Autographiviridae

Autographiviridae
Virus classification
(unranked):	Virus
Realm:	Duplodnaviria
Kingdom:	Heunggongvirae
Phylum:	Uroviricota
Class:	Caudoviricetes
Order:	Caudovirales
Family:	Autographiviridae
Genera
	see text
Synonyms
	T7 supergroup;

Autographiviridae is a family of viruses in the order Caudovirales. Bacteria serve as natural hosts. There are 373 species in this family, assigned to 9 subfamilies and 133 genera.^[1]^[2]

History

Since the 1990s, the term "T7 supergroup" has been coined for the expanding group of bacteriophages related to coliphage T7, as members of the family Podoviridae. Enterobacteriaceae phages SP6 and K1-5 were the first to be considered as an estranged subgroup of the "T7 supergroup".^[3] Pseudomonas phage phiKMV also shared commonalities at the genome organizational level. As such, based on the available morphological and proteomic data, this clade of viruses was established as a subfamily of the family Podoviridae. The subfamily was later raised to the level of family in 2019.^[4]

Applications

Therapeutic Antibiotic Use

Some experiments suggest that Autographiviridae bacteriophages show promise in regulating and stifling the growth of infectious bacteria, like Klebsiella pneumoniae, in humans.^[5] Infectious bacteria like K. pneumoniae have increasingly become more resistant to traditional antibiotics. Some bacteria are even resistant to multiple antibiotics and antibacterial drugs.^[6] This problem prompted researchers to look towards other possible regulators of bacterial growth, like Autographiviridae bacteriophages.^[5] This type of treatment is referred to as phage therapy. Phage therapy is effective against drug-resistant bacteria because bacteriophages are naturally inclined to infect and kill specific bacteria.^[7]

For the past two decades, studying phage therapy has grown in popularity with major research centers opening up in the United States, Poland, Georgia, and Belgium. In turn, many biotechnology companies have shifted their focus to phage therapy, with some like Armata Pharmaceuticals completely dedicating themselves to combating the problem of antibiotic resistance.^[8]

Autographiviridae has also been used in combination with existing antibiotics to effective results. A recent study showed that Autographiviridae combined with antibiotic medication Tigecycline can effectively combat skin and soft tissue infections associated with Acinetobacter baumannii, a bacterium that previously showed resistance to multiple drugs.^[9]

However, phage therapy does pose some potential drawbacks. Antibiotics work by targeting a key part bacterial structure or by impeding a bacterial metabolic function. Because many bacteria have similar metabolic processes and physical structures, an antibiotic could be effective against many different bacteria. Phages on the other hand are much more specific to a single bacteria. This means that scientists would have to put in more work to perfect a phage therapy that only works against one bacteria. Also, some clinical studies involving phage therapy have resulted in low to moderate efficacy rates and in a huge variation of results for different patients.^[10]

Autographiviridae and other lytic phages lyse host bacteria through a process that begins with adsorption.^[11] Once Autographiviridae is adsorbed on the cell surface of the host bacteria, the enzyme located in its tail structure can penetrate the host bacteria's peptidoglycan layer and inner membrane, where it releases genetic material into the interior of the bacteria. When the phage genetic material is integrated with the bacterial host genes, it will replicate to form a new progeny phage with bacteriolytic ability. The infected bacteria are finally lysed and the progeny phages released post-lysis continue to proliferate and lyse surrounding host bacteria.^[12]

Autographiviridae in Phage Cocktail Formulation

“Phage cocktails” are a form of phage therapy that involves employing at least two phages to target a single bacterial strain,^[13] creating a form of therapy with greater ‘depth.’ Phage cocktails are an effective substitute for antibiotics as they create a broader host range and delay the development of phage resistance in bacteria.^[14] Phage cocktails are most commonly used to combat infections caused by Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli.^[15]

Clinical practices have employed phage cocktails to prevent bacterial biofilm formation, which is one of the greatest challenges in the healthcare industry. A recent study showed that formulated phage cocktails that included Autographiviridae under the now-abolished family classification Podoviridae, effectively reduced the growth of Klebsiella pneumoniae.^[13]^[11]

