Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction

Iain Anderson, Jason Rodriguez, Dwi Susanti, Iris Porat, Claudia Reich, Luke E. Ulrich, James G. Elkins, Kostas Mavromatis, Athanasios Lykidis, Edwin Kim, Linda S. Thompson, Matt Nolan, Miriam Land, Alex Copeland, Alla Lapidus, Susan Lucas, Chris Detter, Igor B. Zhulin, Gary J. Olsen, William WhitmanBiswarup Mukhopadhyay, James Bristow, Nikos Kyrpides

Research output: Contribution to journalArticle

Abstract

We report the complete genome of Thermofilum pendens, a deeply branching, hyperthermophilic member of the order Thermoproteales in the archaeal kingdom Crenarchaeota. T. pendens is a sulfur-dependent, anaerobic heterotroph isolated from a solfatara in Iceland. It is an extracellular commensal, requiring an extract of Thermoproteus tenax for growth, and the genome sequence reveals that biosynthetic pathways for purines, most amino acids, and most cofactors are absent. In fact, T. pendens has fewer biosynthetic enzymes than obligate intracellular parasites, although it does not display other features that are common among obligate parasites and thus does not appear to be in the process of becoming a parasite. It appears that T. pendens has adapted to life in an environment rich in nutrients. T. pendens was known previously to utilize peptides as an energy source, but the genome revealed a substantial ability to grow on carbohydrates. T. pendens is the first crenarchaeote and only the second archaeon found to have a transporter of the phosphotransferase system. In addition to fermentation, T. pendens may obtain energy from sulfur reduction with hydrogen and formate as electron donors. It may also be capable of sulfur-independent growth on formate with formate hydrogen lyase. Additional novel features are the presence of a monomethylamine:corrinoid methyltransferase, the first time that this enzyme has been found outside the Methanosarcinales, and the presence of a presenilin-related protein. The predicted highly expressed proteins do not include proteins encoded by housekeeping genes and instead include ABC transporters for carbohydrates and peptides and clustered regularly interspaced short palindromic repeat-associated proteins.

Original languageEnglish (US)
Pages (from-to)2957-2965
Number of pages9
JournalJournal of bacteriology
Volume190
Issue number8
DOIs
StatePublished - Apr 1 2008

Fingerprint

Thermofilaceae
formic acid
Biosynthetic Pathways
Sulfur
Genome
Parasites
Thermoproteales
Thermoproteus
Methanosarcinales
Proteins
Corrinoids
Crenarchaeota
Clustered Regularly Interspaced Short Palindromic Repeats
Carbohydrates
Presenilins
Iceland
Purines
Peptides
ATP-Binding Cassette Transporters
Essential Genes

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology

Cite this

Anderson, I., Rodriguez, J., Susanti, D., Porat, I., Reich, C., Ulrich, L. E., ... Kyrpides, N. (2008). Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. Journal of bacteriology, 190(8), 2957-2965. https://doi.org/10.1128/JB.01949-07

Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. / Anderson, Iain; Rodriguez, Jason; Susanti, Dwi; Porat, Iris; Reich, Claudia; Ulrich, Luke E.; Elkins, James G.; Mavromatis, Kostas; Lykidis, Athanasios; Kim, Edwin; Thompson, Linda S.; Nolan, Matt; Land, Miriam; Copeland, Alex; Lapidus, Alla; Lucas, Susan; Detter, Chris; Zhulin, Igor B.; Olsen, Gary J.; Whitman, William; Mukhopadhyay, Biswarup; Bristow, James; Kyrpides, Nikos.

In: Journal of bacteriology, Vol. 190, No. 8, 01.04.2008, p. 2957-2965.

