Streptomyces
KF Chater, John Innes Centre, Norwich, UK
© 2013 Elsevier Inc. All rights reserved.
This article replaces the previous edition article by J Parker, volume 4, p 1890, © 2001, Elsevier Inc.
Glossary
Actinobacteria Gram-positive bacteria with DNA rich in
G + C.
Antibiotics Secondary metabolites made
by microorganisms, capable of inhibiting
other microorganisms, including the agents of disease.
Hyphae A filamentous form of microbial growth.
Mycelium The mat formed by branching hyphae.
Nonribosomal peptide synthetase Large modular
enzyme catalyzing the nonribosomal assembly of chains
of several amino acyl residues, often giving precursors of
antibiotics.
Streptomycetes belong to the phylum Actinobacteria, which com­
prises Gram-positive bacteria with high GC content in their DNA.
Actinobacteria emerged about 2.3 billion years ago at the time of
the first oxygenation of the Earth’s atmosphere. They include not
only complex, mycelial, sporulating organisms, such as
Streptomyces, but also simple cocci (e.g., Micrococcus luteus), rods
(e.g., Brevibacterium), and organisms of intermediate complexity
(e.g., Nocardia). Many are valuable in biotechnology, especially
those Streptomyces spp. used to produce most antibiotics, but also
Corynebacterium spp. used to produce amino acids, Nocardia and
Rhodococcus spp. used for bioremediation, and Bifidobacterium
spp. used in probiotics. Some actinobacteria are pathogens of
humans, causing intracellular diseases such as leprosy and tuber­
culosis (Mycobacterium spp.), and skin conditions such as acne
(Propionibacterium acnes), among many others. Others interact
with plants, both beneficially (nitrogen-fixing Frankia spp.) and
pathologically (e.g., potato scab caused by Streptomyces scabies,
and sugarcane disease caused by Leifsonia xyli).
Genetic analysis of actinobacteria has broadened consider­
ably in the genomic era, and has benefited greatly from
artificial transformation methods that are used to introduce
DNA, and plasmid cloning vectors that can transfer DNA by
conjugation from Escherichia coli into a very wide range of
other bacteria. Before that, by far, the most-studied actinobac­
terial species was Streptomyces coelicolor A3(2) (Figure 1). In
the 1950s, D. A. Hopwood showed that this organism under­
went natural genetic exchange by conjugation, and he devised
analytical methods to generate a substantial genetic linkage
map. By the 1970s, this provided a basis for studying various
specific aspects of Streptomyces biology, especially including
antibiotic production and morphological differentiation, and
it was found that genes for production of any particular
antibiotic were clustered together, while morphological devel­
opment appeared to be controlled by a relatively small
number of genes scattered along the chromosome. At the
same time, a variety of Streptomyces plasmids (both extrachro­
mosomal and chromosomally integrated) and phages were
studied, leading to the development of vectors for DNA
Brenner’s Encyclopedia of Genetics, 2nd edition, Volume 6 doi:10.1016/B978-0-12-374984-0.01483-2
Polyketide Secondary metabolites made as long carbon
chains by sequential decarboxylative condensation of
activated fatty acid derivatives.
Recombineering Method of introducing precise
mutations, made in short fragments of DNA by the
polymerase chain reaction, into much longer stretches of
DNA, using Escherichia coli strains carrying a gene (lambda
red) that causes abnormally high-frequency recombination.
Secondary metabolism Biochemical process leading to
the production of substances, such as antibiotics, that do
not contribute directly to growth or homeostasis.
Streptomyces Complex actinobacteria that make antibiotics.
cloning. A crucial step in the development of recombinant
DNA techniques for Streptomyces was the exploitation of
Okanishi’s discovery that protoplasts, made by stripping off
the cell wall with lysozyme, could be regenerated on osmoti­
cally suitable media to give normal mycelial colonies: it
turned out that polyethylene glycol treatment of protoplasts
could cause them to take up DNA (under slightly different
conditions, polyethylene glycol also brought about protoplast
fusion, accompanied by a very high frequency of recombina­
tion – a discovery that has been exploited in industrial strain
improvement programs).
