T4 Bacteriophage: Difference between revisions
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[[Image: | [[Image:Bacteriophage T4 electron micrograph a.png|thumb|350px|right|Electron micrograph. Image credit: Fumio Arisaka. Publication: Bacteriophage T4 Genome https://doi.org/10.1128/MMBR.67.1.86-156.2003.]] | ||
==Classification== | ==Classification== | ||
Viruses (Superkingdom); Duplodnaviria (clade); Heunggongvirae (kingdom); Uroviricota (phylum); Caudoviricetes (class); Straboviridae (family); Tevenvirinae (subfamily); Tequatrovirus(genus); Tequatrovirus T4(species) | Viruses (Superkingdom); Duplodnaviria (clade); Heunggongvirae (kingdom); Uroviricota (phylum); Caudoviricetes (class); Straboviridae (family); Tevenvirinae (subfamily); Tequatrovirus(genus); Tequatrovirus T4(species) | ||
''You may notice the absence of a domain in the classification above. This is because bacteriophages, which are viruses, are not alive!'' | |||
===Species=== | ===Species=== | ||
{| | {| | ||
| height=" | | height="15" bgcolor="#FFDF95" | | ||
'''NCBI: | '''NCBI: | ||
[https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1007084&lvl= | [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1007084&lvl= | ||
| Line 14: | Line 18: | ||
|} | |} | ||
''Tequatrovirus T4'' | ''Official name from Taxonomy Browser: Tequatrovirus T4'' | ||
''Current name: Escherichia phage T4'' | |||
''Commonly known as: Bacteriophage T4'' | |||
==Genome Structure== | ==Genome Structure== | ||
Bacteriophage T4 has a linear double stranded DNA genome made of 168,903 base pairs. | |||
==Cell Structure, Metabolism and Life Cycle== | ==Cell Structure, Metabolism and Life Cycle== | ||
[[Image:T4 Bacteriophage infecting Ecoli.png|thumb|390px|right|Helium Ion Micrograph. Image credit: https://doi.org/10.3762/bjnano.12.1]] | |||
The T4 bacteriophage has the classic appearance that most people think of when they hear the term bacteriophage. If you were going to observe a T4 bacteriophage, you would notice two main parts of the virus' body; the head, and the tail. The head is comprised of an icosahedral (20 sided) capsid, that contains T4's | The T4 bacteriophage has the classic appearance that most people think of when they hear the term bacteriophage. If you were going to observe a T4 bacteriophage, you would notice two main parts of the virus' body; the head, and the tail. The head is comprised of an icosahedral (20 sided) capsid, that contains T4's double stranded DNA, and is the proximal part of the virus. The whole tail region has a few more parts, and is located distally to the icosahedral capsid. The proximal end of the tail is where the collar can be observed, and the distal end of the tail is where the baseplate can be observed. Extending laterally from the baseplate are six tail fibers that can be easily mistaken for legs. Despite being a virus, these tail fibers give T4 a very live appearance. Beneath the baseplate there is a spike that the bacteriophage uses to inject its genome into the host for replication. | ||
The T4 bacteriophage is still quite smaller than its host, Escherichia coli. While Escherichia coli is a couple of micrometers, T4 is an entire order of magnitude smaller. The T4 bacteriophage is roughly ______ nM (nanometers) tall. In addition to being smaller than the host, T4 is also much more abundant than its host, outnumber E. coli nearly _____ to one. | The T4 bacteriophage is still quite smaller than its host, Escherichia coli. While Escherichia coli is a couple of micrometers, T4 is an entire order of magnitude smaller. The T4 bacteriophage is roughly ______ nM (nanometers) tall. In addition to being smaller than the host, T4 is also much more abundant than its host, outnumber E. coli nearly _____ to one. | ||
==Ecology and Pathogenesis== | ==Ecology and Pathogenesis== | ||
The term bacteriophage alone can tell you a bit about what T4 does. By breaking down the word to its prefix bacterio- and suffix -phage, you can determine that these organisms "eat" bacteria. Although they don't literally consume bacteria, bacteriophage T4's prey is eliminated as a result of the viral life cycle. | |||
Bacteriophage T4 is a predator (and technically a parasite) of the bacteria Escherichia coli. It is technically considered a parasite because it is incapable of replicating or producing energy without a host cell. | |||
Escherichia coli is the only prey/host species of this bacteriophage. Bacteriophages collectively may replicate by one of two cycles, the lytic cycle, or the lysogenic cycle. The T4 Bacteriophage strictly uses the lytic cycle. In the lytic cycle, T4 will land on the host cell's outer membrane and inject its genome through a surface receptor, such as a transport protein. When injecting the genome, the sheath contracts, making T4 appear shorter. After bacteriophage T4's genome has entered the host cell, it takes over control of the cell machinery that is normally involved in replication of host genetic material, then copying itself and producing enzymes to escape. Eventually T4's genetic material and cellular components are assembled into multiple entire copies of the virus, while lysins (a type of enzyme from bacteriophages) degrade the cell wall. This combination causes the host cell to burst, releasing all of the new replicates of T4. | |||
