''Synechocystis'' sp. PCC6803 is a strain of unicellular, freshwater

cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blu ...

. ''Synechocystis'' sp. PCC6803 is capable of both

phototroph Phototrophs () are organisms that carry out photon capture to produce complex organic compounds (e.g. carbohydrates) and acquire energy. They use the energy from light to carry out various cellular metabolic processes. It is a common misconcep ...

ic growth by oxygenic

photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i ...

during light periods and

heterotrophic A heterotroph (; ) is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but ...

growth by

glycolysis Glycolysis is the metabolic pathway that converts glucose () into pyruvate (). The free energy released in this process is used to form the high-energy molecules adenosine triphosphate (ATP) and reduced nicotinamide adenine dinucleotide (NADH ...

and

oxidative phosphorylation Oxidative phosphorylation (UK , US ) or electron transport-linked phosphorylation or terminal oxidation is the metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing chemical energy in order to produce adenosine tri ...

during dark periods. Gene expression is regulated by a

circadian clock A circadian clock, or circadian oscillator, is a biochemical oscillator that cycles with a stable phase (waves), phase and is synchronized with solar time. Such a clock's ''in vivo'' period is necessarily almost exactly 24 hours (the earth's curre ...

and the organism can effectively anticipate transitions between the light and dark phases.

Evolutionary history

Cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blu ...

are photosynthetic

prokaryotes A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Connec ...

that have existed on

Earth Earth is the third planet from the Sun and the only astronomical object known to harbor life. While large volumes of water can be found throughout the Solar System, only Earth sustains liquid surface water. About 71% of Earth's surfa ...

for an estimated 2.7 billion years. The ability of

to produce oxygen initiated the transition from a planet consisting of high levels of carbon dioxide and little oxygen, to what has been called the

Great Oxygenation Event The Great Oxidation Event (GOE), also called the Great Oxygenation Event, the Oxygen Catastrophe, the Oxygen Revolution, the Oxygen Crisis, or the Oxygen Holocaust, was a time interval during the Paleoproterozoic era when the Earth's atmosphere ...

where large amounts of oxygen gas were produced.

have colonized a wide diversity of habitats, including fresh and salt water ecosystems, and most land environments. Phylogenetically, ''Synechocystis'' branches off later in the cyanobacterial

evolutionary tree A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...

, further from the ancestral root (''Gloeobacter violaceus''). ''Synechocystis'', which is non-diazotrophic, is closely related to another model organism, ''

Cyanothece ''Cyanothece'' is a genus of unicellular, diazotrophic, oxygenic photosynthesizing cyanobacteria. Modern organisms and cellular organization In 1976, Jiří Komárek defined the prokaryotic cyanobacteria genus ''Cyanothece'' as distinct from ' ...

'' ATCC 51442, which is a

diazotroph Diazotrophs are bacteria and archaea that fix gaseous nitrogen in the atmosphere into a more usable form such as ammonia. A diazotroph is a microorganism that is able to grow without external sources of fixed nitrogen. Examples of organisms that d ...

. Thus, it has been proposed that ''Synechocystis'' originally possessed the ability to fix nitrogen gas, but lost the genes required for a fully functioning

nitrogen fixation Nitrogen fixation is a chemical process by which molecular nitrogen (), with a strong triple covalent bond, in the air is converted into ammonia () or related nitrogenous compounds, typically in soil or aquatic systems but also in industry. Atmo ...

(''nif'') gene cluster.

Growth and use as a model organism

are model microorganisms for the study of

carbon Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent In chemistry, the valence (US spelling) or valency (British spelling) of an element is the measure of its combining capacity with o ...

and

nitrogen assimilation Nitrogen assimilation is the formation of organic nitrogen compounds like amino acids from inorganic nitrogen compounds present in the environment. Organisms like plants, fungi and certain bacteria that can fix nitrogen gas (N2) depend on the abil ...

, evolution of plant

plastids The plastid (Greek: πλαστός; plastós: formed, molded – plural plastids) is a membrane-bound organelle found in the cells of plants, algae, and some other eukaryotic organisms. They are considered to be intracellular endosymbiotic cyanobac ...

