Random sequence analysis of genomic DNA of a hyperthermophile: Aquifex pyrophilus

In Geol Choi; Sang Suk Kim; Jae Ryeon Ryu; Ye Sun Han; Won Gi Bang; Sung Hou Kim; Yeon Gyu Yu

doi:10.1007/s007920050025

Random sequence analysis of genomic DNA of a hyperthermophile: Aquifex pyrophilus

In Geol Choi, Sang Suk Kim, Jae Ryeon Ryu, Ye Sun Han, Won Gi Bang, Sung Hou Kim, Yeon Gyu Yu

Research output: Contribution to journal › Article › peer-review

12 Citations (Scopus)

Abstract

Aquifex pyrophilus is one of the hyperthermophilic bacteria that can grow at temperatures up to 95°C. To obtain information about its genomic structure, random sequencing was performed on plasmid libraries containing 0.5-2 kb genomic DNA fragments of A. pyrophilus. Comparison of the obtained sequence tags with known proteins revealed that 123 tags showed strong similarity to previously identified proteins in the PIR or Genebank databases. These included three proteases, two amino acid racemases, and three enzymes utilizing oxygen as substrate. Although the GC ratio of the genome is about 40%, the codon usage of A. pyrophilus showed biased occurrence of G and C at the third position of codons, especially those for amino acids such as asparagine, aspartic acid, cysteine, glutamine, glutamic acid, histidine, lysine, and tyrosine. A higher ratio of positively charged amino acids in A. pyrophilus proteins as compared with proteins from mesophiles suggested that Aquifex proteins might contain increased ion-pair interaction that could help to maintain heat stability.

Original language	English
Pages (from-to)	125-134
Number of pages	10
Journal	Extremophiles
Volume	1
Issue number	3
DOIs	https://doi.org/10.1007/s007920050025
Publication status	Published - 1997
Externally published	Yes

Bibliographical note

Funding Information:
Acknowledgments We thank Dr. K.-S. Kim of the Structural Biology Center of the Korea Institute of Science and Technology for helpful advice on the application of the SEQSEE and BLAST programs. This work is supported by a grant from the Ministry of Science and Technology, Korea. The work of S.-H. Kim has been supported by the Office of Health and Environmental Research, U.S. Department of Energy (DE-AC03-765F00098).

Keywords

Aquifex pyrophilus
Hyperthermophile Genome sequence
Oxidase
Protease
Racemase

ASJC Scopus subject areas

Microbiology
Molecular Medicine

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10.1007/s007920050025

Cite this

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title = "Random sequence analysis of genomic DNA of a hyperthermophile: Aquifex pyrophilus",

abstract = "Aquifex pyrophilus is one of the hyperthermophilic bacteria that can grow at temperatures up to 95°C. To obtain information about its genomic structure, random sequencing was performed on plasmid libraries containing 0.5-2 kb genomic DNA fragments of A. pyrophilus. Comparison of the obtained sequence tags with known proteins revealed that 123 tags showed strong similarity to previously identified proteins in the PIR or Genebank databases. These included three proteases, two amino acid racemases, and three enzymes utilizing oxygen as substrate. Although the GC ratio of the genome is about 40%, the codon usage of A. pyrophilus showed biased occurrence of G and C at the third position of codons, especially those for amino acids such as asparagine, aspartic acid, cysteine, glutamine, glutamic acid, histidine, lysine, and tyrosine. A higher ratio of positively charged amino acids in A. pyrophilus proteins as compared with proteins from mesophiles suggested that Aquifex proteins might contain increased ion-pair interaction that could help to maintain heat stability.",

keywords = "Aquifex pyrophilus, Hyperthermophile Genome sequence, Oxidase, Protease, Racemase",

author = "Choi, {In Geol} and Kim, {Sang Suk} and Ryu, {Jae Ryeon} and Han, {Ye Sun} and Bang, {Won Gi} and Kim, {Sung Hou} and Yu, {Yeon Gyu}",

note = "Funding Information: Acknowledgments We thank Dr. K.-S. Kim of the Structural Biology Center of the Korea Institute of Science and Technology for helpful advice on the application of the SEQSEE and BLAST programs. This work is supported by a grant from the Ministry of Science and Technology, Korea. The work of S.-H. Kim has been supported by the Office of Health and Environmental Research, U.S. Department of Energy (DE-AC03-765F00098).",

year = "1997",

doi = "10.1007/s007920050025",

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AU - Bang, Won Gi

AU - Kim, Sung Hou

AU - Yu, Yeon Gyu

N1 - Funding Information: Acknowledgments We thank Dr. K.-S. Kim of the Structural Biology Center of the Korea Institute of Science and Technology for helpful advice on the application of the SEQSEE and BLAST programs. This work is supported by a grant from the Ministry of Science and Technology, Korea. The work of S.-H. Kim has been supported by the Office of Health and Environmental Research, U.S. Department of Energy (DE-AC03-765F00098).

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N2 - Aquifex pyrophilus is one of the hyperthermophilic bacteria that can grow at temperatures up to 95°C. To obtain information about its genomic structure, random sequencing was performed on plasmid libraries containing 0.5-2 kb genomic DNA fragments of A. pyrophilus. Comparison of the obtained sequence tags with known proteins revealed that 123 tags showed strong similarity to previously identified proteins in the PIR or Genebank databases. These included three proteases, two amino acid racemases, and three enzymes utilizing oxygen as substrate. Although the GC ratio of the genome is about 40%, the codon usage of A. pyrophilus showed biased occurrence of G and C at the third position of codons, especially those for amino acids such as asparagine, aspartic acid, cysteine, glutamine, glutamic acid, histidine, lysine, and tyrosine. A higher ratio of positively charged amino acids in A. pyrophilus proteins as compared with proteins from mesophiles suggested that Aquifex proteins might contain increased ion-pair interaction that could help to maintain heat stability.

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Random sequence analysis of genomic DNA of a hyperthermophile: Aquifex pyrophilus

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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