Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction.
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.
Anderson
Iain
I
Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA 94598, USA. IJAnderson@lbl.gov
Rodriguez
Jason
J
Susanti
Dwi
D
Porat
Iris
I
Reich
Claudia
C
Ulrich
Luke E
LE
Elkins
James G
JG
Mavromatis
Kostas
K
Lykidis
Athanasios
A
Kim
Edwin
E
Thompson
Linda S
LS
Nolan
Matt
M
Land
Miriam
M
Copeland
Alex
A
Lapidus
Alla
A
Lucas
Susan
S
Detter
Chris
C
Zhulin
Igor B
IB
Olsen
Gary J
GJ
Whitman
William
W
Mukhopadhyay
Biswarup
B
Bristow
James
J
Kyrpides
Nikos
N
D019843:Archaeal Proteins / Q000235:genetics; D001482:Base Composition; D053898:Biosynthetic Pathways; D002352:Carrier Proteins / Q000235:genetics; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics*; D004783:Environmental Microbiology; D019766:Genes, Archaeal; D020745:Genome, Archaeal; D007055:Iceland; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D041561:Thermofilaceae / Q000235:genetics* / Q000302:isolation & purification
D019843:Archaeal Proteins; D002352:Carrier Proteins; D019641:DNA, Archaeal