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2006 Annual Science Report

Michigan State University Reporting  |  JUL 2005 – JUN 2006

Genomes of Permafrost Bacteria: Psychrobacter Isolates

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Field Sites

Project Progress

The main objective of this project is to determine what genomic features make a microorganism cold adapted. Towards that goal over the past year we have finished the genome sequencing of Psychrobacter cryohaloentis K5 and we are near full coverage with the genome of Psychrobacter sp. PRw-f1. The genome of Psychrobacter cryohalolentis K5, which is ~ 3.1 megabases in size, contains 2,521 putative proteins and represents the second psychrophilic genome of the Psychrobacter family. P. cryohalolentis, like P.arcticus, grows as low as -10º C and the genome is very similar to the P. arcticus genome with 1778 genes in common and an average amino acid identity (AAI) of 87 %. This genome poses a cold shock genes and a high number of mobile elements similar to P.arcticus. On the other hand, PRw-f1, isolated from the marine fish Lutjanus vivanus in warm water off the north coast of Puerto Rico, is currently in 20 contigs with ~ 2.9 megabases in size and 2,350 candiadate proteins. This strain, that represents a new species within the Psychrobacter family, has a growth range between 0º and 42º C, and has the most distinct genome with an AAI of 66 % when compared to P. arcticus. These results suggest that PRw-f1 proteome could be better adapted to a warmer niche than P.arcticus or P. cryohalolentis , that grow between -10º and 25 º C, providing a good source for genome comparisons.

Genome comparisons have revealed several genomic features of cold adapted microorganisms. Comparison of the G+C content of the three Psychrobacter genomes indicate that the average G+C content of Psychrobacter sp. PRw-f1 is 2% higher (44.8%) than the other two psychrophilic genomes. An increase is G+C content is a typical adaptation for growth on warmer environments. A lower G+C content could facilitate DNA strand separation at lower temperatures. To study cold adaptation at the gene level we have examined patterns of amino acid usage in Psychrobacter arcticus in comparison to a database of mesophilic microorganisms. Proline content, arginine content, arginine/lysine ratio, acidic residues, hydrophobicity and aliphacity were used as indicators of cold adaptation by comparing each Psychrobacter arcticus ORFs against five orthologous genes in the mesophilic datase. Statistical analysis of the data indicates that across all functional gene categories there was a higher proportion of genes that show a statistically significant adaptation towards cold in at least one of the six indicators used. In particular a reduction in proline and arginine content was the most common adaptation towards cold across all gene categories. The reduction of those amino acids increases the flexibility and decreases the stability of the proteins making them more active at low temperatures. Another adaptation observed in the dataset was an increase of the length of the disordered regions in P.arcticus compared to a mesophilic database. All these result suggest that psychrophiles employ a variety of strategies to maintain enzyme activity at low temperatures.