Etymology

The name of this family, termed Autographiviridae, refers to the “auto-graphein” or “self-transcribing” phages which encode their own (single subunit) RNA polymerase, a common characteristic among its members.^{[citation needed]}

Structure

Viruses in Autographiviridae are non-enveloped, with icosahedral and Head-tail geometries, and T=7 symmetry. The diameter is around 60 nm. Genomes are linear, around 40-42kb in length.^[1]

Life cycle

Viral replication is cytoplasmic. DNA templated transcription is the method of transcription. The virus exits the host cell by lysis, and holin/endolysin/spanin proteins. Bacteria serve as the natural host. Transmission routes are passive diffusion.^[1]

Basis for taxonomy

The former family of Podoviridae, which contained many of the viruses that are now classified under Autographiviridae, was defined based on morphology and the presence of short noncontractile tails.^[16] The Podoviridae family, along with Myoviridae and Siphoviridae families, were abolished for being polyphyletic, meaning that viruses under a single family derived from more than one common ancestor and are thus not suitable for placing in the same taxa. However, these terms (Podoviridae, Myoviridae, and Siphoviridae) are still used to refer to the distinct morphological features of certain bacteriophages.^[17]

Taxonomy

The following subfamilies are recognized:^[2]

The following genera are unassigned to a subfamily:^[2]

Aegirvirus
Anchaingvirus
Aqualcavirus
Ashivirus
Atuphduovirus
Ayakvirus
Ayaqvirus
Banchanvirus
Bifseptvirus
Bonnellvirus
Cheungvirus
Chosvirus
Cuernavacavirus
Cyclitvirus
Ermolevavirus
Foturvirus
Foussvirus
Fussvirus
Gajwadongvirus
Gyeongsanvirus
Igirivirus
Jalkavirus
Jiaoyazivirus
Kafavirus
Kajamvirus
Kakivirus
Kalppathivirus
Kelmasvirus
Kembevirus
Krakvirus
Lauvirus
Limelightvirus
Lingvirus
Lirvirus
Lullwatervirus
Maculvirus
Napahaivirus
Nohivirus
Oinezvirus
Paadamvirus
Pagavirus
Pairvirus
Pedosvirus
Pekhitvirus
Pelagivirus
Percyvirus
Piedvirus
Podivirus
Pollyceevirus
Poseidonvirus
Powvirus
Pradovirus
Qadamvirus
Scottvirus
Sednavirus
Serkorvirus
Sieqvirus
Stompelvirus
Stopalavirus
Stopavirus
Stupnyavirus
Tangaroavirus
Tawavirus
Tiamatvirus
Tiilvirus
Tritonvirus
Voetvirus
Votkovvirus
Waewaevirus
Wuhanvirus (not to be confused with severe acute respiratory syndrome coronavirus 2)