, and adaptability to

environmental stress Stress, either physiological, biological or psychological, is an organism's response to a stressor such as an environmental condition. Stress is the body's method of reacting to a condition such as a threat, challenge or physical and psych ...

es. ''Synechocystis'' sp. PCC6803 is one of the most highly studied types of

as it can grow both autotrophically or heterotrophically in the absence of light. It was isolated from a

freshwater Fresh water or freshwater is any naturally occurring liquid or frozen water containing low concentrations of dissolved salts and other total dissolved solids. Although the term specifically excludes seawater and brackish water, it does include ...

lake A lake is an area filled with water, localized in a basin, surrounded by land, and distinct from any river or other outlet that serves to feed or drain the lake. Lakes lie on land and are not part of the ocean, although, like the much large ...

in 1968 and grows best between 32 and 38 degrees

Celsius The degree Celsius is the unit of temperature on the Celsius scale (originally known as the centigrade scale outside Sweden), one of two temperature scales used in the International System of Units (SI), the other being the Kelvin scale. The ...

. ''Synechocystis'' sp. PCC6803 can readily take up exogenous DNA, in addition to up taking DNA via

electroporation Electroporation, or electropermeabilization, is a microbiology technique in which an electrical field is applied to cells in order to increase the permeability of the cell membrane, allowing chemicals, drugs, electrode arrays or DNA to be introdu ...

, ultrasonic transformation and

conjugation Conjugation or conjugate may refer to: Linguistics * Grammatical conjugation, the modification of a verb from its basic form * Emotive conjugation or Russell's conjugation, the use of loaded language Mathematics * Complex conjugation, the chang ...

. The

photosynthetic Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored in c ...

apparatus is very similar to the one found in land plants. The organism also exhibits phototactic movement. ''Synechocystis'' sp. PCC6803 can be grown on either

agar plates An agar plate is a Petri dish that contains a growth medium solidified with agar, used to Microbiological culture, culture microorganisms. Sometimes selective compounds are added to influence growth, such as antibiotics. Individual microorganism ...

or in liquid culture. The most widely used culture medium is a BG-11 salt solution. The ideal pH is between 7 and 8.5. A light intensity of 50 μmol photons m⁻² s⁻¹ leads to best growth. Bubbling with

carbon dioxide Carbon dioxide (chemical formula ) is a chemical compound made up of molecules that each have one carbon atom covalently double bonded to two oxygen atoms. It is found in the gas state at room temperature. In the air, carbon dioxide is transpar ...

enriched air (1–2% CO₂) can increase the growth rate, but may require additional

buffer Buffer may refer to: Science * Buffer gas, an inert or nonflammable gas * Buffer solution, a solution used to prevent changes in pH * Buffering agent, the weak acid or base in a buffer solution * Lysis buffer, in cell biology * Metal ion buffer * ...

to maintain pH Selection is typically performed by

antibiotic resistance Antimicrobial resistance (AMR) occurs when microbes evolve mechanisms that protect them from the effects of antimicrobials. All classes of microbes can evolve resistance. Fungi evolve antifungal resistance. Viruses evolve antiviral resistance. ...

genes. Heidorn et al. 2011 experimentally determined in ''Synechocystis'' sp. PCC6803 the ideal concentrations of

kanamycin Kanamycin A, often referred to simply as kanamycin, is an antibiotic used to treat severe bacterial infections and tuberculosis. It is not a first line treatment. It is used by mouth, injection into a vein, or injection into a muscle. Kanamycin ...

spectinomycin Spectinomycin, sold under the tradename Trobicin among others, is an antibiotic useful for the treatment of gonorrhea infections. It is given by injection into a muscle. Common side effects include pain at the area of injection, rash, nausea, ...

streptomycin Streptomycin is an antibiotic medication used to treat a number of bacterial infections, including tuberculosis, ''Mycobacterium avium'' complex, endocarditis, brucellosis, ''Burkholderia'' infection, plague, tularemia, and rat bite fever. Fo ...

chloramphenicol Chloramphenicol is an antibiotic useful for the treatment of a number of bacterial infections. This includes use as an eye ointment to treat conjunctivitis. By mouth or by injection into a vein, it is used to treat meningitis, plague, cholera, a ...

erythromycin Erythromycin is an antibiotic used for the treatment of a number of bacterial infections. This includes respiratory tract infections, skin infections, chlamydia infections, pelvic inflammatory disease, and syphilis. It may also be used duri ...

