Cyanophage

• Cyanophages are a group of viruses that specifically infect cyanobacteria (formerly called blue-green algae)
• These phages play a significant role in aquatic ecosystems by regulating cyanobacterial populations, influencing biogeochemical cycles, and contributing to gene transfer across microbial communities
• The term "cyanophage" is derived from "cyano" (cyanobacteria) and "phage" (to eat), indicating their parasitic relationship with cyanobacteria. Their presence is critical in controlling harmful algal blooms and maintaining microbial diversity in marine and freshwater habitats.

History 

Discovery

• 1955: First cyanophage discovered by Safferman & Morris in freshwater.
• Named the LPP-1 group (hosts: Lyngbya, Plectonema, Phormidium). 

Morphology Era (1970s–1980s)

• Use of electron microscopy to classify phages.
• Identified tailed viruses (Myoviridae-like).
• Host range expanded to include filamentous and colonial cyanobacteria

Marine Cyanophage Discovery (1990s)

• Isolation of cyanophages infecting Synechococcus and Prochlorococcus.
• Recognized their role in ocean ecology and photosynthesis regulation.

Genomic Breakthroughs (2000s)

• First complete cyanophage genomes sequenced (e.g., S-PM2, P-SSP7).
• Discovery of Auxiliary Metabolic Genes (AMGs) like psbA, mazG, rbcL.
• AMGs revealed viral control of host metabolism during infection.

General Characteristics of Cyanophages

Type	Virus (bacteriophage) – Obligate parasite of cyanobacteria (photosynthetic prokaryotes).
Motility	Non-motile – Movement depends on diffusion/water currents; no flagella or pili.
Morphology	• Myoviridae: Contractile tails. • Podoviridae: Short non-contractile tails. • Siphoviridae: Long non-contractile tails.
Size	Head: 50–100 nm diameter. Tail (if present): 10–200 nm length. (Largest cyanophages: ~200 nm total, e.g., *Ma-LMM01* infecting Microcystis).
Genome Type	Primarily dsDNA (some ssDNA cyanophages hypothesized but not well-documented). Genome size: 40–200 kbp (e.g., Prochlorococcus phage P-SSP7: ~45 kbp).
Structural Features	• Capsid: Icosahedral protein shell. • Tail fibers: Host-specific recognition. • Envelope: Rare (most are non-enveloped).
Replication	• Lytic cycle (most common). • Lysogenic cycle (temperate phages integrate as prophages). • Chronic infection (rare, e.g., filamentous cyanophages).
Host Range	Marine: Prochlorococcus, Synechococcus. Freshwater: Microcystis, Anabaena, Nostoc. Thermal springs: Thermosynechococcus.
Environmental Triggers	• UV radiation. • Nutrient stress. • High host density (bloom conditions).
Optimum Temperature	• Marine phages: 20–30°C. • Freshwater phages: 25–35°C. • Thermophilic phages: Up to 70°C (e.g., Thermosynechococcus phages).
Optimum pH	pH 7–9 (matches cyanobacterial habitats). • Alkaline lakes: Up to pH 10.
Resistance	• Survive UV exposure via photolyase genes. • Tolerate salinity fluctuations (marine vs. freshwater strains).
Habitat	• Oceans (dominant in euphotic zone). • Lakes, rivers, estuaries. • Hot springs, polar ice margins.
Ecological  Impact	• Control cyanobacterial blooms (e.g., Microcystis blooms). • Gene transfer (horizontal transfer of photosynthesis genes like psbA). • Carbon cycling ("viral shunt" releases dissolved organic matter).

Morphology and Structure

Cyanophages exhibit structural diversity but share some common viral traits:

Typical Features:

• Head (capsid): Icosahedral, made of protein, enclosing the genome.
• Tail: Varies by family – may be contractile (Myoviridae), short (Podoviridae), or flexible (Siphoviridae).
• Size: Head diameter ~60–100 nm; tail length varies.

Structural Components:

• Capsid proteins: Protect the nucleic acid.
• Tail fibers: Used for host attachment.
• Base plate and sheath (in Myoviridae): Assist in DNA injection.

Life Cycle of Cyanophage

Cyanophages, like other bacteriophages, follow well-defined viral replication cycles to infect and reproduce within their cyanobacterial hosts. The life cycle of cyanophages generally follows two main patterns:

1. Lytic Cycle (predominant)
2. Lysogenic Cycle (less common)

In some cases, a third, less understood state called pseudolysogeny is observed, particularly in stressful or nutrient-limited conditions.

A. Lytic Cycle (most common)

1. Attachment: Phage tail fibers bind to host surface receptors.
2. Penetration: Phage DNA is injected into host cytoplasm.
3. Replication: Phage hijacks host machinery to replicate its genome.
4. Assembly: Capsids and tails are formed; DNA is packaged.
5. Lysis: Host cell bursts, releasing progeny virions.

B. Lysogenic Cycle (rare in cyanophages)

• Prophage integrates into host genome.
• Replicates passively with host DNA.
• Can switch to lytic under stress.

Some cyanophages show signs of pseudolysogeny, where phage DNA persists in the host without active replication or integration.

Auxiliary Metabolic Genes (AMGs)

    Auxiliary metabolic genes (AMGs) are non-essential viral genes acquired from host genomes, which enhance or modulate host metabolic processes during infection. In cyanophages, AMGs play a critical role in maintaining host photosynthesis, carbon, and nitrogen metabolism, ensuring optimal conditions for viral replication.

