Survey of Genomes - Methanococcus jannaschii

The first group of Archaea were methanogens - microbes that produce methane as a byproduct of their metabolism. The first ever Archaea genome sequenced was from the methanogen Methanococcus jannaschii. Kritika Bhau from the 2019 Hiram College Genetics course walks us through the implications of its genome.

Welcome to Genomics Revolution.  My name is Kritika Bhau and I am a student at Hiram College and currently taking the course called Genetics.  I will be hosting the episode on the organism, Methanococcus jannaschii.  It is also known as methanocaladococcus jannaschii.  I will be calling the organism M. jannaschii throughout the podcast.  M. jannaschii is important because it was also the first archaeon to have its complete genome sequenced.  This sequence help identity many genes unique to domain Archaea.  But, before we get into the genome analysis of this organism, let us talk more about M. Jannaschii to get some background information as to how it was discovered in the first place.  M. jannaschii was first isolated in 1982, in the East Pacific Rise near the western coast of Mexico where it was found from a sample sediment taken from 2600-meter-deep “white smoker” chimney with high temperatures and pressure (1).  But, this organisms survives in these conditions.  This nature of M. Jannaschii is what intrigued scientists. 

When M. Jannaschii’s genome was sequenced, the genomic structure was identified which helped us give more information about the organism’s ability to function in such extreme habitat.  M. jannaschii has three chromosomes: large circular chromosome, large-circular extra chromosome and small circular extra chromosome.  The large circular chromosome is 1.66 megabase pairs long with total 1729 protein-coding regions.  The large circular extra chromosome is 58 kilo base pairs long and has 45 protein coding regions.  Finally, the small circular extra chromosome is 16.5 kilo base pairs with 12 protein codings regions (1). 

M. jannaschii belongs to a group called methanogens.  This means that M. Jannaschii is a methane producer.  M. jannaschii is an autotrophic single cell organism which is specialized in undergoing fueling reactions to produce methane as the end product.  M. jannaschii is strictly anaerobic and uses only carbon dioxide and hydrogen as primary energy sources.  They are very important because they reduce organic products to methane.  Looking at the genome, we can understand the metabolic process, enzymes and proteins involved in M. jannaschii and use it to understand the evolution of domain Archaea.  While analyzing the genome, it was seen that M. jannaschii genome contains all ribosomal proteins that are common to eukaryotes and bacteria.  Moreover, all the subunits found in M. jannaschii show greater similarity to their eukaryotic counterparts than to bacterially subunits meaning that eukaryotes share a common evolutionary trajectory independent to bacteria (1). 

To learn more about how M. jannaschii functions, Tumbula and Whitman conducted in vivo regulation studies to learn that in M. jannaschii “genes of a common pathways are seldom clustered in operons” (2).  They do not know why this is, but they hope to rationalize their findings as more ORF are confirmed.  Additionally, Zhu and et all. Helped identify 963 unique proteins with shotgun proteomic method used in its methanogenesis pathway.  Surprisingly, the proteins that were found represent over half of the whole genome of M. Jannaschii. 95% of those proteins are necessary for amino acid biosynthesis, cellular processes, metabolism and transcription (3).  This is important as with such we can see how effective this organism uses its small genome to survive in such harsh conditions. 

Before, there were two domains based on structure of cells - eukaryotes which have cells with a nucleus like plants and animals. The other domain was prokaryotes which had no nucleus such as bacteria.  But M. jannaschii help create this new third domain: Archaea which is made of single-celled organisms without a nucleus.  With more genetic research using the genome sequence of M. Jannaschii and similar organisms, we hope to find more interesting mechanisms that help us understand the domain Archaea and its evolutionary history. 

(1) Bult, Carol J., et al. (1996). “Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus Jannaschii.” Science, vol. 273, no. 5278, pp. 1058–1073. JSTOR,

(2) Tumbula, D L, and W B Whitman. (1999, July). “Genetics of Methanococcus: Possibilities for Functional Genomics in Archaea.” Molecular Microbiology, U.S. National Library of Medicine,

(3) Zhu, W., Reich, C. I., Olsen, G. J., Giometti, C. S., & Yates, J. R. (2004). Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis. Journal of Proteome Research, 3(3), 538-548.