Streptomyces inside-out: a new perspective on the bacteria that provide us with antibiotics

Abstract

Many of the antibiotics used today are made by a group of bacteria called Streptomyces. Streptomycetes evolved about 450 million years ago as branched filamentous organisms adapted to the utilization of plant remains. They reproduce by sending up specialized aerial branches, which form spores. Aerial growth is parasitic on the primary colony, which is digested and reused for aerial growth. The reproductive phase is coordinated with the secretion of antibiotics, which may protect the colony against invading bacteria during aerial growth. A clue to the integration of antibiotic production and aerial growth is provided by bldA mutants, which are defective in both processes. These mutants lack the ability to translate a particularly rare codon, UUA, in the genetic code. The UUA codon (TTA in DNA) is present in several regulatory genes that control sets of antibiotic production genes, and in one, bldH that controls aerial mycelium formation. The regulatory genes for antibiotic production are all involved in self-reinforcing regulatory systems that potentially amplify the regulatory significance of small changes in the efficiency of translation of UUA codons. One of the regulatory targets of bldH is an extracellular protease inhibitor protein that is likely to delay the digestion of the primary biomass until the colony is ready for aerial growth. The use of the UUA codon to orchestrate different aspects of extracellular biology appeared very early in Streptomyces evolution.

Figure 1

(a) Vertical sections through a Streptomyces colony. Photograph of colony growing on agar (courtesy of Jamie Ryding). (b) Diagram indicating how antibiotic production in the lower part of the colony can protect the nutrients released from dead cells (white) so that they can support aerial growth and sporulation. Living cells are shown as black (after Wildermuth 1970).

Figure 2

The effect of a mutation in the bldA gene. The colony on the left is normal, with a powdery sporulating surface and areas coloured by pigmented antibiotics. The colony on the right lacks the bldA gene, has a wrinkled, shiny, non-sporulating surface, and makes no pigments (photograph by Tobias Kieser).

Figure 3

The role of the tRNA encoded by bldA. The diagram shows the transcription of a short stretch of DNA sequence containing TTA and GGC codons into messenger RNA containing UUA and GGC codons, and their translation, via the bldA tRNA and another tRNA, into leucine and arginine residues in a stretch of protein.

Figure 4

Comparison of a (a) bldA mutant with a (b) wild-type strain by two-dimensional electrophoresis. Proteins in cell extracts were first lined up according to their intrinsic charge by exposing them to an electric potential difference in a long, narrow matrix with a fixed gradient of pH. This matrix was then treated to eliminate the charge differences between proteins, and embedded at one side of a rectangular slab of polyacrylamide gel. A current was applied at right angles to the direction of the first separation, dragging the proteins through the gel. Small proteins pass through the structure of such gels more readily than larger ones, so the resulting gel, after suitable staining of the protein spots, provided a snapshot of the protein composition of the starting cellular material. The arrows indicate a protein spot absent from the mutant. Note that most spots are present in both strains, though the precise positions of spots change somewhat between gels. (Photograph courtesy of Andy Hesketh.)

Figure 5

Role of bldA in autoregulatory circuits for antibiotic production. Three gene sets are illustrated. Shaded ovals represent regulatory proteins. The numbers indicate the sequence of events leading to expression of production genes for actinorhodin (act, a), undecylprodigiosin (red, b) and methylenomycin (mmy, c). In each case the first step involves a gene with a TTA codon (asterisks). The three systems differ in complexity from this point. In the simplest example, the TTA-containing gene (actII-4) encodes a regulatory protein that exerts some kind of positive feedback (act, steps 2 and 3; see text), and thereby accumulates to a level at which it can activate genes for biosynthesis of the end product (step 4). In the case of the TTA-containing redZ, another regulatory gene (redD) is activated (step 3), and this goes through an autoregulatory reinforcement, again uncharacterized (steps 4 and 5; see text), before activating the genes for synthesis of the end product (step 6). In the most complex case, expression of the TTA-containing mmfL, together with mmfH and mmfP, causes accumulation of a small extracellular signal molecule (step 1), which activates further synthesis of itself (steps 2 and 3) to a level that can activate another regulatory gene, mmyB, that also contains a TTA (step 4). If bldA tRNA is available, expression of mmyB can undergo another autoregulatory loop (steps 6 and 7) so that enough of the mmyB gene product accumulates to switch on the genes for synthesis of the final product, methylenomycin (step 8).

Figure 6

Mutants in the bldA and bldH genes behave similarly in a cascade of extracellular signals that leads to aerial growth. The scheme is based on results of Willey et al. (1993), and was adapted from Chater (1998).

Figure 7

The presence of TTA codons in key regulatory genes influences several aspects of the extracellular biology of S. coelicolor. The rectangular box encloses processes taking place inside a hyphal compartment (the underlying image is an electron micrograph of a thin section through hyphae of S. coelicolor). The extracellular cascade thought to activate cannibalization by a trypsin-like protease is indicated by shaded arrows and a shaded cross. Dotted lines indicate processes that have been demonstrated in another species, but have yet to be proven for S. coelicolor.