genetics : Bacterial Proteins, DNA, Bacterial.
- chemical , metabolism : Bacterial Proteins.
- genetics : Clostridium, Genome, Bacterial, Metabolic Networks and Pathways.
- metabolism : Clostridium.
- methods : High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA.
- Amino Acid Sequence, Molecular Sequence Data, Sequence Alignment.
Abstract
Clostridium aceticum is an anaerobic homoacetogen, able to reduce CO2 to multi-carbon products using the reductive acetyl-CoA pathway. This unique ability to use CO2 or CO makes the microbe a potential platform for the biotech industry. However, the development of genetically engineered homoacetogen for the large-scale production of commodity chemicals is hampered by the limited amount of their genetic and metabolic information. Here we exploited next-generation sequencing to reveal C. aceticum genome. The short-read sequencing produced 44,871,196 high quality reads with an average length of 248 bases. Following sequence trimming step, 30,256,976 reads were assembled into 12,563 contigs with 168-fold coverage and 1,971 bases in length using de Bruijn graph algorithm. Since the k-mer hash length in the algorithm is an important factor for the quality of output contigs, a window of k-mers (k-51 to k-201) was tested to obtain high quality contigs. In addition to the assembly metrics, the functional annotation of the contigs was investigated to select the k-mer optimum. Metabolic pathway mapping using the functional annotation identified the majority of central metabolic pathways, such as the glycolysis and TCA cycle. Further, these analyses elucidated the enzymes consisting of Wood-Ljungdahl pathway, in which CO2 is fixed into acetyl-CoA. Thus, the metabolic reconstruction based on the draft genome assembly provides a foundation for the functional genomics required to engineer C. aceticum.
DOI: 10.1166/jnn.2015.9537
PubMed: 26505015
Affiliations:
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Le document en format XML
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Jong" sort="Yu, Seok Jong" uniqKey="Yu S" first="Seok Jong" last="Yu">Seok Jong Yu</name></author><author><name sortKey="Cho, Yongseong" sort="Cho, Yongseong" uniqKey="Cho Y" first="Yongseong" last="Cho">Yongseong Cho</name></author><author><name sortKey="Kim, Sun Chang" sort="Kim, Sun Chang" uniqKey="Kim S" first="Sun Chang" last="Kim">Sun Chang Kim</name></author><author><name sortKey="Cho, Byung Kwan" sort="Cho, Byung Kwan" uniqKey="Cho B" first="Byung-Kwan" last="Cho">Byung-Kwan Cho</name></author></analytic><series><title level="j">Journal of nanoscience and nanotechnology</title><idno type="ISSN">1533-4880</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Bacterial Proteins (genetics)</term><term>Bacterial Proteins (metabolism)</term><term>Clostridium (genetics)</term><term>Clostridium (metabolism)</term><term>DNA, Bacterial (analysis)</term><term>DNA, Bacterial (genetics)</term><term>Genome, Bacterial (genetics)</term><term>High-Throughput Nucleotide Sequencing (methods)</term><term>Metabolic Networks and Pathways (genetics)</term><term>Molecular Sequence Data</term><term>Sequence Alignment</term><term>Sequence Analysis, DNA (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN bactérien (analyse)</term><term>ADN bactérien (génétique)</term><term>Alignement de séquences</term><term>Analyse de séquence d'ADN ()</term><term>Clostridium (génétique)</term><term>Clostridium (métabolisme)</term><term>Données de séquences moléculaires</term><term>Génome bactérien (génétique)</term><term>Protéines bactériennes (génétique)</term><term>Protéines bactériennes (métabolisme)</term><term>Séquence d'acides aminés</term><term>Séquençage nucléotidique à haut débit ()</term><term>Voies et réseaux métaboliques (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>DNA, Bacterial</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Bacterial Proteins</term><term>DNA, Bacterial</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Bacterial Proteins</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>ADN bactérien</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Clostridium</term><term>Genome, Bacterial</term><term>Metabolic Networks and Pathways</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN bactérien</term><term>Clostridium</term><term>Génome bactérien</term><term>Protéines bactériennes</term><term>Voies et réseaux métaboliques</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Clostridium</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Clostridium</term><term>Protéines bactériennes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Molecular Sequence Data</term><term>Sequence Alignment</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Analyse de séquence d'ADN</term><term>Données de séquences moléculaires</term><term>Séquence d'acides aminés</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Clostridium aceticum is an anaerobic homoacetogen, able to reduce CO2 to multi-carbon products using the reductive acetyl-CoA pathway. This unique ability to use CO2 or CO makes the microbe a potential platform for the biotech industry. However, the development of genetically engineered homoacetogen for the large-scale production of commodity chemicals is hampered by the limited amount of their genetic and metabolic information. Here we exploited next-generation sequencing to reveal C. aceticum genome. The short-read sequencing produced 44,871,196 high quality reads with an average length of 248 bases. Following sequence trimming step, 30,256,976 reads were assembled into 12,563 contigs with 168-fold coverage and 1,971 bases in length using de Bruijn graph algorithm. Since the k-mer hash length in the algorithm is an important factor for the quality of output contigs, a window of k-mers (k-51 to k-201) was tested to obtain high quality contigs. In addition to the assembly metrics, the functional annotation of the contigs was investigated to select the k-mer optimum. Metabolic pathway mapping using the functional annotation identified the majority of central metabolic pathways, such as the glycolysis and TCA cycle. Further, these analyses elucidated the enzymes consisting of Wood-Ljungdahl pathway, in which CO2 is fixed into acetyl-CoA. Thus, the metabolic reconstruction based on the draft genome assembly provides a foundation for the functional genomics required to engineer C. aceticum.</div></front></TEI><affiliations><list></list><tree><noCountry><name sortKey="Cho, Byung Kwan" sort="Cho, Byung Kwan" uniqKey="Cho B" first="Byung-Kwan" last="Cho">Byung-Kwan Cho</name><name sortKey="Cho, Suhyung" sort="Cho, Suhyung" uniqKey="Cho S" first="Suhyung" last="Cho">Suhyung Cho</name><name sortKey="Cho, Yongseong" sort="Cho, Yongseong" uniqKey="Cho Y" first="Yongseong" last="Cho">Yongseong Cho</name><name sortKey="Choe, Donghui" sort="Choe, Donghui" uniqKey="Choe D" first="Donghui" last="Choe">Donghui Choe</name><name sortKey="Kim, Sun Chang" sort="Kim, Sun Chang" uniqKey="Kim S" first="Sun Chang" last="Kim">Sun Chang Kim</name><name sortKey="Lee, Sooin" sort="Lee, Sooin" uniqKey="Lee S" first="Sooin" last="Lee">Sooin Lee</name><name sortKey="Song, Yoseb" sort="Song, Yoseb" uniqKey="Song Y" first="Yoseb" last="Song">Yoseb Song</name><name sortKey="Yu, Seok Jong" sort="Yu, Seok Jong" uniqKey="Yu S" first="Seok Jong" last="Yu">Seok Jong Yu</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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