Phage-host coevolution: | Phage-host coevolution: | ||
==History & Significance== | |||
Bacteriophages were discovered just over a century ago, more than a decade before the discovery of penicillin. | |||
Even though penicillin took the spotlight in mainstream medicine, the medicinal potential of bacteriophages has not gone unrecognized. While antibiotics are easier to administer they don't have the same level of precision as a bacteriophage. Penicillin is a broad spectrum antibiotic, meaning it doesn't just kill pathogens but also kills harmless or even beneficial bacteria that are exposed to it. Meanwhile bacteriophages are host specific down to at least a species level. That means that a lytic bacteriophage can kill its host organism, while any other bacteria are simply bystanders and remain unharmed. | |||
==How to draw a T4 Bacteriophage== | |||
[[Image:H2DT4B.png|thumb|430px|left|How to draw the T4 bacteriophage (illustrated). Image credit: Jake Delaney.]] | |||
The Icosahedral capsid | |||
1. Start off by writing the letter M, and spread it slightly horizontally. | |||
2. Add a vertical line stemming from the bottom left, and bottom right of the M. This is the outer edge | |||
3. Connect the tops of the outer edge straight across (or almost straight across) to each other. This line should come in contact with both of the upper peaks from the M | |||
4. Do the same on the bottom, this line should come in contact with the lower peak of the M | |||
5. On the top, make an equilateral triangle stemming from the two peaks of the M. Then make a line from the top of the triangle to the corner above and to the right of the original M - this will produce a scalene triangle. | |||
6. Repeat step 5, going from the top of the equilateral triangle to the corner above and to the left of the original M. | |||
7. Now for the bottom, all you need to do is make a short vertical line stemming from the lower peak of the M. Draw a line connecting this point to the bottom right end of the original M - this should look more like a right triangle. Draw another line connecting the very bottom to the bottom left end of the original M. | |||
- Completing step 7 concludes the drawing of the icosahedral capsid. Icosahedrons have twenty sides, but you should only be able to see ten in a drawing since it is two dimensional. | |||
_________________________________________________________________________________________________ | |||
The collar, sheath, and baseplate. | |||
1. Create a small line stemming from the lower end of the icosahedron, and draw a circle around that. This circle should be like the top of a cylinder drawing. This creates the collar region. | |||
2. Extend the cylinder (really the sheath) and draw a broader circle around the distal end to create the baseplate. | |||
3. Make a custom design on the sheath. T4 is typically illustrated with a sheath horizontally lined, horizontally dotted, helically lined, or helically dotted, but it's cool to make your own drawing extra original. | |||
__________________________________________________________________________________________________ | |||
The whiskers, tail fibers, and spike | |||
1. T4 has six tail fibers that look like legs. Just start from the baseplate in six different spots, extend out and change direction to make the tail fibers look spread out. You can also draw a couple of short tail fibers extending vertically from the bottom of the baseplate. Depending on the size of your drawing, this may not be easy to see. | |||
2. Draw very short lines stemming from the line between the capsid, and the proximal end of the sheath. This creates the a more detailed appearance of the collar region. It may be easier to add the whiskers to the edge of the proximal end of the sheath. | |||
3. Make a very short line from the middle of the baseplate, this creates the spike. Without the spike, your phage won't be able to inject its genome into the host cell drawing! | |||
==References== | ==References== | ||
and | Fenton M, Ross P, McAuliffe O, O'Mahony J, Coffey A. Recombinant bacteriophage lysins as antibacterials. Bioeng Bugs. 2010 Jan-Feb;1(1):9-16. doi: 10.4161/bbug.1.1.9818. PMID: 21327123; PMCID: PMC3035150. | ||
of | |||
Fischetti VA. Development of Phage Lysins as Novel Therapeutics: A Historical Perspective. Viruses. 2018 Jun 7;10(6):310. doi: 10.3390/v10060310. PMID: 29875339; PMCID: PMC6024357. | |||
