Phage lambda - Revision history

Saleksander: /* Adsorbtion and Injection */

2012-01-04T18:34:55Z

Adsorbtion and Injection

← Older revision		Revision as of 18:34, 4 January 2012
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	==== Adsorbtion and Injection ====		==== Adsorbtion and Injection ====
	The [[Phage_lambda_J:Gene_Product(s)\|J protein]], located at the tip of the tail, attaches to the host maltoporin [[lamB]], which is displayed on the outer membrane.<ref name='LIB:Lambda_II'/> The original isolate was able to infect hosts using [[ompF]] as well as [[lamB]].<ref name='LIB:CampbellPhage'/> The dsDNA is stored in the phage head as a linear strand, ~~but~~ is fed through the tail after a conformational change caused by the interaction of the phage tail [[Phage_lambda_J:Gene_Product(s)\|J protein]] with the host protein [[lamB]] <ref name='LIB:Bacteriophages'/>.<ref name='LIB:Lambda_II'/> The genome enters "right" end first and recircularizes immediately upon entry into the host due to complementary 12nt long sticky ends. <ref name='LIB:Lambda_II'/> The sticky ends are each neighbored by packing signals, and the entire site is termed '''co'''hesive end '''s'''ite, or [[Cis_Element:Phage_lambda_cos\|''cos'']].<ref name='LIB:Lambda_II'/> Host DNA ligase is needed to covalently seal the ends together, and host gyrase is required to catalyze the negative supercoiling of the relaxed genome. <ref name='LIB:Lambda_II'/>		The [[Phage_lambda_J:Gene_Product(s)\|J protein]], located at the tip of the tail, attaches to the host maltoporin [[lamB]], which is displayed on the outer membrane.<ref name='LIB:Lambda_II'/> The original isolate was able to infect hosts using [[ompF]] as well as [[lamB]].<ref name='LIB:CampbellPhage'/> The dsDNA is stored in the phage head as a linear strand, and is fed through the tail after a conformational change caused by the interaction of the phage tail [[Phage_lambda_J:Gene_Product(s)\|J protein]] with the host protein [[lamB]] <ref name='LIB:Bacteriophages'/>.<ref name='LIB:Lambda_II'/> The genome enters "right" end first and recircularizes immediately upon entry into the host due to complementary 12nt long sticky ends. <ref name='LIB:Lambda_II'/> The sticky ends are each neighbored by packing signals, and the entire site is termed '''co'''hesive end '''s'''ite, or [[Cis_Element:Phage_lambda_cos\|''cos'']].<ref name='LIB:Lambda_II'/> Host DNA ligase is needed to covalently seal the ends together, and host gyrase is required to catalyze the negative supercoiling of the relaxed genome. <ref name='LIB:Lambda_II'/>

	==== Early Gene Expression ====		==== Early Gene Expression ====

Saleksander: /* Adsorbtion and Injection */

2012-01-04T18:34:29Z

Adsorbtion and Injection

← Older revision		Revision as of 18:34, 4 January 2012
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	==== Adsorbtion and Injection ====		==== Adsorbtion and Injection ====
	The [[Phage_lambda_J:Gene_Product(s)\|J protein]], located at the tip of the tail, attaches to the host maltoporin [[lamB]], which is displayed on the outer membrane.<ref name='LIB:Lambda_II'/> The original isolate was able to infect hosts using [[ompF]] as well as [[lamB]].<ref name='LIB:CampbellPhage'/> The dsDNA is stored in the phage head as a linear strand, ~~then~~ fed through the tail ~~when~~ the phage tail ~~interacts~~ with the ~~inner membrane~~ protein [[~~ptsM~~]]~~; the~~ genome enters "right" end first and recircularizes immediately upon entry into the host due to complementary 12nt long sticky ends. <ref name='LIB:Lambda_II'/> The sticky ends are each neighbored by packing signals, and the entire site is termed '''co'''hesive end '''s'''ite, or [[Cis_Element:Phage_lambda_cos\|''cos'']].<ref name='LIB:Lambda_II'/> Host DNA ligase is needed to covalently seal the ends together, and host gyrase is required to catalyze the negative supercoiling of the relaxed genome. <ref name='LIB:Lambda_II'/>		The [[Phage_lambda_J:Gene_Product(s)\|J protein]], located at the tip of the tail, attaches to the host maltoporin [[lamB]], which is displayed on the outer membrane.<ref name='LIB:Lambda_II'/> The original isolate was able to infect hosts using [[ompF]] as well as [[lamB]].<ref name='LIB:CampbellPhage'/> The dsDNA is stored in the phage head as a linear strand, but is fed through the tail after a conformational change caused by the interaction of the phage tail [[Phage_lambda_J:Gene_Product(s)\|J protein]] with the host protein [[lamB]] <ref name='LIB:Bacteriophages'/>.<ref name='LIB:Lambda_II'/> The genome enters "right" end first and recircularizes immediately upon entry into the host due to complementary 12nt long sticky ends. <ref name='LIB:Lambda_II'/> The sticky ends are each neighbored by packing signals, and the entire site is termed '''co'''hesive end '''s'''ite, or [[Cis_Element:Phage_lambda_cos\|''cos'']].<ref name='LIB:Lambda_II'/> Host DNA ligase is needed to covalently seal the ends together, and host gyrase is required to catalyze the negative supercoiling of the relaxed genome. <ref name='LIB:Lambda_II'/>