Research output: Contribution to journalArticle

Anderson, I, Rodriguez, J, Susanti, D, Porat, I, Reich, C, Ulrich, LE, Elkins, JG, Mavromatis, K, Lykidis, A, Kim, E, Thompson, LS, Nolan, M, Land, M, Copeland, A, Lapidus, A, Lucas, S, Detter, C, Zhulin, IB, Olsen, GJ, Whitman, W, Mukhopadhyay, B, Bristow, J & Kyrpides, N 2008, 'Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction', Journal of bacteriology, vol. 190, no. 8, pp. 2957-2965. https://doi.org/10.1128/JB.01949-07
Anderson, Iain ; Rodriguez, Jason ; Susanti, Dwi ; Porat, Iris ; Reich, Claudia ; Ulrich, Luke E. ; Elkins, James G. ; Mavromatis, Kostas ; Lykidis, Athanasios ; Kim, Edwin ; Thompson, Linda S. ; Nolan, Matt ; Land, Miriam ; Copeland, Alex ; Lapidus, Alla ; Lucas, Susan ; Detter, Chris ; Zhulin, Igor B. ; Olsen, Gary J. ; Whitman, William ; Mukhopadhyay, Biswarup ; Bristow, James ; Kyrpides, Nikos. / Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. In: Journal of bacteriology. 2008 ; Vol. 190, No. 8. pp. 2957-2965.
@article{e8e72128bd564d099359b13349239632,
title = "Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction",
abstract = "We report the complete genome of Thermofilum pendens, a deeply branching, hyperthermophilic member of the order Thermoproteales in the archaeal kingdom Crenarchaeota. T. pendens is a sulfur-dependent, anaerobic heterotroph isolated from a solfatara in Iceland. It is an extracellular commensal, requiring an extract of Thermoproteus tenax for growth, and the genome sequence reveals that biosynthetic pathways for purines, most amino acids, and most cofactors are absent. In fact, T. pendens has fewer biosynthetic enzymes than obligate intracellular parasites, although it does not display other features that are common among obligate parasites and thus does not appear to be in the process of becoming a parasite. It appears that T. pendens has adapted to life in an environment rich in nutrients. T. pendens was known previously to utilize peptides as an energy source, but the genome revealed a substantial ability to grow on carbohydrates. T. pendens is the first crenarchaeote and only the second archaeon found to have a transporter of the phosphotransferase system. In addition to fermentation, T. pendens may obtain energy from sulfur reduction with hydrogen and formate as electron donors. It may also be capable of sulfur-independent growth on formate with formate hydrogen lyase. Additional novel features are the presence of a monomethylamine:corrinoid methyltransferase, the first time that this enzyme has been found outside the Methanosarcinales, and the presence of a presenilin-related protein. The predicted highly expressed proteins do not include proteins encoded by housekeeping genes and instead include ABC transporters for carbohydrates and peptides and clustered regularly interspaced short palindromic repeat-associated proteins.",
author = "Iain Anderson and Jason Rodriguez and Dwi Susanti and Iris Porat and Claudia Reich and Ulrich, {Luke E.} and Elkins, {James G.} and Kostas Mavromatis and Athanasios Lykidis and Edwin Kim and Thompson, {Linda S.} and Matt Nolan and Miriam Land and Alex Copeland and Alla Lapidus and Susan Lucas and Chris Detter and Zhulin, {Igor B.} and Olsen, {Gary J.} and William Whitman and Biswarup Mukhopadhyay and James Bristow and Nikos Kyrpides",
year = "2008",
month = "4",
day = "1",
doi = "10.1128/JB.01949-07",
language = "English (US)",
volume = "190",
pages = "2957--2965",
journal = "Journal of Bacteriology",
issn = "0021-9193",
publisher = "American Society for Microbiology",
number = "8",

}

TY - JOUR

T1 - Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction

AU - Anderson, Iain

AU - Rodriguez, Jason

AU - Susanti, Dwi

AU - Porat, Iris

AU - Reich, Claudia

AU - Ulrich, Luke E.

AU - Elkins, James G.

AU - Mavromatis, Kostas

AU - Lykidis, Athanasios

AU - Kim, Edwin

AU - Thompson, Linda S.