References

^ ^a ^b ^c "Viral Zone". ExPASy. Retrieved 1 July 2015.
^ ^a ^b ^c "Virus Taxonomy: 2020 Release". International Committee on Taxonomy of Viruses (ICTV). March 2021. Retrieved 11 May 2021.
^ D., Scholl; J., Kieleczawa; Kemp, P.; Rush, J.; Richardson, C. C.; Merril, C.; Adhya, S.; Molineux, I. J. (2004). "Genomic analysis of bacteriophages SP6 and K1-5, an estranged subgroup of the T7 supergroup". Journal of Molecular Biology. 335 (5): 1151–71. doi:10.1016/j.jmb.2003.11.035. PMID 14729334.
^ Kumar, R.; Tao, M. (1975-11-20). "Multiple forms of casein kinase from rabbit erythrocytes". Biochimica et Biophysica Acta (BBA) - Enzymology. 410 (1): 87–98. doi:10.1016/0005-2744(75)90209-0. ISSN 0006-3002. PMID 76.
^ ^a ^b Gorodnichev, RB; Kornienko, MA; Kuptsov, NS; Malakhova, MV; Bespiatykh, DA; Veselovsky, VA; Shitikov, EA; Ilina, EN (2021). "Molecular genetic characterization of three new Klebsiella pneumoniae bacteriophages suitable for phage therapy". Medicine of Extreme Situations (in Russian). 2021 (3). doi:10.47183/mes.2021.035. Retrieved 2024-05-07.
^ Li, Yanping; Kumar, Suresh; Zhang, Lihu; Wu, Hongjie; Wu, Hongyan (2023-01-01). "Characteristics of antibiotic resistance mechanisms and genes of Klebsiella pneumoniae". Open Medicine. 18 (1). doi:10.1515/med-2023-0707. ISSN 2391-5463. PMC 10183727. PMID 37197355.
^ "What is Phage Therapy? - IPATH". UC San Diego School of Medicine. Retrieved 2024-05-07.
^ "Company Overview - Armata Pharmaceuticals". Armata Pharmaceuticals. Retrieved 2024-05-07.
^ Wintachai, Phitchayapak; Surachat, Komwit; Singkhamanan, Kamonnut (February 2022). "Isolation and Characterization of a Novel Autographiviridae Phage and Its Combined Effect with Tigecycline in Controlling Multidrug-Resistant Acinetobacter baumannii-Associated Skin and Soft Tissue Infections". Viruses. 14 (2): 194. doi:10.3390/v14020194. ISSN 1999-4915. PMC 8878389. PMID 35215788.
^ Nilsson, Anders S. (2019-11-14). "Pharmacological limitations of phage therapy". Upsala Journal of Medical Sciences. 124 (4): 218–227. doi:10.1080/03009734.2019.1688433. ISSN 2000-1967. PMC 6968538. PMID 31724901.
^ ^a ^b Li, Fei; Tian, Fengjuan; Nazir, Amina; Sui, Shujing; Li, Mengzhe; Cheng, Dongxiao; Nong, Siqin; Ali, Azam; KaKar, Mohib-Ullah; Li, Lu; Feng, Qiang; Tong, Yigang (October 2022). "Isolation and genomic characterization of a novel Autographiviridae bacteriophage IME184 with lytic activity against Klebsiella pneumoniae". Virus Research. 319: 198873. doi:10.1016/j.virusres.2022.198873. ISSN 0168-1702. PMID 35868353.
^ Xu, Hao-Ming; Xu, Wen-Min; Zhang, Long (2022-10-03). "Current Status of Phage Therapy against Infectious Diseases and Potential Application beyond Infectious Diseases". International Journal of Clinical Practice. 2022: e4913146. doi:10.1155/2022/4913146. ISSN 1368-5031. PMC 9550513. PMID 36263241.
^ ^a ^b Mani, Indra (2023), "Phage and phage cocktails formulations", Phage Therapy - Part A, Progress in Molecular Biology and Translational Science, vol. 200, Elsevier, pp. 159–169, doi:10.1016/bs.pmbts.2023.04.007, ISBN 978-0-323-95563-8, PMID 37739554, retrieved 2024-05-07
^ Ribeiro, Jhonatan Macedo; Pereira, Giovana Nicolete; Durli Junior, Itamar; Teixeira, Gustavo Manoel; Bertozzi, Mariana Marques; Verri, Waldiceu A.; Kobayashi, Renata Katsuko Takayama; Nakazato, Gerson (2023-08-11). "Comparative analysis of effectiveness for phage cocktail development against multiple Salmonella serovars and its biofilm control activity". Scientific Reports. 13 (1): 13054. Bibcode:2023NatSR..1313054R. doi:10.1038/s41598-023-40228-z. ISSN 2045-2322. PMC 10421930. PMID 37567926.
^ Kornienko, Maria; Kuptsov, Nikita; Gorodnichev, Roman; Bespiatykh, Dmitry; Guliaev, Andrei; Letarova, Maria; Kulikov, Eugene; Veselovsky, Vladimir; Malakhova, Maya; Letarov, Andrey; Ilina, Elena; Shitikov, Egor (2020-10-29). "Contribution of Podoviridae and Myoviridae bacteriophages to the effectiveness of anti-staphylococcal therapeutic cocktails". Scientific Reports. 10 (1): 18612. Bibcode:2020NatSR..1018612K. doi:10.1038/s41598-020-75637-x. ISSN 2045-2322. PMC 7596081. PMID 33122703.
^ Ackermann, H.-W. (May 2003). "Bacteriophage observations and evolution". Research in Microbiology. 154 (4): 245–251. doi:10.1016/S0923-2508(03)00067-6. PMID 12798228.
^ Turner, Dann; Shkoporov, Andrey N.; Lood, Cédric; Millard, Andrew D.; Dutilh, Bas E.; Alfenas-Zerbini, Poliane; van Zyl, Leonardo J.; Aziz, Ramy K.; Oksanen, Hanna M.; Poranen, Minna M.; Kropinski, Andrew M.; Barylski, Jakub; Brister, J Rodney; Chanisvili, Nina; Edwards, Rob A. (February 2023). "Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee". Archives of Virology. 168 (2): 74. doi:10.1007/s00705-022-05694-2. ISSN 0304-8608. PMC 9868039. PMID 36683075.