	==== Early Gene Expression ====		==== Early Gene Expression ====

Saleksander: /* Morphology */

2012-01-04T18:16:10Z

Morphology

← Older revision		Revision as of 18:16, 4 January 2012
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	== Morphology ==		== Morphology ==
	The λ phage has an icosahedral head (with T=7) about 50 nm in diameter, and a flexible, long noncontractile tail about 150nm in length.<ref name='LIB:Lambda_II'/><ref name='PMID:1439823'/><ref name='LIB:CampbellPhage'/> The head is formed from the proteins [[Phage_lambda_E:Gene_Product(s)\|E]], [[Phage_lambda_D:Gene_Product(s)\|D]], [[Phage_lambda_B:Gene_Product(s)\|B]], [[Phage_lambda_W:Gene_Product(s)\|W]], [[Phage_lambda_FII:Gene_Product(s)\| FII]], B*, X1, and X2. <ref name="Basic Virology"> Edward K. Wagner et al (2007) Basic Virology (Wiley-Blackwell) ISBN 978-1-4051-4715-6</ref> The head is the capsid, and contains a single double-stranded DNA molecule about 48 kb in length; by weight the genome is about 32x10<sup>6</sup> Da and comprises about half of the phage's weight.<ref name='LIB:Lambda_II'/> The tail consists of a 135nm hollow tube finished with a 15nm conical cap.<ref name='LIB:Lambda_II'/> The inside diameter of the tail is about 3nm, with an outside diameter of 9-18nm due to knob-like structures that make the tail appear rough.<ref name='LIB:Lambda_II'/> The wt λ does not have tail fibers, although these may be present on certain strains.<ref name='PMID:1439823'/>		The λ phage has an icosahedral head (with T=7) about 50-60 nm in diameter, and a flexible, long noncontractile tail about 150nm in length.<ref name='LIB:Lambda_II'/><ref name='PMID:1439823'/><ref name='LIB:CampbellPhage'/><ref name='LIB:Bacteriophages'/> The head is formed from the proteins [[Phage_lambda_E:Gene_Product(s)\|E]], [[Phage_lambda_D:Gene_Product(s)\|D]], [[Phage_lambda_B:Gene_Product(s)\|B]], [[Phage_lambda_W:Gene_Product(s)\|W]], [[Phage_lambda_FII:Gene_Product(s)\| FII]], B*, X1, and X2. <ref name="Basic Virology"> Edward K. Wagner et al (2007) Basic Virology (Wiley-Blackwell) ISBN 978-1-4051-4715-6</ref> The head is the capsid, and contains a single double-stranded DNA molecule about 48 kb in length; by weight the genome is about 32x10<sup>6</sup> Da and comprises about half of the phage's weight.<ref name='LIB:Lambda_II'/> The tail consists of a 135nm hollow tube finished with a 15nm conical cap.<ref name='LIB:Lambda_II'/> The inside diameter of the tail is about 3nm, with an outside diameter of 9-18nm due to knob-like structures that make the tail appear rough.<ref name='LIB:Lambda_II'/> The wt λ does not have tail fibers, although these may be present on certain strains.<ref name='PMID:1439823'/>