AU - Nolan, Matt

AU - Land, Miriam

AU - Copeland, Alex

AU - Lapidus, Alla

AU - Lucas, Susan

AU - Detter, Chris

AU - Zhulin, Igor B.

AU - Olsen, Gary J.

AU - Whitman, William

AU - Mukhopadhyay, Biswarup

AU - Bristow, James

AU - Kyrpides, Nikos

PY - 2008/4/1

Y1 - 2008/4/1

N2 - We report the complete genome of Thermofilum pendens, a deeply branching, hyperthermophilic member of the order Thermoproteales in the archaeal kingdom Crenarchaeota. T. pendens is a sulfur-dependent, anaerobic heterotroph isolated from a solfatara in Iceland. It is an extracellular commensal, requiring an extract of Thermoproteus tenax for growth, and the genome sequence reveals that biosynthetic pathways for purines, most amino acids, and most cofactors are absent. In fact, T. pendens has fewer biosynthetic enzymes than obligate intracellular parasites, although it does not display other features that are common among obligate parasites and thus does not appear to be in the process of becoming a parasite. It appears that T. pendens has adapted to life in an environment rich in nutrients. T. pendens was known previously to utilize peptides as an energy source, but the genome revealed a substantial ability to grow on carbohydrates. T. pendens is the first crenarchaeote and only the second archaeon found to have a transporter of the phosphotransferase system. In addition to fermentation, T. pendens may obtain energy from sulfur reduction with hydrogen and formate as electron donors. It may also be capable of sulfur-independent growth on formate with formate hydrogen lyase. Additional novel features are the presence of a monomethylamine:corrinoid methyltransferase, the first time that this enzyme has been found outside the Methanosarcinales, and the presence of a presenilin-related protein. The predicted highly expressed proteins do not include proteins encoded by housekeeping genes and instead include ABC transporters for carbohydrates and peptides and clustered regularly interspaced short palindromic repeat-associated proteins.

AB - We report the complete genome of Thermofilum pendens, a deeply branching, hyperthermophilic member of the order Thermoproteales in the archaeal kingdom Crenarchaeota. T. pendens is a sulfur-dependent, anaerobic heterotroph isolated from a solfatara in Iceland. It is an extracellular commensal, requiring an extract of Thermoproteus tenax for growth, and the genome sequence reveals that biosynthetic pathways for purines, most amino acids, and most cofactors are absent. In fact, T. pendens has fewer biosynthetic enzymes than obligate intracellular parasites, although it does not display other features that are common among obligate parasites and thus does not appear to be in the process of becoming a parasite. It appears that T. pendens has adapted to life in an environment rich in nutrients. T. pendens was known previously to utilize peptides as an energy source, but the genome revealed a substantial ability to grow on carbohydrates. T. pendens is the first crenarchaeote and only the second archaeon found to have a transporter of the phosphotransferase system. In addition to fermentation, T. pendens may obtain energy from sulfur reduction with hydrogen and formate as electron donors. It may also be capable of sulfur-independent growth on formate with formate hydrogen lyase. Additional novel features are the presence of a monomethylamine:corrinoid methyltransferase, the first time that this enzyme has been found outside the Methanosarcinales, and the presence of a presenilin-related protein. The predicted highly expressed proteins do not include proteins encoded by housekeeping genes and instead include ABC transporters for carbohydrates and peptides and clustered regularly interspaced short palindromic repeat-associated proteins.

UR - http://www.scopus.com/inward/record.url?scp=41949089913&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=41949089913&partnerID=8YFLogxK

U2 - 10.1128/JB.01949-07

DO - 10.1128/JB.01949-07

M3 - Article

C2 - 18263724

AN - SCOPUS:41949089913

VL - 190

SP - 2957

EP - 2965

JO - Journal of Bacteriology

JF - Journal of Bacteriology

SN - 0021-9193

IS - 8

ER -