, and

gentamicin Gentamicin is an antibiotic used to treat several types of bacterial infections. This may include bone infections, endocarditis, pelvic inflammatory disease, meningitis, pneumonia, urinary tract infections, and sepsis among others. It is not e ...

. Cultures can be kept on

for approximately 2 weeks and re-streaked indefinitely. For long term storage, liquid cell cultures should be stored in a 15%

glycerol Glycerol (), also called glycerine in British English and glycerin in American English, is a simple triol compound. It is a colorless, odorless, viscous liquid that is sweet-tasting and non-toxic. The glycerol backbone is found in lipids known ...

solution at -80 degrees

Genome

The

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...

of ''Synechocystis'' sp. PCC6803 is contained within approximately 12 copies of a single

chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...

(3.57 megabases), three small

plasmids A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...

: pCC5.2 (5.2 kb) pCA2.4 (2.4 kb), and pCB2.4 (2.4 kb) and four large plasmids: pSYSM (120 kb), pSYSX (106 kb), pSYSA (103kb), and pSYSG (44 kb). The genome of ''Synechocystis'' sp. PCC6803 is the fourth genome to be completely sequenced, and the first phototrophic organism to have its genome fully sequenced.

Additional strains

The primary strain of ''Synechocystis'' sp. is PCC6803. Further modifications of the parent PCC6803 strain have been created, such as a sub-strain lacking

photosystem 1 Photosystem I (PSI, or plastocyanin–ferredoxin oxidoreductase) is one of two photosystems in the photosynthetic light reactions of algae, plants, and cyanobacteria. Photosystem I is an integral membrane protein complex that uses ...

(PSI). The other widely used sub-strain of ''Synechocystis'' sp. is a

glucose Glucose is a simple sugar with the molecular formula . Glucose is overall the most abundant monosaccharide, a subcategory of carbohydrates. Glucose is mainly made by plants and most algae during photosynthesis from water and carbon dioxide, using ...

tolerant strain, ATCC 27184. The parent PCC 6803 strain cannot utilize external glucose.

Light-activated heterotrophy

''Synechocystis'' sp. PCC6803, sub-strain ATCC 27184 can live heterotrophically in the dark on the carbon source

, but for yet unknown reasons requires a minimum of 5 to 15 minutes (blue) light per day. This regulatory role of light is intact in both

PSI Psi, PSI or Ψ may refer to: Alphabetic letters * Psi (Greek) (Ψ, ψ), the 23rd letter of the Greek alphabet * Psi (Cyrillic) (Ѱ, ѱ), letter of the early Cyrillic alphabet, adopted from Greek Arts and entertainment * "Psi" as an abbreviatio ...

and

PSII Photosystem II (or water-plastoquinone oxidoreductase) is the first protein complex in the light-dependent reactions of oxygenic photosynthesis. It is located in the thylakoid membrane of plants, algae, and cyanobacteria. Within the photosyste ...

deficient strains. Some

glycolytic Glycolysis is the metabolic pathway that converts glucose () into pyruvate (). The free energy released in this process is used to form the high-energy molecules adenosine triphosphate (ATP) and reduced nicotinamide adenine dinucleotide (NADH ...

genes are regulated by the gene''sll1330'' under light and glucose-supplemented conditions. One of the most important glycolytic genes is fructose-1,6-bisphosphate aldolase (''fbaA''). The mRNA level of ''fbaA'' is increased under light and glucose-supplemented conditions.

Native CRISPR-Cas system

The

CRISPR CRISPR () (an acronym for clustered regularly interspaced short palindromic repeats) is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. These sequences are derived from DNA fragments of bacte ...