Mathews K. Bacteriophage T4. eLS. 2015 Aug 14. https://doi.org/10.1002/9780470015902.a0000784.pub4 | |||
Taylor, M.W. (2014). The Discovery of Bacteriophage and the d’Herelle Controversy. In: Viruses and Man: A History of Interactions. Springer, Cham. p 53-61 https://doi.org/10.1007/978-3-319-07758-1_4 | |||
NCBI NLM Taxonomy Browser. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi | |||
NIH NCBI Virus. https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Escherichia%20phage%20T4,%20taxid:2681598 | |||
Miller, Eric & Kutter, Elizabeth & Mosig, Gisela & Arisaka, Fumio & Kunisawa, Takashi & Rüger, Wolfgang. (2003). Bacteriophage T4 Genome. Microbiology and molecular biology reviews : MMBR. 67. 86-156, table of contents. 10.1128/MMBR.67.1.86-156.2003. | |||
Schmidt, Matthias & Byrne, James & Maasilta, Ilari. (2021). Bio-imaging with the helium-ion microscope: A review. Beilstein Journal of Nanotechnology. 12. 1-23. 10.3762/bjnano.12.1. | |||
==Author== | ==Author== | ||
Page authored by Jake Delaney, student of Prof. Bradley Tolar at UNC Wilmington. | Page authored by Jake Delaney, student of Prof. Bradley Tolar at UNC Wilmington. | ||
<!-- Do not remove this line-->[[Category:Pages edited by students of Bradley Tolar at UNC Wilmington]] | <!-- Do not remove this line-->[[Category:Pages edited by students of Bradley Tolar at UNC Wilmington]] | ||
Latest revision as of 22:31, 20 December 2022
Classification
Viruses (Superkingdom); Duplodnaviria (clade); Heunggongvirae (kingdom); Uroviricota (phylum); Caudoviricetes (class); Straboviridae (family); Tevenvirinae (subfamily); Tequatrovirus(genus); Tequatrovirus T4(species)
You may notice the absence of a domain in the classification above. This is because bacteriophages, which are viruses, are not alive!
Species
|
NCBI: [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1007084&lvl= 3&lin=f&keep=1&srchmode=1&unlock] |
Official name from Taxonomy Browser: Tequatrovirus T4
Current name: Escherichia phage T4
Commonly known as: Bacteriophage T4
Genome Structure
Bacteriophage T4 has a linear double stranded DNA genome made of 168,903 base pairs.
Cell Structure, Metabolism and Life Cycle
The T4 bacteriophage has the classic appearance that most people think of when they hear the term bacteriophage. If you were going to observe a T4 bacteriophage, you would notice two main parts of the virus' body; the head, and the tail. The head is comprised of an icosahedral (20 sided) capsid, that contains T4's double stranded DNA, and is the proximal part of the virus. The whole tail region has a few more parts, and is located distally to the icosahedral capsid. The proximal end of the tail is where the collar can be observed, and the distal end of the tail is where the baseplate can be observed. Extending laterally from the baseplate are six tail fibers that can be easily mistaken for legs. Despite being a virus, these tail fibers give T4 a very live appearance. Beneath the baseplate there is a spike that the bacteriophage uses to inject its genome into the host for replication.
The T4 bacteriophage is still quite smaller than its host, Escherichia coli. While Escherichia coli is a couple of micrometers, T4 is an entire order of magnitude smaller. The T4 bacteriophage is roughly ______ nM (nanometers) tall. In addition to being smaller than the host, T4 is also much more abundant than its host, outnumber E. coli nearly _____ to one.
Ecology and Pathogenesis
The term bacteriophage alone can tell you a bit about what T4 does. By breaking down the word to its prefix bacterio- and suffix -phage, you can determine that these organisms "eat" bacteria. Although they don't literally consume bacteria, bacteriophage T4's prey is eliminated as a result of the viral life cycle.
Bacteriophage T4 is a predator (and technically a parasite) of the bacteria Escherichia coli. It is technically considered a parasite because it is incapable of replicating or producing energy without a host cell.
Escherichia coli is the only prey/host species of this bacteriophage. Bacteriophages collectively may replicate by one of two cycles, the lytic cycle, or the lysogenic cycle. The T4 Bacteriophage strictly uses the lytic cycle. In the lytic cycle, T4 will land on the host cell's outer membrane and inject its genome through a surface receptor, such as a transport protein. When injecting the genome, the sheath contracts, making T4 appear shorter. After bacteriophage T4's genome has entered the host cell, it takes over control of the cell machinery that is normally involved in replication of host genetic material, then copying itself and producing enzymes to escape. Eventually T4's genetic material and cellular components are assembled into multiple entire copies of the virus, while lysins (a type of enzyme from bacteriophages) degrade the cell wall. This combination causes the host cell to burst, releasing all of the new replicates of T4.
