An Introduction to Streptomyces

Practical Streptomyces Genetics

This book is the bible of Streptomyces work; a must have for any Streptomyces
researcher. Written by team leaders of Streptomyces research at the John Innes
Centre, Norwich Research Park, UK; it covers almost everything from basic
information to maps of different strains, media and buffer recipes, genetics
methods, metabolism, antibiotic production and development.

For further details and to acquire a copy, visit:

http://www.jic.ac.uk/SCIENCE/molmicro/Strepmanual/Manual.htm

Kieser, T., Bibb, M.J., Buttner, M.J., Chater, K.F. & Hopwood, D.A., (2000).
Practical Streptomyces Genetics. Norwich, UK: John Innes Foundation.
ISBN 0-7084-0623-8

Genomes
Several Streptomyces genomes have been sequenced and some mapped, various
degrees of annotation apply to each.

Streptomyces ambofaciens

Information: Partial sequencing of the linear chromosome is currently

being undertaken. Approximately 25% of the genome will
be sequenced when the terminal regions are completed.
This information will be made public.

Sequence held at: Genoscope, Centre National de Séquençage, Evry, France.

http://www.genoscope.cns.fr/externe/English/Projets/

Streptomyces avermitilis MA-4860

Reference: Complete genome sequence and comparative analysis of the

industrial microorganism Streptomyces avermitilis.
Ikeda, H., Ishikawa, J., Hanamoto, A., Shinose, M.,
Kikuchi, H., Shiba, T., Sakaki, Y., Hattori, M., Omura,
S.
Nat Biotechnol. 2003 May; 21(5):526-31.
PMID: 12692562

Sequence held at: National Center for Biotechnology Information, U.S.

National Library of Medicine, Bethesda, MD, USA.
http://www.ncbi.nlm.nih.gov/sites/entrez?
db=genome&cmd=Retrieve&dopt=Overview&list_uids=294

Size, G+C% & genes: The chromosome is 9,025,608bp long with a G+C content of
70.70% and encodes a predicted 7,574 genes.
Streptomyces coelicolor A3(2)

Reference: Complete genome sequence of the model actinomycete

Streptomyces coelicolor A3(2).
Bentley, S.D., Chater, K.F., Cerdeño-Tárraga, A.M.,
Challis, G.L., Thomson, N.R., James, K.D., Harris, D.E.,
Quail, M.A., Kieser, H., Harper, D., Bateman, A., Brown,
S., Chandra, G., Chen, C.W., Collins, M., Cronin, A.,
Fraser, A., Goble, A., Hidalgo, J., Hornsby, T.,
Howarth, S., Huang, C.H., Kieser, T., Larke, L., Murphy,
L., Oliver, K., O'Neil, S., Rabbinowitsch, E.,
Rajandream, M.A., Rutherford, K., Rutter, S., Seeger,
K., Saunders, D., Sharp, S., Squares, R., Squares, S.,
Taylor, K., Warren, T., Wietzorrek, A., Woodward, J.,
Barrell, B.G., Parkhill, J., Hopwood, D.A.
Nature. 2002 May; 417(6885):141-7.
PMID: 12000953

Sequence held at: The Sanger Institute, Cambridge, UK.

http://www.sanger.ac.uk/Projects/S_coelicolor/
Other hosts: The Institute for Genomic Research - Comprehensive
Microbial Resource`
National Center for Biotechnology Information

Size, G+C% & genes: The chromosome is 8,667,507bp long with a G+C content of
72.10% and encodes a predicted 7,825 genes.

Streptomyces diversa / Streptomyces venezuelae

Information: This is a proprietary genome funded by the Diversa

Corporation. The genome has been completed, but is not
yet available to the public, however; some researchers
do have access to the data.
Diversa underwent a merger with Celunol in February
2007, the new company is now called Verenium
Corporation. The name Diversa is no longer used.

Streptomyces griseus

Reference: Physical map of the linear chromosome of Streptomyces

griseus.
Lezhava, A., Mizukami, T., Kajitani, T., Kameoka, D.,
Redenbach, M., Shinkawa, H., Nimi, O., Kinashi, H.
J Bacteriol. 1995 Nov; 177(22):6492-8.
PMID: 7592425

Size, G+C% & genes: The chromosome is ~7,800,000bp, G+C% - N/A, genes – N/A.