-Cas (Clustered Regularly Interspaced Short Palindrome Repeats – CRISPR associated proteins) system provides

adaptive immunity The adaptive immune system, also known as the acquired immune system, is a subsystem of the immune system that is composed of specialized, systemic cells and processes that eliminate pathogens or prevent their growth. The acquired immune system ...

archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...

and

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

. ''Synechocystis'' sp. PCC6803 contains three different CRISPR-Cas systems: type I-D, and two versions of type III. All three CRISPR-Cas systems are localize on the pSYSA plasmid. All

are lacking the type II system, which has been widely adapted for genetic engineering purposes across many species.

RNA polymerase and sigma factors

RNA polymerase In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that synthesizes RNA from a DNA template. Using the enzyme helicase, RNAP locally opens the ...

(RNAP) and

sigma factor A sigma factor (σ factor or specificity factor) is a protein needed for initiation of transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is ho ...

s are necessary proteins for

transcription Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the fir ...

of DNA into

messenger RNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during the p ...

(mRNA). Eubacterial RNAP holoenzymes consist of a core with four major subunits α2 ββ'. In cyanobacteria, β' is formed from two smaller subunits (у and β'), which corresponds to RNAPs in plant

chloroplasts A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant cell, plant and algae, algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, ...

. The

beta subunits Beta (, ; uppercase , lowercase , or cursive Greek, cursive ; grc, βῆτα, bē̂ta or ell, βήτα, víta) is the second letter of the Greek alphabet. In the system of Greek numerals, it has a value of 2. In Modern Greek, it represents th ...

are responsible for binding the RNAP to the DNA, preventing premature dissociation. In ''Escherichia coli'', the beta "clamp" first binds loosely and tightens as the RNAP approaches the start codon (AUG). In cyanobacteria, the beta clamp binds tightly at initial binding. The effect of this difference is that synthetic repressible promoters do not function as expected in ''Synechocystis'' sp. PCC6803. In ''E. coli'', a repressor binds the DNA operon and dislodges RNAP due to the loosely bound beta clamp, whereas in ''Synechocystis'', the RNAP is tightly bound leading the reverse phenomenon where the repressor is knocked off the DNA. Thus the gene is not effectively repressed. ''Synechocystis'' possesses the 70S

(σ70), which can be divided into three groups. Group 1

s are critical for cell viability. Group 2, similar in structure to Group 1, is not essential for cell vitality. Group 3 is structurally different and involved with survival under stress conditions. ''Synechocystis'' sp. PCC6803 lacks the σN factor found in other organisms, such as ''

Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escher ...

'', which is involved with transcribing genes related to nitrogen, but is nonetheless able to metabolize nitrogen.

Natural genetic transformation

''Synechocystis'' sp. PCC6803 is capable of natural genetic transformation. For

transformation Transformation may refer to: Science and mathematics In biology and medicine * Metamorphosis, the biological process of changing physical form after birth or hatching * Malignant transformation, the process of cells becoming cancerous * Trans ...

to take place, the recipient bacteria must be in a competent state. A gene, ''comF'', was shown to be involved in competence development in ''Synechocystis'' sp. PCC6803.

Synthetic biology/genetic engineering

''Synechocystis'' sp. PCC6803 is considered a

model organism A model organism (often shortened to model) is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workin ...

, yet there exist few synthetic parts that can be used for

genetic engineering Genetic engineering, also called genetic modification or genetic manipulation, is the modification and manipulation of an organism's genes using technology. It is a set of technologies used to change the genetic makeup of cells, including t ...

. As cyanobacteria in general have slow

doubling time The doubling time is the time it takes for a population to double in size/value. It is applied to population growth, inflation, resource extraction, consumption of goods, compound interest, the volume of malignant tumours, and many other things th ...

s (4.5 to 5 h in ''Synechocystis'' sp. PCC6301 ), it is more efficient to perform as much DNA cloning as possible in a fast growing host, such as ''

''. In order to create

—stable, replicating circular pieces of DNA—that will function successfully in multiple species, a broad-host-range shuttle vector (see Replicative Plasmids below) is needed. Gene promoters, which control gene expression, need to also predictably work in multiple hosts (see Promoters below).

