2004 Annual Science Report
Michigan State University Reporting | JUL 2003 – JUN 2004
Genomes of Permafrost Bacteria
A major objective of our research team is to determine the repertoire of genes necessary for bacteria to live in the permafrost environment. Central to this effort is determining (in collaboration with the Joint Genome Institute and the Lawrence Livermore National Laboratory) the complete genome sequences of two bacteria that we have isolated from Siberian permafrost: Psychrobacter strain 273-4 and Exiguobacterium strain 255-15, psychrophilic bacteria isolated from permafrost soils thought to have been constantly frozen for some 40,000 and 3 million years, respectively.
Sequencing of the Psychrobacter genome has been completed. Considerable effort over the past year went into a “manual curation” of each open reading frame (ORF) to yield the first completely annotated genome of a psychroactive microorganism. A number of interesting findings have emerged. The genome is 2.64-megabases in size, contains 2,147 ORFs including a 20,145 base pair (bp) tandem repeat that encodes an extremely large hypothetical protein of 6,715 amino acids. The genome encodes four histone-like proteins that potentially have roles in cold tolerance as well as enzymes for a complete glyoxylate shunt pathway enabling growth of an acetate. Analysis of genes that were found to be up-regulated in response to low temperature (see transcriptome and proteome projects) revealed the existence of a novel 139 bp sequence present 294 times in the genome that may have roles in cold-regulated gene expression. Phylogenetic analysis has also revealed that an isocitrate lyase encoded by Psychrobacter forms a unique cluster with cold-induced isocitrate lyases of the psychrophile Colwellia maris and three other microbes that grow at low temperatures. Significantly, this cluster of sequences contains three insertions that may increase flexibility of the enzymes and reduce activation energy, an important factor for function at low temperature.
Significant progress has also been made in sequencing the Exiguobacterium 255-15 genome, estimated to be about 2.9 Mb in size. Currently, the sequences are assembled into 70 contigs predicted to encode 2,977 proteins. Approximately 75% of the Exiguobacterium ORFs encode putative homologs of Psychrobacter proteins and there appear to be many ORFs that encode putative homologues of genes from Bacillus and other genera that are known to be expressed at cold temperatures including proteins involved in ribosomal binding, membrane alteration, metabolism, DNA replication, and transcription.
PROJECT INVESTIGATORS:David Gilichinsky
Project InvestigatorMichael Thomashow
Project InvestigatorJames Tiedje
Project InvestigatorJames Cole
PROJECT MEMBERS:Patrick Chain
RELATED OBJECTIVES:Objective 5.1
Environment-dependent, molecular evolution in microorganisms
Biochemical adaptation to extreme environments
Adaptation and evolution of life beyond Earth