Streptomyces hygroscopicus 10-22

Reference: Physical map of the linear chromosome of Streptomyces

hygroscopicus 10-22 deduced by analysis of overlapping
large chromosomal deletions.
Pang, X., Zhou, X., Sun, Y., Deng, Z.
J Bacteriol. 2002 Apr; 184(7):1958-65.
PMID: 11889104

Size, G+C% & genes: The chromosome is ~7,360,000bp, G+C% - N/A, genes – N/A.
Streptomyces lividans 66 ZX7

Reference: Physical map of the Streptomyces lividans 66 genome and

comparison with that of the related strain Streptomyces
coelicolor A3(2).
Leblond, P., Redenbach, M., and Cullum, J.
J Bacteriol. 1993 June; 175(11):3422–3429.
PMID: 8501047

Size, G+C% & genes: The chromosome is ~8,000,000bp, G+C% - N/A, genes – N/A.

Streptomyces noursei ATCC 11455

Information: This proprietary genome is funded by QIAGEN. No further

information available.

Streptomyces peucetius ATCC 27952

Information: This species is currently being sequenced. Not much is

known except it is researched at the Institute of
Biomolecule Reconstruction, Sunmoon University, Korea.

Streptomyces rimosus R6-501

Reference: Physical mapping shows that the unstable oxytetracycline

gene cluster of Streptomyces rimosus lies close to one
end of the linear chromosome.
Pandza, K., Pfalzer, G., Cullum, J., Hranueli, D.
Microbiology. 1997 May; 143(5):1493-501.
PMID: 9168599

Size, G+C% & genes: The chromosome is ~8,000,000bp, G+C% - N/A, genes – N/A.

Streptomyces scabies 87-22

Reference: Unpublished, due 2007.

Sequence held at: The Sanger Institute, Cambridge, UK.

http://www.sanger.ac.uk/Projects/S_scabies/

Size, G+C% & genes: The chromosome is 10,148,695bp with a G+C content of
71.45% and encodes a predicted 8,990 genes.
Actinobacteria
Streptomyces coelicolor is a member of the class of bacteria called the
Actinobacteria (older name: Actinomycetes). A taxonomic classification is
available from the Global Biodiversity Information Facility

 Kingdom: Bacteria
 Phylum: Actinobacteria
 Class: Actinobacteria
 Order: Actinomycetales
 Family: Streptomycetaceae
 Genus: Streptomyces
 Species: Streptomyces coelicolor

For years this class of bacteria has been the centre of research and discussion
due to their diversity and complex life cycles.
Organisms are assigned to this class on the basis of their chemotaxonomy, their
high G+C context and the similarities in the sequences of their 16S ribosomal
ribonucleic acid (Hain, 1997).
In the early steps of microbiology, many organisms now belonging to the class of
Actinobacteria, such as Mycobacterium leprae were considered as species
somewhere between fungi and bacteria (Hopwood, 1999). In the light of new
discoveries such as the: composition of the Actinobacteria cell wall (like that
of typical Gram positive bacteria); the fact that their nuclear material was not
delimited by any membrane and from their genome context itself, they were
characterised as bacteria. This gave biologists a great field of exploration for
bacterial development.
Unlike most bacteria, Streptomycetes possess linear chromosomes (Lin, 1993). The
genome of Streptomyces coelicolor displays great similarity at gene to gene
level with other important Actinomycetales. Examples such as Mycobacterium
tuberculosis and Mycobacterium leprae, the causative agents of tuberculosis and
leprosy respectively; making learning by genome comparison easier since
Streptomyces coelicolor is non pathogenic (Bentley, 2002 genome).