External links

[ViralZone-1] "Viral Zone". ExPASy. Retrieved 1 July 2015.

[ICTV-2] "Virus Taxonomy: 2020 Release". International Committee on Taxonomy of Viruses (ICTV). March 2021. Retrieved 11 May 2021.

[3] D., Scholl; J., Kieleczawa; Kemp, P.; Rush, J.; Richardson, C. C.; Merril, C.; Adhya, S.; Molineux, I. J. (2004). "Genomic analysis of bacteriophages SP6 and K1-5, an estranged subgroup of the T7 supergroup". Journal of Molecular Biology. 335 (5): 1151–71. doi:10.1016/j.jmb.2003.11.035. PMID 14729334.

[4] Kumar, R.; Tao, M. (1975-11-20). "Multiple forms of casein kinase from rabbit erythrocytes". Biochimica et Biophysica Acta (BBA) - Enzymology. 410 (1): 87–98. doi:10.1016/0005-2744(75)90209-0. ISSN 0006-3002. PMID 76.

[:0-5] Gorodnichev, RB; Kornienko, MA; Kuptsov, NS; Malakhova, MV; Bespiatykh, DA; Veselovsky, VA; Shitikov, EA; Ilina, EN (2021). "Molecular genetic characterization of three new Klebsiella pneumoniae bacteriophages suitable for phage therapy". Medicine of Extreme Situations (in Russian). 2021 (3). doi:10.47183/mes.2021.035. Retrieved 2024-05-07.

[6] Li, Yanping; Kumar, Suresh; Zhang, Lihu; Wu, Hongjie; Wu, Hongyan (2023-01-01). "Characteristics of antibiotic resistance mechanisms and genes of Klebsiella pneumoniae". Open Medicine. 18 (1). doi:10.1515/med-2023-0707. ISSN 2391-5463. PMC 10183727. PMID 37197355.

[7] "What is Phage Therapy? - IPATH". UC San Diego School of Medicine. Retrieved 2024-05-07.

[8] "Company Overview - Armata Pharmaceuticals". Armata Pharmaceuticals. Retrieved 2024-05-07.

[9] Wintachai, Phitchayapak; Surachat, Komwit; Singkhamanan, Kamonnut (February 2022). "Isolation and Characterization of a Novel Autographiviridae Phage and Its Combined Effect with Tigecycline in Controlling Multidrug-Resistant Acinetobacter baumannii-Associated Skin and Soft Tissue Infections". Viruses. 14 (2): 194. doi:10.3390/v14020194. ISSN 1999-4915. PMC 8878389. PMID 35215788.