Because antibiotic production generally requires that the
producer should be resistant to its own products, streptomy­
cetes are a rich source of antibiotic resistance genes, and these
were very easy to clone and were used in the construction of
convenient cloning vectors. The thiostrepton-resistance gene
(tsr) of Streptomyces azureus proved particularly useful. During
the 1980s and 1990s, genomic libraries cloned into such vec­
tors were used to complement representative mutants that had
been studied in the precloning days. Thus, many S. coelicolor
genes for antibiotic production and morphological differentia­
tion were cloned. From then on, Streptomyces genetics went
molecular, and followed two main directions: on the one
hand, dissecting biological and biochemical questions, and,
on the other hand, comparative genomic analysis.
Genomic studies were facilitated by the preparation of an
ordered library of large S. coelicolor chromosomal DNA inserts
in an E. coli cosmid vector (Supercos 1). The library then
provided the material for sequencing the entire genome,
which is exceptionally large (at �8 Mb, about twice that of
E. coli). Meanwhile, it had emerged that, like some plasmids
of Streptomyces spp., including SCP1 of S. coelicolor A3(2), the
chromosome was linear, with ends that were long inverted
repeats of each other, and a terminal protein (Ter) attached to
each 5′-end. This was unexpected, since the genetic map is
circular – a paradox that is still not completely explained,
though contributory factors may include the apparently partial
zygotes formed in conjugation (i.e., only part of the
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566 Streptomyces
Figure 1 Fuzzy sporulating colonies of S. coelicolor producing the blue
polyketide antibiotic actinorhodin. Courtesy of M. J. Bibb and A. Davis,
John Innes Centre.
chromosome is donated to a recipient) and the likely associa­
tion with each other of the Ter proteins at each end. Although
chromosome replication is initiated bidirectionally from a
point near the center of the chromosome, the Ter proteins
and the complex secondary structure of the chromosome
ends are important in providing a priming mechanism from
the otherwise unreplicatable 5′-ends.
In the past 10 years, more Streptomyces genomes have been
sequenced, including those of Streptomyces griseus, famous as
the producer of streptomycin; Streptomyces avermitilis, the pro­
ducer of avermectins, which is used to treat river blindness;
Streptomyces venezuelae, the producer of chloramphenicol,
which has been put forward as an ideal organism for physio­
logical studies and for biochemical analysis of differentiation,
since it grows in a dispersed fashion and sporulates very rapidly
and completely in submerged culture; and Streptomyces scabies,
which causes potato scab. A useful and well-maintained data­
base (StrepDB) of completed genome sequences can be found
at strepdb.streptomyces.org.uk. Most of the genomes are in the
7–10 Mb range, with terminal inverted repeats ranging from a
few to more than a million base pairs (recombination between
ends can cause them to expand or contract, or even to bring
about replacement of one chromosome end by an end from a
linear plasmid). The genes in each genome include very large
numbers (typically, >10%) encoding regulatory or signal trans­
duction mechanisms, with genes for sigma factors and
regulatory protein kinases being exceptionally abundant. The
genomes reveal evidence of a very active extracellular biology,
with many secreted proteins and small molecules, as well as
large numbers of transport systems and other membrane pro­
teins. Most Streptomyces genomes have many (typically 20–30)
gene clusters predicted to encode the biosynthesis of secondary
metabolites, including antibiotics, metal siderophores, and sig­
naling molecules. Most of these gene clusters are relatively
species-specific, and so the total number of potentially novel
natural products that could be produced by these gene clusters
is enormous. Some of the large linear plasmids of streptomy­
cetes also contain such gene clusters, suggesting that
plasmid–chromosome genetic exchange may have brought
about the movement of clusters between streptomycetes and
the evolution of new clusters.
Since the availability of genome sequences, practical
Streptomyces genetics has changed in character. Mutants are
mostly generated either by targeted gene knockouts (mostly
exploiting lambda red-based recombineering) or by transposon
mutagenesis followed by high-throughput sequencing to iden­
tify inserts in any particular gene. Both methods involve
primary mutagenesis of sequenced cosmid clones in E. coli.
The mutated DNA, typically marked with an antibiotic resis­
tance gene, is then transferred into Streptomyces by conjugation
or transformation, where double crossover recombination
allows the mutant allele to be introduced into the chromo­
some. Proteomics and microarray-based procedures provide
molecular insights into the phenotypes of such mutants.
