In a lecture delivered at Harvard University almost three decades ago, Francis Crick declared that he had become disenchanted with the view that life arose on Earth. Instead, he espoused a Theory of Panspermia, which holds that life was sent to Earth from elsewhere in the Universe, and he proposed that the seed of life would have been an extraordinarily resistant spore of the kind produced by Bacillus subtilis and related bacteria. In response, Matthew Meselson pointed out that, if this were so, surely the extraterrestrial civilization would have sent a message in the spore. If only mankind was able to sequence DNA, he wistfully conjectured, then we could learn the secret of the Universe from the nucleotide sequence of the contemporary genome of the spore-forming bacterium. Now we have such a sequence, for on page 249of this issue1 a worldwide consortium report the 4,214,810-nucleotide sequence of the single chromosome of B. subtilis. If the sequence contains a cosmic revelation, it has evidently escaped the scrutiny of the 151 collaborators in this impressive sequencing project. Nonetheless, the B. subtilis genome sequence is a milestone in microbiology and of fundamental importance to industry, medicine and basic science.
The complement of genes making up the B. subtilis genome contains many surprises. The regulation of gene expression in this organism is known to be quite different from that in Escherichia coli. But the finding of genes encoding 18 sigma factors (prokaryotic regulators of gene transcription) is still surprising. It suggests that B. subtilis regulates many of its genes in small groups. The expansion of certain gene families (paralogues) is also remarkable, resulting in, for example, 77 different members of the ABC family of transporter proteins. These transporters are vital pumping systems that use energy from the hydrolysis of ATP to import cell nutrients and signalling molecules into bacteria, and to export toxic by-products of metabolism and noxious agents, such as antibiotics. The large number of ABC transporters in B. subtilis indicates that this organism has evolved an elaborate and finely tuned system for chemical communication with its environment. At the other extreme, one-quarter of the genes are present as a single copy and bear no obvious similarity to any other gene discovered so far. Presumably, they play some useful role in B. subtilis physiology under conditions that have not yet been mimicked in the laboratory. The presence of several antibiotic-production pathways — including a polyketide pathway occupying two per cent of the genome — indicates that this microorganism can defend its ecological niche. The genes of unknown function, comprising 42% of the genome, are the subject of a worldwide functional analysis programme that will define whether they are expressed and will attempt to assign a function to their products.
One of the valuable legacies that will stem from this work lies in B. subtilis being an exemplar for Gram-positive bacteria, a group that includes Staphylococcus aureus, Streptococcus pneumoniae and the enterococci. Gram-positive pathogens are the leading cause of death from bacterial infections and are the agents of diphtheria, scarlet fever, toxic-shock syndrome, botulism, listeriosis, pneumonia and tuberculosis, to name a few. Many are becoming resistant to well-known antibiotics, and these threaten the very existence of antibiotic therapy, especially in hospitals. The genome sequence of B. subtilis provides a solid basis for understanding the genes and genomes of other Gram-positive microorganisms.
Understanding the functions of newly identified genes through their close similarity (homology) to genes of known function is the basis of bioinformatics; the success of this is entirely dependent on how accurately the known genes have been characterized. With the completion of the E. coligenome sequence earlier this year2, we now have the pre-eminent organisms of both Gram-positive and Gram-negative groups as reference standards for gene identification. Forty years of intensive studies into the genetics, biochemistry and physiology of B. subtilis provides a high degree of confidence in such comparisons, especially for Gram-positive microorganisms where E. coliinformation may be of only limited usefulness. Because of the large differences in the cell walls, cell membranes and surface structures of Gram-positive and Gram-negative bacteria, there will be discrete groups of genes unique to each (orthologues) that are likely to hold a rich repository of new targets for antibacterial agents. If the lesson from the B. subtilis genome sequence of multiple transport systems is a general phenomenon, then efforts to develop new classes of antibiotics against Gram-positive pathogens should be directed towards the discovery of agents that prevent these bacteria from exporting antibacterial compounds.
A driving force behind genetic, biochemical and cytological studies in B. subtilis has been interest in the mechanisms regulating sporulation3,4, a developmental process where a cell undergoes metamorphosis into a dormant spore form that can resist extremes of environment (including, perhaps, those of interstellar travel). Because of this, we know more about gene expression during the post-exponential phase of growth in B. subtilis than in any other bacteria. Yet we are only now beginning to understand how sporulation is linked to DNA replication and the cell cycle. A fundamental question in bacteria, which lack a spindle apparatus, is how they segregate newly duplicated chromosomes. Recent advances in visualizing chromosome movement in B. subtilis and other bacteria has prompted a search for the chromosome segregation machinery5, 6, 7, 8.
The septation process during cell division also remains a mystery in all bacteria, but particularly in B. subtilis, which undergoes symmetric division (binary fission) during growth and asymmetric division during sporulation (Fig. 1a). A hallmark of sporulation is the process of engulfment (phagocytosis) in which the nascent spore is wholly pinched off within the nurturing mother cell to create a cell-within-a-cell (Fig. 1b). Yet little is understood about how the bacterial membranes mediate this remarkable example of prokaryotic phagocytosis. These and other fundamental problems pose challenges in research, the solutions to which will be greatly accelerated by the availability of the entire sequence of the B. subtilis genome.
Figure 1: Asymmetric division (sporulation) and symmetric division (binary fission) in B. subtilis.
b, During sporulation the nascent B. subtilis spore is pinched off within the mother cell to create a cell-within-a-cell. In the photomicrograph, the outer membrane surrounding the spore fluoresces green because of the presence of green fluorescent protein fused to a sporulation protein that localizes around the developing spore. (Courtesy of K. Price, Harvard University.)
High resolution image and legend (0K)
