Physical map of alkaliphilic Bacillus firmus OF4 and detection of a large endogenous plasmid

Abstract

Extremely alkaliphilic Bacillus firmus OF4 is among the best characterized of this group of alkaliphiles. Together with alkaliphilic Bacillus C-125 and numerous non-alkaliphilic Bacillus species whose chromosomes and gene organizations are currently being studied in detail, work on B. firmus OF4 offers the opportunity to discern whether there are features of chromosome and gene organization that are associated with alkaliphily. A physical map of the B. firmus OF4 is consistent with a circular chromosome of approximately 4 Mb, with an extrachromosomal element of 110 kb also detected. The previously identified cadmium-resistance locus and transposition functions in B. firmus OF4 were localized to the extrachromosomal element, whose genes exhibit a slightly different pattern of codon usage from chromosomal genes. No clustering of genes thus far identified with roles in alkaliphily has been found. Direct repeat sequences (DRS) were previously reported upstream of a gene encoding a Na+/H+ antiporter that has a role in pH homeostasis. In the current analyses, these sequences were found to be present in multiple copies on the chromosome, most of which are present in one 920-kb fragment. Such sequences might play a role in DNA rearrangements that allow amplification of important genes in this region.

Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4

“…The genome of B. pseudofirmus OF4 consists of a 3 858 997 bp circular chromosome and two plasmids; pBpOF4-01 (285 222 bp) and pBpOF4-02 (109 029 bp) ( Table 1). The sizes of the main chromosome and the small plasmid are consistent with earlier chromosomal mapping (Gronstad et al, 1998) whereas the presence of the large plasmid has not been previously reported. The average GC content of the chromosome is 40.4% whereas the large and small plasmids have an average GC content of 36% and 35.5% respectively.…”

“…During the sequencing effort, independent preparations of DNA were used. One of them lacked the large pBpOF4‐01 plasmid, as had the earlier sample used in a physical mapping study (Gronstad et al ., 1998). Like the mapping study sample, the cells from which this sample was isolated had been shipped from one collaborating laboratory to another, suggesting that particular manipulations or stresses might lead to loss of the large plasmid of B. pseudofirmus OF4.…”

Alkaliphiles: Some Applications of Their Products for Biotechnology

“…Alkaliphiles have clearly gained large amounts of genetic information by evolutionary processes and exhibit an ability in their genes to cope with particular environments; therefore their genes are a potentially valuable source of information waiting to be explored and exploited by the biotechnologists. Genes responsible for the alkaliphily of Bacillus halodurans C-125 and Bacillus firmus OF4 have been analyzed (49,181). Recently, the complete genome of B. halodurans C-125 has been sequenced to obtain more information on industrial applications and on the molecular basis of alkaliphily.…”

“…Krulwich et al (49,51,76,114,171,172) have focused their studies on the facultative alkaliphile Bacillus firmus OF4, which is routinely grown on malate-containing medium at either pH 7.5 or 10.5. Current work is directed toward clarification of the characteristics and energetics of membrane-associated proteins that must catalyze inward proton movements.…”

pGIAK1, a Heavy Metal Resistant Plasmid from an Obligate Alkaliphilic and Halotolerant Bacterium Isolated from the Antarctic Concordia Station Confined Environment

“…Although little is known about extrachromosomal elements from alkaliphilic bacteria, plasmid profiles from several alkaliphilic bacteria have been reported to harbor both small (<20 kb) and large (>20 kb) plasmids [14], [15]. Similarly, the development of genomic sequencing has revealed the presence of plasmids in several alkaliphic bacteria [16], [17], [18], [19], [20], [21], [22] although their actual functions have so far remained unclear.…”