August 10, 1999

JAMSTEC

The Frontier Research Program for Deep-sea Extremophiles of the Japan Marine Science and Technology Center (JAMSTEC, Chief Director: Takuya Hirano) has completed the sequencing of the whole genome of the alkaliphilic Bacillus halodurans (Photo 1) within one year and three months from May 1998 to July, 1999.

In the DNA sequencing of the genome, we used the new and developing method: the whole-genome shotgun method. The application of this method to a bacterial genome that exceeds four million bases has rarely been reported. During this project, we have developed a total genome analysis system called the GAMBLER (Genome assembly and genome information research) system in order to handle the massive DNA sequence data.

This research results have been made public in the international science journal and through the presentation at the 9th European Congress on Biotechnology on July 1999 in Brussels, Belgium and was very acclaimed (Reference 1).

The industrially-useful Bacillus halodurans is an alkaliphilic bacterium found by Dr. Koki Horikoshi that produces many industrially useful alkaliphilic enzymes such as, protease (protein degrading enzyme), cellulase (cellulose degrading enzyme) and amylase (starch degrading enzyme). These enzymes are widely used as additives to laundry detergents. Bacillus halodurans also produces keratin decomposing enzyme which devolves keratinous proteins such as hair (Photo 2), nail and cock feathers which is troubling the world for its disposal. Bacillus halodurans are now actively investigated for further industrial applications.

Bacillus halodurans which is closely related to Bacillus subtilis whose genome has been completely sequenced by the joint project between Japan and European Community. Accordingly, it was expected that the genome structure of B. halodurans was similar to that of B. subtilis, but it has just become the gene order in B. halodurans shows significant difference from that of Bacillus subtilis..

From these results, it was also found that 20%~30% of all genes assigned in the B. halodurans genome did not show any similarity to any other gene so far reported. Thus it is considered that the genome sequence of B. halodurans will play an important role as a supplier of new genome information.

Bacillus halodurans also produces xylanase that bleaches pulp in the process of paper-making. The low productivity is hindering commercialization of potential enzymes. It is earnestly expected to clarify the regulation mechanism of the enzyme production in alkaliphilic Bacillus genus, which will contribute to the further industrialization of useful enzymes that Bacillus halodurans and other related microbes produce.

The whole genome (4.25 million bases) was once fragmented randomly to 1~2 thousand bases and assembled back to the genome based on the sequence information of each fragment. This method is called the whole-genome shotgun method.

The whole-genome shotgun method has rarely been applied to the whole-genome sequencing of a bacterial genome that exceeds four million bases. By systemizing the sequencing procedure, we have succeeded to sequence the whole genome by nine men in a world recording speed.

As previously described Bacillus halodurans was sequenced by the whole-genome shotgun method. The whole-genome shotgun method is the method for genome sequencing by random fragmentation to 1~2 thousand bases and assemble them back to the genome by the sequence information of the fragments. In order to analyze these massive data of a bacterial genome that exceeds four million bases, a computerized system that automates the procedures, from assembling and analyzing the genome sequence to submitting the large genome data, is necessary.

The Frontier Research Program for Deep-sea Extremophiles of JAMSTEC has developed a total genome analysis system, so-called GAMBLER system, to contribute on the speed-up of the future genome analysis projects in Japan. The system automates the processes done by man and enables rapid genetic analyses. The GAMBLER system can handle large bacterial genome up to the size of 10 million bases and we strongly believe that the system will contribute to the future of genome analyses in Japan.