Replicative plasmids

Currently there is only one broad-host-range shuttle vector, RSF1010, that successfully replicates in ''Synechocystis'' sp. PCC6803. RSF1010 is a mobilization plasmid that facilitates

between cells, allowing the

horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offsprin ...

of DNA. Additionally, RSF1010 encodes its own replication machinery, so that it does not depend on its host to possess the necessary proteins and assorted factors.

Promoters

Gene promoters are responsible for recruiting

RNAP In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that synthesizes RNA from a DNA template. Using the enzyme helicase, RNAP locally opens the ...

and facilitating

of DNA. Type I promoters consists of a consensus -35 and -10 region (

Pribnow box The Pribnow box (also known as the Pribnow-Schaller box) is a sequence of ''TATAAT'' of six nucleotides (thymine, adenine, thymine, etc.) that is an essential part of a promoter site on DNA for transcription to occur in bacteria. It is an ideal ...

) upstream of the gene start site. Heidorn et al. 2011 compiled a list of native ''Synechocystis'' sp. PCC6803 promoters that have been used in synthetic constructs, although this leads to cross talk and non-orthogonal or non-specific gene expression. A handful of Anderson promoters (a group of constitutive promoters collected from a combinatorial library based on the consensus -35 (5'-TTGACA-3) and -10 (5’-TATAAT-3’) regions), represented best by BBa_J23101, have been demonstrated to function in ''Synechocystis'' sp. PCC6803. The iGem Registry hosts these promoter sequences as part of the BioBrick initiative to create interchangeable genetic parts. For

synthetic biology Synthetic biology (SynBio) is a multidisciplinary area of research that seeks to create new biological parts, devices, and systems, or to redesign systems that are already found in nature. It is a branch of science that encompasses a broad ran ...

, it is critical to have inducible promoters, or genes that can be turned on/off on demand. Several popular inducible promoters in ''

E. coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escher ...

'' are the pBad, pTet, and pLac promoters, all of which repress gene expression by a repressor molecule that binds the gene operator and blocks RNAP progression. Progress in engineering ''Synechocystis'' sp. PCC6803 is currently hampered by promoter issues. As noted above in RNA Polymerase and Sigma Factors, the beta clamp proteins within the RNAP complex have a higher initial

binding affinity In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. The etymology stems from ''ligare'', which means 'to bind'. In protein-ligand binding, the ligand is usually a mol ...

in ''Synechocystis'' sp. versus other eubacterial models. Thus promoters that turn on/off in response to small binding molecules are less effective in ''Synechocystis'' since the RNAP can knock them off the DNA strand. Camsund, Heidorn and Lindblad 2014 attempted to enhance pLac repression in ''Synechocystis'' sp. PCC6803 by engineering a promoter with multiple operons, thus facilitating DNA looping. Their attempt was too effective, as it was now too difficult to induce transcription in highly repressed variants. Huang and Lindblad 2013 created a library of modified pTet promoters with varying levels of repression and dynamic range in the

tolerant ''Synechocystis'' sp. ATCC 27184. Another option are promoters that are inducible by heavy metals, such as:

zinc Zinc is a chemical element with the symbol Zn and atomic number 30. Zinc is a slightly brittle metal at room temperature and has a shiny-greyish appearance when oxidation is removed. It is the first element in group 12 (IIB) of the periodi ...

cadmium Cadmium is a chemical element with the symbol Cd and atomic number 48. This soft, silvery-white metal is chemically similar to the two other stable metals in group 12, zinc and mercury. Like zinc, it demonstrates oxidation state +2 in most of ...

cobalt Cobalt is a chemical element with the symbol Co and atomic number 27. As with nickel, cobalt is found in the Earth's crust only in a chemically combined form, save for small deposits found in alloys of natural meteoric iron. The free element, pr ...

