From studies with E. coli, it was learned that cells have many regulons involved in sur-vival responses during difficult circumstances. The catabolite repression regulon just described is in essence a means by which the cell can optimize its synthesis of catabolic enzymes by making only those that contribute to growth. But this regulon can also be viewed as a survival device, helping the cell to respond to the nutritional stress of running out of glucose. If an alternative source of carbon is present in the environment, the cell can redirect its pattern of gene expression to make a suitable adjustment to the nutritional stress.
Perhaps more obvious as a stress response is the SOS system, a set of 17 genes that are turned on when the cell suffers damage to its DNA. The products of these genes are involved in several processes that repair damaged DNA and prevent cell division during the repair.
Another prominent bacterial cell stress regulon is responsible for the heat-shock re-sponse. It encompasses some 20 genes, which are transcriptionally activated on an upwardshift in temperature or on imposition of several kinds of chemical stress, including alcohol. In the case of E. coli, the heat-shock regulator protein is a special subunit of RNA poly-merase, σ-32, which replaces the normal σ-70 subunit and locates the special promoters of the heat-shock genes. At least half of the heat-shock genes encode proteins that either are proteases or are protein chaperones that assist in the processing, maturation, or export of other proteins. It is thought that these chaperones and proteases are needed for normal pro-tein processing at all temperatures but are required in higher amounts to counteract the effects of high temperature on protein folding and protein – protein interactions. The bacte-rial chaperones are highly similar to their mammalian counterparts. For example, HtpG, DnaK, and GroEL of E. coli correspond to the mammalian hsp90, hsp70, and hsp60 fami-lies of chaperones, respectively. The precise involvement of the heat-shock response in in-fectious disease is still being explored, but it is striking that antibodies directed against bacterial heat-shock proteins constitute a major component of the serologic response of humans to infection or vaccine administration. Fever in humans can elevate body tempera-ture sufficiently to induce the heat-shock response, and it is suspected that this response may affect the outcome of various infections. Also, some viruses both of bacteria and of humans use the heat-shock proteins of their host cells to promote their own replication.
Other regulons deal with cell survival in the face of such stresses as osmotic shock, high or low pH, oxidation damage, presence of toxic metal ions, and restrictions for fun-damental nutrients (phosphate, nitrogen, sulfur, and carbon). A large number of these re-sponses involve teams of proteins that sense the environment, generate a signal, transmit that signal by protein – protein interactions, and activate the appropriate response regulon. In a striking number of cases, a response system includes a protein kinase that becomes phosphorylated by ATP on a particular conserved histidine residue in response to an envi-ronmental stimulus. This kinase is teamed with a second protein called a phosphorylatedresponse regulator. The phosphate residue from the kinase is transferred to an asparticacid residue of the response regulator, usually converting this protein into an activator of transcription of the appropriate genes. Members of these two families of signal transduc-tion proteins share highly conserved domains throughout distantly related bacteria.
Two of the most elaborate bacterial survival responses involve the transition of growing cells into a form that can survive long periods without growth. In a few Gram-positive bacterial species, this involves sporulation, the production of an endospore. This process, extensively studied in a few species, involves cascades of RNA polymerase subunits, each sequentially activating several interrelated regulons that co-operate to produce the elaborately encased spore, which though metabolically inert and extremely resistant to environmental stress, is capable of germinating into a growing (vegetative) cell.
For all other bacteria, adaptation to a nongrowing state involves formation of a differenti-ated cell called the stationary phase cell. The product is certainly far different morpho-logically from an endospore, but a tough, resistant, and metabolically quiescent cell is produced that looks distinct from its growing counterpart. Its envelope is made tougher by many modification of its structure, its chromosome is aggregated, and its metabolism is adjusted to a maintenance mode. Producing this resistance involves a process surpris-ingly analogous to sporulation, because, as in sporulation, cascades of signals and re-sponses involving the sequential activation of sets of genes appear to be involved. One of the many global regulators involved is RpoS, a subunit of RNA polymerase.
Motility in most bacterial species is the property of swimming by means of flagellar propulsion. The complex structure of a flagellum — its filament, hook, and basal body. The helical filament functions as a propeller, the hook possibly as a universal joint, and the basal body with its rod and rings as a motor anchored in the envelope. The flagellar motors turn the filaments using energy directly from the electro-chemical gradient (proton-motive force) of the cell membrane rather than from ATP. The filament can be rotated either clockwise or counterclockwise. Whatever the number of fla-gella on a cell and whatever their arrangement on the surface (polar, peritrichous, or lophotrichous), they are synchronized to rotate simultaneously in the same direction. Only counterclockwise rotation results in productive vectorial motion, called a run. Clockwise rotation of the flagella causes the cell totumble in place. The flagella alternate between periods of clockwise and counterclockwise rotation according to an endogenous schedule. As a result, motile bacteria move in brief runs interrupted by periods of tumbling.
Chemotaxis is directed movement toward chemical attractants and away fromchemical repellents. It is accomplished by a remarkable molecular sensory system that possesses many of the characteristics that would be expected of behavioral systems in higher animals, including memory and adaptation. Beside the genes of the flagellar pro-teins (called fla, for flagella) more than 30 genes (called mot, for motility, and che, for chemotaxis) encode the proteins that make this system work: receptors, signalers, trans-ducers, tumble regulators, and motors.
Whether a cell is moving toward an attractant or away from a repellent, chemotaxis is achieved by biased random walks. These result from alterations in the frequency of tum-bling. When a cell is, by chance, progressing toward an attractant, tumbling is suppressed and the run is long; if it is swimming away, tumbling occurs sooner and the run is brief. It is sheer chance in what direction a cell is pointed at the end of a tumble, but by regulating the frequency of tumbles in this manner, directed progress is made.
The mechanism of chemotaxis is fairly well understood from work with E. coli. It is complex and can be summarized as follows. Binding of an attractant alters the endoge-nous routine schedule of runs and tumbles by interrupting a phosphorylation cascade and thus prolonging the run. Accommodation by a methylation system restores the en-dogenous schedule and resets the cell’s sensitivity to the attractant to require a higher concentration to prolong the run. This constitutes a molecular memory. The bacterial cell senses a concentration gradient not by measuring a difference between the concentra-tion at each end of the cell but by a molecular memory that enables it to compare the con-centration now with what it was a short time ago. Escape from a repellent occurs in an analogous fashion.
Chemotaxis is both a survival device (for avoiding toxic substances) and a growth-promoting device (for finding food). It can also be a virulence factor in facilitating colo-nization of the human host by bacteria.