Secondary Metabolism
The biochemistry of Streptomycetes is truly remarkable, considering their
production of secondary metabolites, many of which account for almost half of
all known antibiotics (Berdy, 1964). Many of these compounds have important
applications in human medicine as antibacterial, antitumour and antifungal
agents. Also, in agriculture these compounds act as growth promoters, agents for
plant protection, antiparasitic agents and herbicides (Hopwood, 1995).
The onset of antibiotic production of Streptomyces cultures grown on agar
usually coincides with the early stages of morphological differentiation.
One of the best known and understood Streptomycetes is Streptomyces coelicolor
A3(2). In May 2002 the complete genome sequence of this model Actinobacteria
was published. It has a single linear chromosome, instead of a circular
chromosome that is common to bacteria. The complete sequence reveals a length of
8,667,507bp, and 7,825 predicted genes making it one of the largest bacterial
genome to be sequenced to date. It is nearly twice the size of Escherichia coli
(Blattner, 1997), Bacillus subtilis (Kunst, 1997) and Mycobacterium tuberculosis
(Cole, 1998). It also has a greater number of genes than the lower eukaryote
Saccharomyces cerevisiae, which has 6,183 genes (http://www.yeastgenome.org/).
These findings however, are not entirely surprising given that Streptomyces
coelicolor has a complex life cycle and exists in an environment in which it
must be able to constantly adapt.
There are at least five distinct secondary metabolites in S.coelicolor and four
of these have antibiotic activity: The coloured and visually detected
actinorhodin (Act) and undecylprodigiosin (Red); methylenomycin (Mmy) and the
calcium dependent antibiotic (CDA). The aromatic polyketide actinorhodin (Act)
provides probably the best studied example of all Streptomyces antibiotics with
its colour being dependent on the pH of the environment: blue in neutral and
alkaline solutions and red in acidic. It was Act which gave the trigger for
investigation as well as the name of Streptomyces coelicolor (Hopwood, 1999)
The Life cycle of Streptomyces coelicolor

Germination  Vegetative Growth  Aerial Growth  Sporulation

The life cycle of Streptomyces begins with the germination of a single spore.
This spore produces one or more multi-nucleoid filaments (Hardisson, 1978). This
will elongate and branch on the surface and into the culture medium to form a
vegetative mycelium. Hyphal growth is by quasi-exponential growth kinetics
(Chater, 1993). This complex network of filaments will continue penetrating the
medium, utilising the available organic molecules with the use of extracellular
hydrolytic enzymes.
This motility of the Streptomyces vegetative filaments gives it a big advantage
to other less motile bacteria when it comes to colonizing solid substrates in
the soil.
In response to appropriate signals, believed to include the exhaust of nutrient
supplies in the surrounding environment, the substrate mycelium will break the
surface barrier and aerial hyphae are formed. Aerial growth coincides with the
onset of secondary metabolism in cultures grown on solid media (Chater, 1989).
The continuation of the aerial growth is supported by the utilization of the
vegetative mycelium.
When the extension of the aerial hyphae stops; their multigenomic tips undergo
synchronous, multiple septation to give rise to unigenomic prespore compartments
(Schwedock, 1997; Ryding, 1998).
Mature spores are held together in chains of about 50 and they develop a
characteristic grey pigment as they mature (Davis, 1990).
Unlike the endospores of other Gram-positive bacteria, such as Bacillus and
Clostridium, Streptomyces exospores are not resistant to extreme heat or pH and
are less dormant; however, they are fairly resistant to desiccation.

Figure 1.
The life cycle of Streptomyces coelicolor.
From a single spore a vegetative mycelium germinates, this is followed by aerial
growth with the production of aerial hyphae. These hyphae in turn will undergo
synchronous septation to produce unigenomic spore compartments, which will
disperse and thus commence a new cycle (McGregor, 1954).
References
Bentley, S.D., Chater, K.F., Cerdeno-Tarraga, A.M., Challis, G.L., Thomson,
N.R., James, K.D., Harris, D.E., Quail, M.A., Kieser, H., Harper, D., Bateman,
A., Brown, S., Chandra, G., Chen, C.W., Collins, M., Cronin, A., Fraser, A.,
Goble, A., Hidalgo, J., Hornsby, T., Howarth, S., Huang, C.H., Kieser, T.,
Larke, L., Murphy, L., Oliver, K., O'Neil, S., Rabbinowitsch, E., Rajandream,
M.A., Rutherford, K., Rutter, S., Seeger, K., Saunders, D., Sharp, S., Squares,
R., Squares, S., Taylor, K., Warren, T., Wietzorrek, A., Woodward, J., Barrell,
B.G., Parkhill, J., Hopwood, D.A.
Complete genome sequence of the model actinomycete Streptomyces coelicolor
A3(2).
Nature. 2002 May; 417(6885):141-7.
PMID: 12000953

Berdy, J., Horvath, I., Szentirmai, A.