arsenic Arsenic is a chemical element with the symbol As and atomic number 33. Arsenic occurs in many minerals, usually in combination with sulfur and metals, but also as a pure elemental crystal. Arsenic is a metalloid. It has various allotropes, but ...

nickel Nickel is a chemical element with symbol Ni and atomic number 28. It is a silvery-white lustrous metal with a slight golden tinge. Nickel is a hard and ductile transition metal. Pure nickel is chemically reactive but large pieces are slow to ...

and

chromium Chromium is a chemical element with the symbol Cr and atomic number 24. It is the first element in group 6. It is a steely-grey, lustrous, hard, and brittle transition metal. Chromium metal is valued for its high corrosion resistance and hardne ...

. Several such promoters were evaluated in ''Synechocystis'' sp. PCC6803 by Peca 2007. These promoters are not ideal, as

metal ions A metal (from Greek μέταλλον ''métallon'', "mine, quarry, metal") is a material that, when freshly prepared, polished, or fractured, shows a lustrous appearance, and conducts electricity and heat relatively well. Metals are typicall ...

are critical in ''Synechocystis''’ metabolic pathways and altering concentrations can lead to compounding undesired side effects. Additionally, working with these promoters produces waste contaminated with

heavy metals upright=1.2, Crystals of osmium, a heavy metal nearly twice as dense as lead">lead.html" ;"title="osmium, a heavy metal nearly twice as dense as lead">osmium, a heavy metal nearly twice as dense as lead Heavy metals are generally defined as ...

, increasing disposal costs

Ribosome binding site (RBS)

The ribosome binding site (RBS) is the location where a

ribosome Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to ...

binds a strand of

mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA is ...

and begins

translation Translation is the communication of the Meaning (linguistic), meaning of a #Source and target languages, source-language text by means of an Dynamic and formal equivalence, equivalent #Source and target languages, target-language text. The ...

. In

, the RBS includes a Shine-Dalgarno sequence. Little is known about the translation efficiency of RBSs in ''Synechocystis'' sp. PCC6803. Heidorn et al. 2011 scanned the ''Synechocystis'' sp. PCC6803 genome and created a consensus RBS sequence (TAGTGGAGGT), which had 5 times higher output than the consensus ''E. coli'' sequence.

Terminators

Terminators are the DNA signal which halts

. Native ''Synechocystis'' sp. PCC6803 termination sites have been characterized.

Transcription unit (TU)

Transcription units (TUs) of ''Synechocystis'' sp. PCC6803 have been assigned using transcription start sites (TSSs) and transcript 3'-end positions (TEPs).

Biofuel production

have been used in several ways to produce renewable biofuel. The original method was to grow cyanobacteria for the

biomass Biomass is plant-based material used as a fuel for heat or electricity production. It can be in the form of wood, wood residues, energy crops, agricultural residues, and waste from industry, farms, and households. Some people use the terms bi ...

, which could be converted through

liquefaction In materials science, liquefaction is a process that generates a liquid from a solid or a gas or that generates a non-liquid phase which behaves in accordance with fluid dynamics. It occurs both naturally and artificially. As an example of the ...

into liquid fuel. Current estimates suggest that

biofuel Biofuel is a fuel that is produced over a short time span from biomass, rather than by the very slow natural processes involved in the formation of fossil fuels, such as oil. According to the United States Energy Information Administration (E ...

production from cyanobacteria is unfeasible, as the energy return on energy invested (EROEI) is unfavorable. The

EROEI In energy economics and ecological energetics, energy return on investment (EROI), also sometimes called energy returned on energy invested (ERoEI), is the ratio of the amount of usable energy (the ''exergy'') delivered from a particular energy re ...

is not advantageous as numerous large, closed loop

bioreactors A bioreactor refers to any manufactured device or system that supports a biologically active environment. In one case, a bioreactor is a vessel in which a chemical reaction, chemical process is carried out which involves organisms or biochemistry, ...

with ideal growth conditions (sunlight, fertilizers, concentrated carbon dioxide, oxygen) need to be constructed and operated, which consumes

fossil fuels A fossil fuel is a hydrocarbon-containing material formed naturally in the Earth's crust from the remains of dead plants and animals that is extracted and burned as a fuel. The main fossil fuels are coal, oil, and natural gas. Fossil fuels ...

