Synechococcus elongatus

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A Microbial Biorealm page on the genus Synechococcus elongatus



Higher order taxa

Bacteria; Cyanobacteria; Chroococcales; Synechococcus


Synechococcus elongatus

NCBI: Taxonomy Genome

Description and significance

The genus Synechococcus encompasses cyanobacteria in both freshwater and marine environments. In the typical marine environment, they are approximately responsible for 25% of the primary production, making them one of the most significant photosynthetic bacteria (6). In eutrophic habitats or habitats with high nutrients, blooms of cyanobacteria can occur, producing harmful neurotoxins that effect the nerve cells of other organisms (4). Synechococcus elongatus is a freshwater unicellular cyanobacterium. Cyanobacteria, sometimes referred to as blue-green algae, are prokaryotes that are able to obtain their energy through photosynthesis. Synechococcus elongatus has a rod-shaped appearance and is oligotrophic, having the ability to survive in freshwater environments with low nutrients. Living habitats include freshwater hot springs and other freshwater habitats preferably with a mesophilic or moderate temperature range (9). Geitler first identified Synechococcus elongatus in Germany during the year 1925. Later, Frenkel et. al. in 1950 discovered Synechococcus elongatus in small rain-filled pools on Angelica Rock, located in Massachusetts. Frenkel and his colleagues took a suspension of the water and identified the blue-green algae as Synechococcus elongatus. They cultured Synechococcus elongatus and ran tests to confirm its ability to photosynthesize (1). Currently, two complete Synechococcus elongatus (previously known as Anacystis nidulans) genomes have been sequenced, Synechococcus elongatus PCC 6301 and Synechococcus elongatus PCC 7942.

Genome structure

Synechococcus elongatus has one circular chromosome and two plasmids. Two genomic strains of these cyanobacteria have been sequenced: Synechococcus elongatus PCC 6301 and Synechococcus elongatus PCC 7942. Both strains are closely related to each other. Synechococcus elongatus PCC 6301 contains a circular chromosome 2,696,255 bp long with a GC content of 55.5 percent. The Synechococcus elongatus PCC 6301 chromosome contains the genes for 2,527 proteins and 55 RNAs (7). Synechococcus elongatus PCC 7942 also contains a circular chromosome approximately 2,700,000 bp long with a GC content of 55.5 percent. The Synechococcus elongatus PCC 7942 chromosome contains the genes for 2,612 proteins and 53 RNAs. One plasmid of Synechococcus elongatus PCC 7942 is currently being sequenced by Dr. Golden’s lab at Texas A&M University in conjunction with the DOE Joint Genome Institute.

Cell structure and metabolism

Synechococcus elongatus is unicellular, rod-shaped, and may appear in the environment as isolated, paired, linearly connected, or in small clusters. Synechococcus elongatus is a Gram-negative bacterium with an inner and outer cell membrane enveloping a cell wall (3). This cyanobacterium is able to swim or glide despite lacking flagella or cilia. It moves in a wave-like manner and this movement is possibly accomplished via projections from the cell surface (9). Also, its movement is not influenced by light stimulation. Synechococcus elongatus is a photoautotroph, due to its ability to undergo photosynthesis using energy from sunlight, carbon dioxide, and water (9). Through photosynthesis, Synechococcus elongatus may perform biosynthesis and respiration. A very significant by-product of Synechococcus elongatus photosynthesis is oxygen. Synechococcus elongatus uses carbon dioxide (CO2) as its carbon source through the Calvin cycle. During photosynthesis, Synechococcus elongatus uses water (H2O) for the electron donor, which produces oxygen (O2) as the by-product. Carbon dioxide is then converted to glucose through the Calvin cycle and is used for biosynthesis or other energetic needs. Photosynthesis occurs at the cell membrane inside thylakoids, which are compartments containing the photosynthetic pigments. The coupling of photosystems I and II in the thylakoid membrane drives photosynthesis and the oxidation of H2O, providing energy for carbon fixation (12). Chlorophyll a is the primary pigment required for photosynthesis in Synechococcus elongatus. Chlorophyll a is also extremely common in eukaryotic organisms such as plants. Other accessory pigments include phycobiliproteins, which give the blue-green coloration or pigmentation of Synechococcus elongatus as well as other cyanobacteria (2).