Antibiotics produced by Streptomyces. II. The tautomeric transformation of
Xanthomycin.
Z Allg Mikrobiol. 1964; 61:232-5.
PMID: 14296570

Blattner, F.R., Plunkett, G. 3rd, Bloch, C.A., Perna, N.T., Burland, V., Riley,
M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., Gregor, J.,
Davis, N.W., Kirkpatrick, H.A., Goeden, M.A., Rose, D.J., Mau, B., Shao, Y.
The complete genome sequence of Escherichia coli K-12.
Science. 1997 Sep; 277(5331):1453-74.
PMID: 9278503

Chater, K.F.
Multilevel regulation of Streptomyces differentiation.
Trends Genet. 1989 Nov; 5(11):372-7.
PMID: 2692245

Chater, K.F.
Genetics of differentiation in Streptomyces.
Annu Rev Microbiol. 1993; 47:685-713.
PMID: 7504906

Cole, S.T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D.,
Gordon, S.V., Eiglmeier, K., Gas, S., Barry, C.E. 3rd, Tekaia, F., Badcock, K.,
Basham, D., Brown, D., Chillingworth, T., Connor, R., Davies, R., Devlin, K.,
Feltwell, T., Gentles, S., Hamlin, N., Holroyd, S., Hornsby, T., Jagels, K.,
Krogh, A., McLean, J., Moule, S., Murphy, L., Oliver, K., Osborne, J., Quail,
M.A., Rajandream, M.A., Rogers, J., Rutter, S., Seeger, K., Skelton, J.,
Squares, R., Squares, S., Sulston, J.E., Taylor, K., Whitehead, S., Barrell,
B.G.
Deciphering the biology of Mycobacterium tuberculosis from the complete genome
sequence.
Nature. 1998 Jun; 393(6685):537-44.
PMID: 9634230

Davis, N.K., Chater, K.F.

Spore colour in Streptomyces coelicolor A3(2) involves the developmentally
regulated synthesis of a compound biosynthetically related to polyketide
antibiotics.
Mol Microbiol. 1990 Oct; 4(10):1679-91.
PMID: 2077356

Hain, T., Ward-Rainey, N., Kroppenstedt, R.M., Stackebrandt, E., Rainey, F.A.
Discrimination of Streptomyces albidoflavus strains based on the size and number
of 16S-23S ribosomal DNA intergenic spacers.
Int J Syst Bacteriol. 1997 Jan; 47(1):202-6.
PMID: 8995823
Hardisson, C., Manzanal, M.B., Salas, J.A., Suarez, J.E.
Fine structure, physiology and biochemistry of arthrospore germination in
Streptomyces antibioticus.
J Gen Microbiol. 1978 Apr;105(2):203-14.
PMID: 347027

Hopwood, D.A.
Forty years of genetics with Streptomyces: from in vivo through in vitro to in
silico.
Microbiology. 1999 Sep; 145(9):2183-202.
PMID: 10517572

Hopwood, D.A., Chater, K.F., Bibb, M.J.

Genetics of antibiotic production in Streptomyces coelicolor A3(2), a model
streptomycete.
Biotechnology. 1995; 28:65-102.
PMID: 8688641

Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., Azevedo, V.,
Bertero, M.G., Bessieres, P., Bolotin, A., Borchert, S., Borriss, R., Boursier,
L., Brans, A., Braun, M., Brignell, S.C., Bron, S., Brouillet, S., Bruschi,
C.V., Caldwell, B., Capuano, V., Carter, N.M., Choi, S.K., Codani, J.J.,
Connerton, I.F., Danchin, A.
The complete genome sequence of the gram-positive bacterium Bacillus subtilis.
Nature. 1997 Nov; 390(6657):249-56.
PMID: 9384377

Lin, Y.S., Kieser, H.M., Hopwood, D.A., Chen, C.W.

The chromosomal DNA of Streptomyces lividans 66 is linear.
Mol Microbiol. 1993 Dec; 10(5):923-33.
PMID: 7934869

McGregor, J.F.
Nuclear division and the life cycle in a Streptomyces sp.
J Gen Microbiol. 1954 Aug; 11(1):52-6.
PMID: 13192301

Ryding, N.J., Kelemen, G.H., Whatling, C.A., Flardh, K., Buttner, M.J., Chater,
K.F.
A developmentally regulated gene encoding a repressor-like protein is essential
for sporulation in Streptomyces coelicolor A3(2).
Mol Microbiol. 1998 Jul; 29(1):343-57.
PMID: 9701826

Schwedock, J., McCormick, J.R., Angert, E.R., Nodwell, J.R., Losick, R.

Assembly of the cell division protein FtsZ into ladder-like structures in the
aerial hyphae of Streptomyces coelicolor.
Mol Microbiol. 1997 Sep; 25(5):847-58.
PMID: 9364911