Origin and Evolution of AMGs

• AMGs are believed to have originated through horizontal gene transfer (HGT) from cyanobacteria.
• Once acquired, they evolve independently in phage genomes.
• They often display signs of genomic streamlining (shorter gene length, reduced introns) to suit viral replication efficiency.

Function of AMGs in Cyanophage Infection

• Support host metabolism during viral takeover.
• Stabilize photosynthesis and energy generation during infection.
• Help divert host resources toward nucleotide and protein synthesis needed for phage assembly.
• Enhance fitness of phages by prolonging host survival during the lytic cycle.

Key points:

• These genes (psbA, psbD, hli, petE) help sustain ATP and NADPH production, crucial for viral DNA synthesis.
• These (rbcL/rbcS , cp12, talc) AMGs reroute carbon flux to provide precursors for nucleotide biosynthesis.
• These genes (mazG, nrdA/nrdB, thyX, dcm) enable de novo nucleotide synthesis when host resources are low.
• By maintaining host function under stress, these (sodC, gpx, groES/groEL) AMGs extend the window for viral replication.
• These genes (phoH , pstS) boost phosphate uptake, essential for nucleic acid synthesis during phage replication.

Ecological Significance

Cyanophages are critical players in marine and freshwater ecology:

Population Control

• Regulate cyanobacterial blooms (including toxic ones).
• Maintain balance in microbial communities.

Nutrient Cycling

• Viral shunt: Lysis of cyanobacteria releases DOM (dissolved organic matter), fueling microbial loops.
• Influence nitrogen, phosphorus, and carbon cycling.

Genetic Exchange

• Facilitate horizontal gene transfer (HGT) via transduction.
• Spread AMGs, increasing genetic diversity and adaptability of cyanobacteria.

Biogeochemical Impacts

• Affect primary production.
• Influence atmospheric carbon fixation and oceanic nutrient dynamics.

MCQ's : 

1. Which of the following best defines cyanophages?
   a) Bacteria that lyse cyanobacteria
   b) Viruses that infect photosynthetic eukaryotes
   c) Viruses specifically targeting cyanobacteria *
   d) Bacteriophages infecting heterotrophic bacteria
2. The LPP-1 group of cyanophages primarily infects which hosts?
   a) Prochlorococcus and Synechococcus
   b) Lyngbya, Plectonema, and Phormidium *
   c) Microcystis and Anabaena
   d) Thermosynechococcus
3. Which family of cyanophages is characterized by a long, flexible, non-contractile tail?
   a) Myoviridae
   b) Podoviridae
   c) Siphoviridae *
   d) Tectiviridae

4. Auxiliary Metabolic Genes (AMGs) like psbA and psbD in cyanophages are critical because they:
   a) Degrade host DNA to release nucleotides
   b) Maintain host photosynthesis during viral replication *
   c) Inhibit host CRISPR-Cas defense systems
   d) Encode structural proteins for virion assembly
5. The "viral shunt" in marine ecosystems refers to:
   a) Transfer of genes between cyanobacteria via transduction
   b) Release of dissolved organic matter through phage-induced lysis *
   c) Fixation of atmospheric CO₂ by cyanobacterial hosts
   d) Formation of viral lysogens in nutrient-limited conditions
6. Which of the following cyanophages is most likely to infect Prochlorococcus, a dominant marine picocyanobacterium?
   a) S-CBS1 (Siphoviridae)
   b) P-SSP7 (Podoviridae) *
   c) Ma-LMM01 (Myoviridae)
   d) LPP-1 (Myoviridae)

7. CRISPR-Cas systems in cyanobacteria primarily function to:
   a) Enhance viral replication efficiency
   b) Provide resistance against cyanophage infection *
   c) Facilitate horizontal gene transfer of AMGs
   d) Degrade host photosynthetic proteins
8. Which technique revolutionized the discovery of uncultured marine cyanophages in the 2000s?
   a) Electron microscopy
   b) Metagenomics *
   c) Southern blotting
   d) Polymerase Chain Reaction (PCR)
9. A researcher observes that a cyanophage-infected Synechococcus culture maintains photosynthesis longer than uninfected cells. This is likely due to:
   a) Viral inhibition of host ribosomes
   b) Phage-encoded AMGs like psbA *
   c) Downregulation of host carbon fixation genes
   d) Lysogenic conversion of the host

10. How might climate change impact cyanophage-host dynamics in oceans?
    a) Warming waters will eliminate all cyanophages
    b) Increased UV exposure will reduce phage infectivity
    c) Shifts in host abundance may alter phage-mediated carbon cycling *
    d) Acidification will enhance lysogenic conversion rates
11. Which of the following is a potential biotechnological application of cyanophages?
    a) Production of antibiotics using phage lysins
    b) Control of toxic Microcystis blooms *
    c) Development of viral vaccines for fish
    d) Bioengineering of algal biofuels via transduction
12. A cyanophage genome is found to encode rbcL (RuBisCO large subunit). This gene most likely:
    a) Degrades host chloroplasts
    b) Redirects carbon flux toward nucleotide synthesis *
    c) Blocks host photosynthetic electron transport
    d) Promotes prophage integration