Synechococcus elongatus is a freshwater photoautotroph and insignificantly contributes to primary production in the world. However, marine unicellular photoautotrophs of genus Synechococcus make a major and significant contribution to primary production. As noted earlier, they are approximately responsible for 25% of the primary production in the marine environment (9). Since Synechococcus are photoautrophs and require light to perform photosynthesis, they reside in well lit depths of the water with enough sunlight for photosynthesis. This depth of water is known at the photic zone. An equal distribution of Synechococcus is seen throughout the mixed layer with favored habitation in the photic zone (2). The mixed layer is the layer from the ocean surface to a certain depth where density is approximately similar to the surface. Synechococcus seems to be more abundant in nutrient rich marine environments than oligotrophic marine environments that contain a minimal amount of nutrients. However, Synechococcus have been found to flourish in environments with variable salinity and temperatures as well as certain oligotrophic environments (2). Their ability to survive in oligotrophic environments may be partly due to the closely packed colonies they form to allow the recycling of used nutrients (2). In areas of high nutrients such as coastal plumes or contributions of pollutions, Synechococcus blooms may occur, producing harmful neurotoxins as mentioned earlier (2).


Synechococcus elongatus is currently not known to cause any diseases.

Application to Biotechnology

Synechococcus elongatus is not yet known to produce any useful compounds or enzymes.

Current Research

One current study is the function of the GlgX protein in Synechococcus elongatus PCC 7942. This study was accomplished by disrupting the glgx gene using an inserstional inactivation technique. By disrupting the glgx gene, GlgX protein was not produced. As a result, the glycogen content of the glgx mutant cell had short chains. The research determined the GlgX protein plays a role in forming the “branching pattern” of polysaccharides such as glycogen (8). Another study involves the analysis of three dnaK homologues (dnaK1, dnaK2, and dnaK3) and their stress responses in Synechococcus elongatus PCC 7942. The experiment involved creating a reporter assay to show that under stress conditions, only the dnaK2 gene was induced. This suggested each dnaK homologue had a specific function (5). This last study is a review of known genetic components of the circadian clock rhythm of cyanobacteria including Synechococcus elongatus PCC 7942. This cyanobacterium has an “endogenous timing mechanism” so can create and maintain a 24 hour clock period. The circadian clock proteins include KaiA, KaiB, and KaiC. Despite past research, not much is known on how the circadian clock mechanism functions and its connection to the environment in terms of regulating gene expression (10).


1. Frenkel, Albert et al. “Photosynthesis and photoreduction by the blue green alga, Synechococcus elongatus, Nag.” Biology Bulletin. 1950. Volume 99. p. 157-162.

2. Olson, R. J. et al. “Pigment size and distribution of Synechococcus in the North Atlantic and Pacific oceans.” Limnol Oceanogr. 1990. Volume 35. p. 45-58.

3. Perkins, F .O. et al. “Ultrastructure of a marine Synechococcus possessing spinae.” Can. J. Microbiol. 1981. Volume 27. p. 318-329.

4. Rippka, R. “Neurotoxins in axenic oscillatorian cyanobacteria: coexistence of anatoxin-a and homoanatoxin-a determined by ligand-binding assay and GC/MS.” Microbiology. 2005. Volume 151. p. 1263-1273.

5. Sato, M. et al. “Expression analysis of multiple dnaK genes in the cyanobacterium Synechococcus elongatus PCC 7942.” Journal of Microbiology. 2007. Volume 189. p. 3751-3758.

6. Scanlan, D. J. and Nyree, J. W. “Molecular ecology of the marine cyanobacterial genera Prochlorococcus and Synechococcus.” FEMS Microbiology Ecology. 2002. Volume 40. p. 1-12.

7. Sugita, C. et al. "Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization.", Photosynth Res. 2007.

8. Suzuki, E. et al. “Role of the GlgX protein in glycogen metabolism of the cyanobacterium, Synechococcus elongatus PCC 7942.” Biochim Biophys Acta. 2007. Volume 1770. p. 763-773.

9. Waterbury, J. B. et al. “Biological and ecological characterization of the marine unicellular cyanobacterium Synechococcus.” Can. Bull. Fish. Aquat. Sci. 1986. Volume 214. p. 71-120.

10. Williams, S.B. “A circadian timing mechanism in the cyanobacteria.” Adv Microb Physiol. 2007. Volume 52. p. 229-296.


12. Yang, Mino et al. “Energy Transfer in Photosystem I of Cyanobacteria Synechococcus elongatus: Model Study with Structure-Based Semi-Empirical Hamiltonian and Experimental Spectral Density.” Biophysical Journal. 2003. Volume 85. p. 140-158.


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