Recombineering also permits the ready construction of fusions
of target proteins to cytological reporters such as various fluor­
escent proteins. This has led to a breakthrough in our ability to
track the location and movement of proteins at the subcellular
level during growth and development.
Not surprisingly, antibiotic production has been a major
focus of interest, and hundreds of biosynthetic gene clusters
have been sequenced. Among the many classes of antibiotics,
two have received particular attention: those made by modular
polyketide synthases and those assembled by modular nonri­
bosomal peptide synthetases. The modularity of these often
huge enzymes has allowed them to be modified by genetic
engineering, leading to the design and production of novel
antibiotics. Antibiotics of many other classes have also been
modified by genetic manipulation. Studies on the regulation of
secondary metabolism have also been pursued as a route to
increasing the efficiency of industrial production. Some special
regulatory mechanisms have been discovered, including the
involvement of small extracellular molecules (often lactones
with hydrophobic side chains). The most famous of these,
A-factor, has been shown to trigger a regulatory cascade that
activates streptomycin production in S. griseus. Another remark­
able regulatory device is the use of a very rare codon (UUA, one
of six leucine codons) by many regulatory genes associated
with biosynthetic gene clusters: the abundance of the transfer
RNA (tRNA) for this codon is regulated differently from that of
all other tRNAs.
Although early genetic studies suggested that possibly as few
as 10–20 genes were the key determinants of aerial growth and
sporulation, molecular genetics has shown this to be a consider­
able underestimate. Many regulatory and signal transduction
genes play roles that may become evident only under particular
growth conditions. Complex regulatory cascades culminate in the
production of secreted hydrophobic proteins and peptides that
cover the hyphal surface at the air interface, permitting hyphae to
grow away from the substrate. Continued extension away from
the nutrients is supported by cannibalizing of the substrate myce­
lium, in part through the activation of diverse proteases in an
extracellular cascade involving protease inhibitors. Aerial growth
is also fueled by the degradation of storage polysaccharides and
oils. Aerial hyphae are converted to long chains of spores by
changes in the abundance and behavior of several cytoskeletal
proteins, including the major cell division protein FtsZ and the
ParA, B, J chromosomal partitioning proteins. Changes in the
location and composition of the cell wall biosynthetic complex
are brought about by the actin-like proteins MreB and Mbl, and
also involve a family of Ssg proteins as key players.

The major challenges for the future in Streptomyces genetics
include the integration through systems approaches of the already
vast data sets coming from postgenomic technologies, the identi­
fication of the signals to which the many regulators of important
processes respond, and the revolutionizing of industrial antibiotic
discovery and production, notably by finding the means to ‘wake
up’ the silent gene clusters revealed by gene sequencing and so
obtain access to a gamut of new natural products.
See also: Circular Linkage Map; Cosmids; Inverted Terminal
Repeats; Microbial Genetics; Microbial Genomics;
Recombineering: A Modern Approach to Genetic Engineering;
Streptomycin.
Further Reading
Chater KF, Biro S, Lee KJ, Palmer T, and Schrempf H (2010) The evolution of
Streptomyces has involved an amazingly complex extracellular biology. FEMS
Microbiology Reviews 24: 171–198.
Streptomyces 567
Dyson P (ed.) (2011) Streptomyces Molecular Biology and Biotechnology. Norfolk:
Caister Academic Press.
Gust B, Chandra G, Jakimowicz D, et al. (2004) Lambda red-mediated genetic
manipulation of antibiotic-producing Streptomyces. Advances in Applied
Microbiology 54: 107–128.
Hopwood DA (2007) Streptomyces in Nature and Medicine: The Antibiotic Makers. New
York: Oxford University Press.
Kieser T, Bibb MJ, Buttner MJ, Chater KF, and Hopwood DA (2000) Practical
Streptomyces Genetics. Norwich: John Innes Foundation.
Relevant Websites
http://www.biocyc.org/SCO/organism-summary – BIOCYC is a collection of pathway/
genome databases including several streptomycetes – the link given is that for
S. coelicolor A3(2).
http://microbewiki.kenyon.edu/index.php/Streptomyces – General account of
Streptomyces biology.
http://www.streptomyces.org.uk – Well-maintained site including server for several
Streptomyces genome sequences, and information about recombineering in
Streptomyces.
http://en.wikipedia.org/wiki/Streptomyces – Wikipedia article containing general facts
about Streptomyces.