. Additionally, further post processing of cyanobacterial products is necessary, which requires additional fossil fuels. ''Synechocystis'' sp. PCC6803 has been used as a model to increase cyanobacterial energy yields through genetic engineering by the following manipulations: broadening the range of photosynthetic light

absorption Absorption may refer to: Chemistry and biology * Absorption (biology), digestion **Absorption (small intestine) *Absorption (chemistry), diffusion of particles of gas or liquid into liquid or solid materials *Absorption (skin), a route by which ...

, altering antenna size in

photosystem II Photosystem II (or water-plastoquinone oxidoreductase) is the first protein complex in the light-dependent reactions of oxygenic photosynthesis. It is located in the thylakoid membrane of plants, algae, and cyanobacteria. Within the photosystem ...

, increasing

bicarbonate In inorganic chemistry, bicarbonate (IUPAC-recommended nomenclature: hydrogencarbonate) is an intermediate form in the deprotonation of carbonic acid. It is a polyatomic anion with the chemical formula . Bicarbonate serves a crucial biochemic ...

uptake, modifying the

Rubisco Ribulose-1,5-bisphosphate carboxylase-oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme () involved in the first major step of carbon fixation, a process by which atmospheric carbon dioxide is con ...

enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...

to increase

carbon fixation Biological carbon fixation or сarbon assimilation is the process by which inorganic carbon (particularly in the form of carbon dioxide) is converted to organic compounds by living organisms. The compounds are then used to store energy and as ...

, and introduction of biofuel producing

metabolic pathways In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reac ...

. It is not yet clear whether cyanobacterial biofuels will be a viable future alternative to non-renewable fossil fuels.

Databases

SynechoNET
integrated protein-protein interaction database of a model

cyanobacterium Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blue ...

''Synechocystis'' sp. PCC 6803. SynechoNET is a specialized cyanobacterial protein-protein interaction database. It shows feasible cyanobacterial domain-domain interactions, as well as their protein level interactions using the model cyanobacterium, ''Synechocystis'' sp. PCC 6803. Additionally, SynechoNET provides transmembrane topology and domain information, as well as interaction networks in graphical web interfaces.
CyanoBase
Cyanobacteria carry a complete set of genes for oxygenic photosynthesis, which is the most fundamental life process on Earth. This organism is also interesting from an evolutionary viewpoint, for it arose in a very ancient age and has survived in various environments. The algal and land plant chloroplast evolved from cyanobacterial ancestors which developed an

endosymbiotic An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within" ...

relationship with a

eukaryotic Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...

host cell. CyanoBase provides an easy way of accessing the sequences and all-inclusive annotation data on the structures of the cyanobacterial genomes. This database was originally developed by Makoto Hirosawa, Takakazu Kaneko and Satoshi Tabata, and the current version of CyanoBase has been developed and maintained by Yasukazu Nakamura, Takakazu Kaneko, and Satoshi Tabata at Kazusa DNA Research Institute.
STRING
STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources: Genomic Context, High-throughput Experiments, (Conserved) Coexpression, and Previous Knowledge. The database currently contains 1,513,782 proteins in 373 species. Especially, the database provides interactions for ''Synechocystis'' sp. PCC 6803.
cTFbase
cTFbase contains 1288 putative

transcription factors In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The func ...

(TFs) identified from 21 fully sequenced cyanobacterial genomes. Through its user-friendly interactive interface, users can employ various criteria to retrieve all TF sequences and their detailed annotation information, including sequence features, domain architecture and sequence similarity against the linked databases. Furthermore, cTFbase also provides

phylogenetic trees A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...

of individual TF family, multiple sequence alignments of the DNA-binding domain and

ortholog Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a spec ...

identification from any selected

genomes In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding gen ...

References

{{Taxonbar, from=Q21384143 Synechococcales Undescribed species