[10] Nilsson, Anders S. (2019-11-14). "Pharmacological limitations of phage therapy". Upsala Journal of Medical Sciences. 124 (4): 218–227. doi:10.1080/03009734.2019.1688433. ISSN 2000-1967. PMC 6968538. PMID 31724901.

[:1-11] Li, Fei; Tian, Fengjuan; Nazir, Amina; Sui, Shujing; Li, Mengzhe; Cheng, Dongxiao; Nong, Siqin; Ali, Azam; KaKar, Mohib-Ullah; Li, Lu; Feng, Qiang; Tong, Yigang (October 2022). "Isolation and genomic characterization of a novel Autographiviridae bacteriophage IME184 with lytic activity against Klebsiella pneumoniae". Virus Research. 319: 198873. doi:10.1016/j.virusres.2022.198873. ISSN 0168-1702. PMID 35868353.

[12] Xu, Hao-Ming; Xu, Wen-Min; Zhang, Long (2022-10-03). "Current Status of Phage Therapy against Infectious Diseases and Potential Application beyond Infectious Diseases". International Journal of Clinical Practice. 2022: e4913146. doi:10.1155/2022/4913146. ISSN 1368-5031. PMC 9550513. PMID 36263241.

[:2-13] Mani, Indra (2023), "Phage and phage cocktails formulations", Phage Therapy - Part A, Progress in Molecular Biology and Translational Science, vol. 200, Elsevier, pp. 159–169, doi:10.1016/bs.pmbts.2023.04.007, ISBN 978-0-323-95563-8, PMID 37739554, retrieved 2024-05-07

[14] Ribeiro, Jhonatan Macedo; Pereira, Giovana Nicolete; Durli Junior, Itamar; Teixeira, Gustavo Manoel; Bertozzi, Mariana Marques; Verri, Waldiceu A.; Kobayashi, Renata Katsuko Takayama; Nakazato, Gerson (2023-08-11). "Comparative analysis of effectiveness for phage cocktail development against multiple Salmonella serovars and its biofilm control activity". Scientific Reports. 13 (1): 13054. Bibcode:2023NatSR..1313054R. doi:10.1038/s41598-023-40228-z. ISSN 2045-2322. PMC 10421930. PMID 37567926.

[15] Kornienko, Maria; Kuptsov, Nikita; Gorodnichev, Roman; Bespiatykh, Dmitry; Guliaev, Andrei; Letarova, Maria; Kulikov, Eugene; Veselovsky, Vladimir; Malakhova, Maya; Letarov, Andrey; Ilina, Elena; Shitikov, Egor (2020-10-29). "Contribution of Podoviridae and Myoviridae bacteriophages to the effectiveness of anti-staphylococcal therapeutic cocktails". Scientific Reports. 10 (1): 18612. Bibcode:2020NatSR..1018612K. doi:10.1038/s41598-020-75637-x. ISSN 2045-2322. PMC 7596081. PMID 33122703.

[16] Ackermann, H.-W. (May 2003). "Bacteriophage observations and evolution". Research in Microbiology. 154 (4): 245–251. doi:10.1016/S0923-2508(03)00067-6. PMID 12798228.

[17] Turner, Dann; Shkoporov, Andrey N.; Lood, Cédric; Millard, Andrew D.; Dutilh, Bas E.; Alfenas-Zerbini, Poliane; van Zyl, Leonardo J.; Aziz, Ramy K.; Oksanen, Hanna M.; Poranen, Minna M.; Kropinski, Andrew M.; Barylski, Jakub; Brister, J Rodney; Chanisvili, Nina; Edwards, Rob A. (February 2023). "Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee". Archives of Virology. 168 (2): 74. doi:10.1007/s00705-022-05694-2. ISSN 0304-8608. PMC 9868039. PMID 36683075.

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Autographiviridae

History

Applications

Therapeutic Antibiotic Use

Autographiviridae in Phage Cocktail Formulation

Etymology

Structure

Life cycle

Basis for taxonomy

Taxonomy

References

External links

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