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Title: Draft genome sequence of Actinotignum schaalii DSM 15541 T: Genetic insights into the lifestyle, cell fitness and virulence

Abstract

The permanent draft genome sequence of Actinotignum schaalii DSM 15541 T is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogensis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA) pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS) were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM) systems, type II toxin-antitoxin (TA), CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contributemore » to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA) and topisomerase IV (ParC) enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH-flavin oxidoreductase.« less

Authors:
ORCiD logo [1];  [2];  [3];  [3];  [3];  [3];  [2];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [4]
  1. Univ. of Bonn, Bonn (Germany)
  2. Klinik und Poliklinik fur Hals-Nasen-Ohrenheilkunde/Chirurgie, Bonn (Germany)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Univ. Paris-Sud (France)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1544031
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 12; Journal Issue: 12; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Science & Technology; Other Topics

Citation Formats

Yassin, Atteyet F., Langenberg, Stefan, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Mukherjee, Supratim, Reddy, T. B. K., Daum, Chris, Shapiro, Nicole, Ivanova, Natalia, Woyke, Tanja, Kyrpides, Nikos C., and Virolle, Marie -Joelle. Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence. United States: N. p., 2017. Web. doi:10.1371/journal.pone.0188914.
Yassin, Atteyet F., Langenberg, Stefan, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Mukherjee, Supratim, Reddy, T. B. K., Daum, Chris, Shapiro, Nicole, Ivanova, Natalia, Woyke, Tanja, Kyrpides, Nikos C., & Virolle, Marie -Joelle. Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence. United States. doi:10.1371/journal.pone.0188914.
Yassin, Atteyet F., Langenberg, Stefan, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Mukherjee, Supratim, Reddy, T. B. K., Daum, Chris, Shapiro, Nicole, Ivanova, Natalia, Woyke, Tanja, Kyrpides, Nikos C., and Virolle, Marie -Joelle. Thu . "Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence". United States. doi:10.1371/journal.pone.0188914. https://www.osti.gov/servlets/purl/1544031.
@article{osti_1544031,
title = {Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence},
author = {Yassin, Atteyet F. and Langenberg, Stefan and Huntemann, Marcel and Clum, Alicia and Pillay, Manoj and Palaniappan, Krishnaveni and Varghese, Neha and Mikhailova, Natalia and Mukherjee, Supratim and Reddy, T. B. K. and Daum, Chris and Shapiro, Nicole and Ivanova, Natalia and Woyke, Tanja and Kyrpides, Nikos C. and Virolle, Marie -Joelle},
abstractNote = {The permanent draft genome sequence of Actinotignum schaalii DSM 15541T is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogensis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA) pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS) were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM) systems, type II toxin-antitoxin (TA), CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA) and topisomerase IV (ParC) enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH-flavin oxidoreductase.},
doi = {10.1371/journal.pone.0188914},
journal = {PLoS ONE},
number = 12,
volume = 12,
place = {United States},
year = {2017},
month = {12}
}

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Works referenced in this record:

Catalytic Promiscuity in Dihydroxy-Acid Dehydratase from the Thermoacidophilic Archaeon Sulfolobus solfataricus
journal, March 2006

  • Kim, Seonghun; Lee, Sun Bok
  • The Journal of Biochemistry, Vol. 139, Issue 3, p. 591-596
  • DOI: 10.1093/jb/mvj057