Nanoarchaeum equitans

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A Microbial Biorealm page on the genus Nanoarchaeum equitans


Higher order taxa

Archaea; Nanoarchaeota; Nanoarchaeum


Nanoarchaeum equitans

Description and significance

Nanoarchaeum equitans, which means "riding the fire sphere", is a hyperthermophile that also acts as an obligate symbiont to the archaea Ignicoccus hospitalis. It is spherical and is only 400 nm in diameter, making it one of the smallest known living organisms. It is also the only known archaeal parasite. (3) (5)

It was first discovered in 2002 in an undersea hydrothermal vent off the coast of Iceland by Karl Stetter. It was first seen as tiny dots on the surface of Ignicoccus hospitalis. Its genome is extremely small, making it one of the smallest non-viral genomes ever sequenced. The significance of its genome was that ss rRNA-based sequencing comparisons placed its branching point early in the archaeal lineage, representing the new archaeal kingdom Nanoarchaeota. As such, it is the only known member of this lineage. (1)

Genome structure

Nanoarchaeum equitans has one of the smallest genomes of any sequenced microbe with only 490,885 base pairs. It was first sequenced in 2003. This sequenced genome was of strain Kin4-M which was found in hot-water geysers on the ocean floor near Iceland.

The genome has one circular chromosome, about 550 protein genes, 46 RNA genes, and has a GC content of 31.6%. The genome encodes the machinery for information processing and repair, but lacks genes for lipid, cofactor, amino acid, or nucleotide biosynthesis. It is also one of the most compact genomes, with 95% of the DNA used to encode proteins or stable RNAs. Unlike the similarly small genomes of bacterial parasites that are undergoing reductive evolution, Nanoarchaeum equitans has few pseudogenes or extensive regions of noncoding DNA. Another interesting feature is that there are many split genes that code for different functional domains of the encoded protein and are found in different places along the chromosome. To get full function, the two domains must be synthesized independently and brought together. (4) (9)

Cell structure and metabolism

Nanoarchaeum equitans is spherical and extremely small, with a size of only 400 nm in diameter. This marks it as one of the smallest known living cells. It has no flagella and can only grow attached to the specific archaeal host Ignicoccus hospitalis. Due to the lack of genes encoding several vital metabolic pathways, Nanoarchaeum equitans relies on its host to acquire many biomolecules such as lipids, amino acids, and nucleotides. (1) (2)


Nanoarchaeum equitans is a hyperthermophile, with its ideal environment having a temperature of 90 degrees Celsius. It also prefers to be in places rich in sulfur, hydrogen, and carbon dioxide since it lacks the means to metabolize these compounds on its own. Nanoarchaeum equitans has no significant contribution or effect on its environment.

Nanoarchaeum equitans acts as an obligate symbiont that lives on the surface of the crenarchaeon Ignicoccus hospitalis. Since Nanoarchaeum equitans cannot live apart from this host, it represents the only known example of an archaeal parasite. (4) (5)


Nanoarchaeum equitans is not a pathogen. However, it does act as a parasite to Ignicoccus hospitalis and cannot survive without it. This relationship appears to involve only molecular recognition, with signaling and exchange between the two archaea. (1) (3)

Application to Biotechnology

Although it may not produce any useful compounds or enzymes, Nanoarchaeum equitans may be useful in biotechnology. This is because its small genome and small number of genes could make it easier to genetically engineer which will help for future research into industrial chemicals that work well in extreme environments, such as enzymes that break down harmful substances in oil wells. (3)

Current Research

1) The genome and proteome composition of Nanoarchaeum equitans was analyzed and compared to that of other mesophiles, hyperthermophiles, and obligatory host-associated organisms to determine any significant differences that may have resulted from evolution. The study resulted in revealing that the composition is marked with the signatures of dual adaptation- one to high temperature and another to obligatory parasitism. The comparative study of the compositional characteristics of mesophiles, hyperthermophiles, and obligatory host-associated organisms demonstrates the generality of such strategies in the microbial world. (8)

2) The analysis of the genome sequence of Nanoarchaeum equitans has not revealed genes encoding vital tRNA species. After searching for widely separated genes encoding tRNA halves, it was discovered that the genome contains nine genes that encode tRNA halves. Reverse transcriptase polymerase chain reaction and aminoacylation experiments of the tRNA demonstrated maturation to full-size tRNA. (7)

3) In order to analyze the contents and nature of the membrane lipids of Nanoarchaeum equitans, its host cell, Ignicoccus hospitalis was grown at 90 degrees C, as well as Ignicoccus hospitalis without any parasites at its lowest and highest growth temperatures of 75 degrees C and 95 degrees C respectively. Both organisms contained identical assemblages of glycerol ether lipids, showing only differences in the amounts of certain components. Analysis of the total lipid extracts revealed that archaeol and caldarchaeol were the main core lipids. Sugar residues were mainly mannose and small amounts of glucose. (6)


(1) "A Genomic Perspective of the Nanoarchaeum Equitans-Ignicoccus Sp Archaeal Association." JGI. 6 Sept. 2005. he Regents of the University of California. 25 Aug. 2007 <>.

(2)Ahel, I. "HAMAP: Nanoarchaeum Equitans Complete Proteome." HAMAP. 2 May 2003. ExPASy. 24 Aug. 2007 <>.

(3)"Archaea Genomes-NANOARCHAEUM EQUITANS." EMBL-EBI. 1 May 2003. European Bioinformatics Institute. 26 Aug. 2007 <>.

(4)Gene, Mike. "Extreme Evolution: a View From Three Perspectives." ID THINK. 15 Sept. 2005. 24 Aug. 2007 <>.

(5)Huber, H, Mj Hohn, R Rachel, T Fuchs, Vc Wimmer, and Ko Stetter. "A New Phylum of Archaea Represented by a Nanosized Hyperthermophilic Symbiont." PubMed. 2 May 2002. NCBI. 25 Aug. 2007 <>.

(6)Jahn, U, R Summons, H Sturt, E Grosjean, and H Huber. "Composition of the Lipids of Nanoarchaeum Equitans and Their Origin From Its Host Ignicoccus Sp. Strain KIN4/I." PubMed. 14 Sept. 2004. NCBI. 27 Aug. 2007 <>.

(7)Randau, Lennart, Richard Munch, Micheal J. Hohn, Dieter Jahn, and Dieter Soil. "Nanoarchaeum Equitans Creates Functional TRNAs From Separate Genes for Their 5'- and 3'-Halves." Nature. 3 Feb. 2005. NPG. 28 Aug. 2007 <>.

(8)Sabyasachi, Das, Paul Sandip, Bag K. Sumit, and Dutta Chitra. "Analysis of Nanoarchaeum Equitans Genome and Proteome Composition: Indications for Hyperthermophilic and Parasitic Adaptation." BMC Genomics. 25 July 2006. BioMed Central. 27 Aug. 2007 <>.

(9)Waters, E. "The Genome of Nanoarchaeum Equitans: Insights Into Early Archaeal Evolution and Derived Parasitism." PubMed. 28 Oct. 2003. NCBI. 26 Aug. 2007 <>.

Edited by Robert Rishwain, student of Rachel Larsen and Kit Pogliano