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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 [1]

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


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

Information: Completed - Reference [2]
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)

Information: Completed - Reference [3]
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

http://cmr.tigr.org/tigr-scripts/CMR/GenomePage.cgi?database=ntsc02
National Center for Biotechnology Information
http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=Retrieve&dopt=Overview&list_uids=238

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

Information: Mapped - Reference [4]
Size, G+C% & genes: The chromosome is ~7,800,000bp, G+C% - N/A, genes – N/A.

Streptomyces hygroscopicus 10-22

Information: Mapped - Reference [5]
Size, G+C% & genes: The chromosome is ~7,360,000bp, G+C% - N/A, genes – N/A.

Streptomyces lividans 66 ZX7

Information: Mapped - Reference [6]
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

Information: Mapped - Reference [7]
Size, G+C% & genes: The chromosome is ~8,000,000bp, G+C% - N/A, genes – N/A.

Streptomyces scabies 87-22

Information: Completed - 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 [8]. 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 [9]. 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 [10]. 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 [3].


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 [11]. 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 [12]. 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 genomes sequenced to date. It is nearly twice the size of Escherichia coli [13], Bacillus subtilis [14] 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 [9].


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 [15]. 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 [16]. 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 [17]. 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 [18] [19]. Mature spores are held together in chains of about 50 and they develop a characteristic grey pigment as they mature [20]. 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 [21].



References

  1. Practical streptomyces genetics. John Innes Foundation. ISBN:0708406238 [Kieser-PracticalStreptomycesGenetics-2000]
  2. Kieser, T., Bibb, M.J., Buttner, M.J., Chater, K.F. & Hopwood, D.A., (2000). Practical Streptomyces Genetics. Norwich, UK: John Innes Foundation. Click Here for more Information [Kieser-PracticalStreptomycesGenetics-2000]
  3. Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, and Omura S. Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol. 2003 May;21(5):526-31. DOI:10.1038/nbt820 | PubMed ID:12692562 | HubMed [Ikeda-NatBiotechnol-2003]
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All Medline abstracts: PubMed | HubMed