Annual Review of Microbiology - Volume 54, 2000

In microbial cells, inorganic polyphosphate (polyP) plays a significant role in increasing cell resistance to unfavorable environmental conditions and in regulating different biochemical processes. polyP is a polyfunctional compound. The most important of its functions are the following: phosphate and energy reservation, cation sequestration and storage, membrane channel formation, participation in phosphate transport, involvement in cell envelope formation and function, gene activity control, regulation of enzyme activities, and a vital role in stress response and stationary-phase adaptation. The functions of polyP have changed greatly during the evolution of living organisms. In prokaryotes, the most important functions are as an energy source and a phosphate reserve. In eukaryotic microorganisms, the regulatory functions predominate. Therefore, a great difference is observed between prokaryotes and eukaryotes in their polyP-metabolizing enzymes. Some key prokaryotic enzymes are not present in eukaryotes, and conversely, eukaryotes have developed new polyP-metabolizing enzymes that are not present in prokaryotes. The synthesis and degradation of polyP in each specialized organelle and compartment of eukaryotic cells are mediated by different sets of enzymes. This is consistent with the endosymbiotic hypothesis of eukaryotic cell origin.

Type III secretion systems allow Yersinia spp., Salmonella spp., Shigella spp., Bordetella spp., and Pseudomonas aeruginosa and enteropathogenic Escherichia coli adhering at the surface of a eukaryotic cell to inject bacterial proteins across the two bacterial membranes and the eukaryotic cell membrane to destroy or subvert the target cell. These systems consist of a secretion apparatus, made of ∼25 proteins, and an array of proteins released by this apparatus. Some of these released proteins are “effectors,” which are delivered into the cytosol of the target cell, whereas the others are “translocators,” which help the effectors to cross the membrane of the eukaryotic cell. Most of the effectors act on the cytoskeleton or on intracellular-signaling cascades. A protein injected by the enteropathogenic E. coli serves as a membrane receptor for the docking of the bacterium itself at the surface of the cell. Type III secretion systems also occur in plant pathogens where they are involved both in causing disease in susceptible hosts and in eliciting the so-called hypersensitive response in resistant or nonhost plants. They consist of 15–20 Hrp proteins building a secretion apparatus and two groups of effectors: harpins and avirulence proteins. Harpins are presumably secreted in the extracellular compartment, whereas avirulence proteins are thought to be targeted into plant cells. Although a coherent picture is clearly emerging, basic questions remain to be answered. In particular, little is known about how the type III apparatus fits together to deliver proteins in animal cells. It is even more mysterious for plant cells where a thick wall has to be crossed. In spite of these haunting questions, type III secretion appears as a fascinating trans-kingdom communication device.

It is becoming increasingly clear that the complex machines involved in transcription and translation, the two major activities leading to gene expression, communicate directly with one another by sharing proteins. For some proteins, such as ribosomal proteins S10 and L4, there is strong evidence of their participation in both processes, and much is known about their role in both activities. The exact roles and interactions of other proteins, such as Nus factors B and G, in both transcription and translation remain a mystery. Although there are not, at present, many examples of such shared proteins, the importance of understanding their behavior and intimate involvement with two major cellular machines is beginning to be appreciated. Studies related to the dual activities of these proteins and searches for more examples of proteins shared between the transcription and translation machines should lead to a better understanding of the communication between these two activities and the purposes it serves.

Two proteins, an endolysin and a holin, are essential for host lysis by bacteriophage. Endolysin is the term for muralytic enzymes that degrade the cell wall; endolysins accumulate in the cytosol fully folded during the vegetative cycle. Holins are small membrane proteins that accumulate in the membrane until, at a specific time that is “programmed” into the holin gene, the membrane suddenly becomes permeabilized to the fully folded endolysin. Destruction of the murein and bursting of the cell are immediate sequelae. Holins control the length of the infective cycle for lytic phages and so are subject to intense evolutionary pressure to achieve lysis at an optimal time. Holins are regulated by protein inhibitors of several different kinds. Holins constitute one of the most diverse functional groups, with >100 known or putative holin sequences, which form >30 ortholog groups.

Throughout the first 90 years after their discovery, sulfate-reducing bacteria were thought to be strict anaerobes. During the last 15 years, however, it has turned out that they have manifold properties that enable them to cope with oxygen. Sulfate-reducing bacteria not only survive oxygen exposure for at least days, but many of them even reduce oxygen to water. This process can be a true respiration process when it is coupled to energy conservation. Various oxygen-reducing systems are present in Desulfovibrio species. In Desulfovibrio vulgaris and Desulfovibrio desulfuricans, oxygen reduction was coupled to proton translocation and ATP conservation. In these species, the periplasmic fraction, which contains hydrogenase and cytochrome c3, was found to catalyze oxygen reduction with high rates. In Desulfovibrio gigas, a cytoplasmic rubredoxin oxidase was identified as an oxygen-reducing terminal oxidase. Generally, the same substrates as with sulfate are oxidized with oxygen. As additional electron donors, reduced sulfur compounds can be oxidized to sulfate. Sulfate-reducing bacteria are thus able to catalyze all reactions of a complete sulfur cycle. Despite a high respiration rate and energy coupling, aerobic growth of pure cultures is poor or absent. Instead, the respiration capacity appears to have a protective function. High numbers of sulfate-reducing bacteria are present in the oxic zones and near the oxic-anoxic boundaries of sediments and in stratified water bodies, microbial mats and termite guts. Community structure analyses and microbiological studies have shown that the populations in those zones are especially adapted to oxygen. How dissimilatory sulfate reduction can occur in the presence of oxygen is still enigmatic, because in pure culture oxygen blocks sulfate reduction. Behavioral responses to oxygen include aggregation, migration to anoxic zones, and aerotaxis. The latter leads to band formation in oxygen-containing zones at concentrations of ≤20% air saturation.

The gram-positive bacterium Bacillus subtilisis capable of using numerous carbohydrates as single sources of carbon and energy. In this review, we discuss the mechanisms of carbon catabolism and its regulation. Like many other bacteria, B. subtilis uses glucose as the most preferred source of carbon and energy. Expression of genes involved in catabolism of many other substrates depends on their presence (induction) and the absence of carbon sources that can be well metabolized (catabolite repression). Induction is achieved by different mechanisms, with antitermination apparently more common in B. subtilis than in other bacteria. Catabolite repression is regulated in a completely different way than in enteric bacteria. The components mediating carbon catabolite repression in B. subtilis are also found in many other gram-positive bacteria of low GC content.

The ability of pathogens to obtain iron from transferrins, ferritin, hemoglobin, and other iron-containing proteins of their host is central to whether they live or die. To combat invading bacteria, animals go into an iron-withholding mode and also use a protein (Nramp1) to generate reactive oxygen species in an attempt to kill the pathogens. Some invading bacteria respond by producing specific iron chelators—siderophores—that remove the iron from the host sources. Other bacteria rely on direct contact with host iron proteins, either abstracting the iron at their surface or, as with heme, taking it up into the cytoplasm. The expression of a large number of genes (>40 in some cases) is directly controlled by the prevailing intracellular concentration of Fe(II) via its complexing to a regulatory protein (the Fur protein or equivalent). In this way, the biochemistry of the bacterial cell can accommodate the challenges from the host. Agents that interfere with bacterial iron metabolism may prove extremely valuable for chemotherapy of diseases.