Characterization and development of phage PhiCh1, an archaeal Natrialba magadii virus with unusual genomic features

Spontaneous lysis of the haloalkalophilic archaeon Natrialba magadii revealed a new phage called phi-Ch1. Phi- Ch1 is the first described bacteriophage specific for this species. Electron microscopic investigations show that phi- Ch1 has an icosaheadral head and a well defined structured contractible tall. Its morphology as well as the significant dependence on high ionic strength (at least 2 M NaC1) for structural stability and infectivity identify phi-Ch1 as a typical halophage corresponding to the physiological situation of its host. The capsid is composed of 4 major and 5 minor proteins with a molecular weight range of 14 to 80 kDa named A to 1 and with extraordinarily low isoelectric points between pH 3.3 and pH 5.2. Sequencing of the coding region of several structural proteins indicate that protein E shows homology to protein hp32, a coat protein of the archaeal phage (DH. In contrast to protein E, proteins A and H share no homologies with phi-H. Characterization of nucleic acid revealed that the phage contains DNA and RNA in its capsid. Analysis of the genome of phi-Ch1 revealed linear, 55 kb double stranded DNA and RNA fragments, co-isolated with the DNA. For these RNA fragments, sizes of about 80 to 700 bases could be detected. The function of this RNA type is not clear. Investigation of the origin of the RNA species, isolated from mature phage particles, by hybridization experiments revealed that these RNAs are more likely to be encoded by the host N. magadii rather than by the phage itself. Using the phage as a model system, answers will be given to the problem of gene regulation in Archaea. As ft has been shown recently, the sequencing of different genomes of members of the Archaea revealed that genes involved in cell division, energy metabolism are closely related to those found in Bacteria genes involved In gene regulation and replication to those found in Eukarya. The sequencing of the phage genome therefore is one of the main topic of this study. As described for Methanococcus janaaschii, where about 50% of the genes are related to known genes from Bacteria. and Eukarya, homology study with the sequence of phage phi-Ch1 will give further insights into regulation events. The establishing of a transformation system is the basis to work genetically with N. magadii and related organisms. So far, such a system does not exist for haloalkalophilc Archaea. The introduction of foreign genes, the possibility to delete genes from the host chromosome as well as from the phage in its lysogenic stage will be the background to study gene regulation and expression in detail. Additionally, the use of these organisms for fermentation procedures or the treatment of special waste water with N. magadii will be enhanced by the additional production of products normally not found in N. magadii.