Phage-host coevolution:
History & Significance
Bacteriophages were discovered just over a century ago, more than a decade before the discovery of penicillin.
Even though penicillin took the spotlight in mainstream medicine, the medicinal potential of bacteriophages has not gone unrecognized. While antibiotics are easier to administer they don't have the same level of precision as a bacteriophage. Penicillin is a broad spectrum antibiotic, meaning it doesn't just kill pathogens but also kills harmless or even beneficial bacteria that are exposed to it. Meanwhile bacteriophages are host specific down to at least a species level. That means that a lytic bacteriophage can kill its host organism, while any other bacteria are simply bystanders and remain unharmed.
How to draw a T4 Bacteriophage
The Icosahedral capsid
1. Start off by writing the letter M, and spread it slightly horizontally.
2. Add a vertical line stemming from the bottom left, and bottom right of the M. This is the outer edge
3. Connect the tops of the outer edge straight across (or almost straight across) to each other. This line should come in contact with both of the upper peaks from the M
4. Do the same on the bottom, this line should come in contact with the lower peak of the M
5. On the top, make an equilateral triangle stemming from the two peaks of the M. Then make a line from the top of the triangle to the corner above and to the right of the original M - this will produce a scalene triangle.
6. Repeat step 5, going from the top of the equilateral triangle to the corner above and to the left of the original M.
7. Now for the bottom, all you need to do is make a short vertical line stemming from the lower peak of the M. Draw a line connecting this point to the bottom right end of the original M - this should look more like a right triangle. Draw another line connecting the very bottom to the bottom left end of the original M.
- Completing step 7 concludes the drawing of the icosahedral capsid. Icosahedrons have twenty sides, but you should only be able to see ten in a drawing since it is two dimensional. _________________________________________________________________________________________________
The collar, sheath, and baseplate.
1. Create a small line stemming from the lower end of the icosahedron, and draw a circle around that. This circle should be like the top of a cylinder drawing. This creates the collar region.
2. Extend the cylinder (really the sheath) and draw a broader circle around the distal end to create the baseplate.
3. Make a custom design on the sheath. T4 is typically illustrated with a sheath horizontally lined, horizontally dotted, helically lined, or helically dotted, but it's cool to make your own drawing extra original.
__________________________________________________________________________________________________
The whiskers, tail fibers, and spike
1. T4 has six tail fibers that look like legs. Just start from the baseplate in six different spots, extend out and change direction to make the tail fibers look spread out. You can also draw a couple of short tail fibers extending vertically from the bottom of the baseplate. Depending on the size of your drawing, this may not be easy to see.
2. Draw very short lines stemming from the line between the capsid, and the proximal end of the sheath. This creates the a more detailed appearance of the collar region. It may be easier to add the whiskers to the edge of the proximal end of the sheath.
3. Make a very short line from the middle of the baseplate, this creates the spike. Without the spike, your phage won't be able to inject its genome into the host cell drawing!
References
Fenton M, Ross P, McAuliffe O, O'Mahony J, Coffey A. Recombinant bacteriophage lysins as antibacterials. Bioeng Bugs. 2010 Jan-Feb;1(1):9-16. doi: 10.4161/bbug.1.1.9818. PMID: 21327123; PMCID: PMC3035150.
Fischetti VA. Development of Phage Lysins as Novel Therapeutics: A Historical Perspective. Viruses. 2018 Jun 7;10(6):310. doi: 10.3390/v10060310. PMID: 29875339; PMCID: PMC6024357.
Mathews K. Bacteriophage T4. eLS. 2015 Aug 14. https://doi.org/10.1002/9780470015902.a0000784.pub4
Taylor, M.W. (2014). The Discovery of Bacteriophage and the d’Herelle Controversy. In: Viruses and Man: A History of Interactions. Springer, Cham. p 53-61 https://doi.org/10.1007/978-3-319-07758-1_4
NCBI NLM Taxonomy Browser. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi
NIH NCBI Virus. https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Escherichia%20phage%20T4,%20taxid:2681598
Miller, Eric & Kutter, Elizabeth & Mosig, Gisela & Arisaka, Fumio & Kunisawa, Takashi & Rüger, Wolfgang. (2003). Bacteriophage T4 Genome. Microbiology and molecular biology reviews : MMBR. 67. 86-156, table of contents. 10.1128/MMBR.67.1.86-156.2003.
Schmidt, Matthias & Byrne, James & Maasilta, Ilari. (2021). Bio-imaging with the helium-ion microscope: A review. Beilstein Journal of Nanotechnology. 12. 1-23. 10.3762/bjnano.12.1.
Author
Page authored by Jake Delaney, student of Prof. Bradley Tolar at UNC Wilmington.