	== Genome Organization ==		== Genome Organization ==

Saleksander: /* Lysogenic State */

2011-11-10T22:28:11Z

Lysogenic State

← Older revision		Revision as of 22:28, 10 November 2011
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	=== Lysogenic State ===		=== Lysogenic State ===
	The lysogenic lifecycle does not result in the production of a large number of progeny phage, nor is the host cell destroyed. Instead, recombination of the λ DNA with the host genome creates a ''prophage'' which is replicated as part of the host chromosome with each cell division.<ref name='LIB:BofV'/><ref name='LIB:Lambda_II'/> The single recombination event occurs between specific sites: the ''att''P (for '''att'''achment '''p'''hage) on the λ DNA and the ''att''B (for '''att'''achment '''b'''acteria) loci.<ref name='LIB:BofV'/> The genes that cause lysis must be repressed in order for a lysogen to integrate. <ref name='LIB:CampbellPhage'/> Most of the phage genes are silenced, as very few genes are required to keep the phage DNA integrated.<ref name='LIB:BofV'/> Prophage and descendant prophage are capable of producing phage when the λ DNA is induced to excise from the host DNA. <ref name='PMID:17247494'/>		The lysogenic lifecycle does not result in the production of a large number of progeny phage, nor is the host cell destroyed. Instead, recombination of the λ DNA with the host genome creates a ''prophage'' which is replicated as part of the host chromosome with each cell division.<ref name='LIB:BofV'/><ref name='LIB:Lambda_II'/>
			The single recombination event occurs between specific sites: the ''att''P (for '''att'''achment '''p'''hage) on the λ DNA and the ''att''B (for '''att'''achment '''b'''acteria) loci.<ref name='LIB:BofV'/> The genes that cause lysis must be repressed in order for a lysogen to integrate. <ref name='LIB:CampbellPhage'/> Most of the phage genes are silenced, as very few genes are required to keep the phage DNA integrated.<ref name='LIB:BofV'/> Prophage and descendant prophage are capable of producing phage when the λ DNA is induced to excise from the host DNA. <ref name='PMID:17247494'/>

	=== Lysis-Lysogeny Switch ===		=== Lysis-Lysogeny Switch ===

Saleksander: /* Lysogenic State */

2011-11-10T21:00:37Z

Lysogenic State

← Older revision		Revision as of 21:00, 10 November 2011
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	=== Lysogenic State ===		=== Lysogenic State ===
	The lysogenic lifecycle does not result in the production of a large number of progeny phage, nor is the host cell destroyed. Instead, recombination of the λ DNA with the host genome creates a ''prophage'' which is replicated as part of the host chromosome with each cell division.<ref name='LIB:BofV'/><ref name='LIB:Lambda_II'/> The recombination occurs between specific sites: the ''att''P (for '''att'''achment '''p'''hage) on the λ DNA and the ''att''B (for '''att'''achment '''b'''acteria) loci.<ref name='LIB:BofV'/> The genes that cause lysis must be repressed in order for a lysogen to integrate. <ref name='LIB:CampbellPhage'/> Most of the phage genes are silenced, as very few genes are required to keep the phage DNA integrated.<ref name='LIB:BofV'/> Prophage and descendant prophage are capable of producing phage when the λ DNA is induced to excise from the host DNA. <ref name='PMID:17247494'/>		The lysogenic lifecycle does not result in the production of a large number of progeny phage, nor is the host cell destroyed. Instead, recombination of the λ DNA with the host genome creates a ''prophage'' which is replicated as part of the host chromosome with each cell division.<ref name='LIB:BofV'/><ref name='LIB:Lambda_II'/> The single recombination event occurs between specific sites: the ''att''P (for '''att'''achment '''p'''hage) on the λ DNA and the ''att''B (for '''att'''achment '''b'''acteria) loci.<ref name='LIB:BofV'/> The genes that cause lysis must be repressed in order for a lysogen to integrate. <ref name='LIB:CampbellPhage'/> Most of the phage genes are silenced, as very few genes are required to keep the phage DNA integrated.<ref name='LIB:BofV'/> Prophage and descendant prophage are capable of producing phage when the λ DNA is induced to excise from the host DNA. <ref name='PMID:17247494'/>

	=== Lysis-Lysogeny Switch ===		=== Lysis-Lysogeny Switch ===

Saleksander: /* Middle Gene Expression */

2011-11-10T20:59:20Z

Middle Gene Expression

← Older revision		Revision as of 20:59, 10 November 2011
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	==== Middle Gene Expression ====		==== Middle Gene Expression ====
	The middle phase of gene expression occurs about 3-9 minutes after host infection.<ref name='LIB:BofV'/> The early gene product [[Phage_lambda_N:Gene_Product(s)\|N]] behaves like an antiterminator by working in tandem with host [[nusA:Gene_Product(s)\|nusA]] and causes RNA polymerase to read past ''t''<sub>L1</sub> and ''t''<sub>R1</sub><ref name='LIB:BofV'/>; as well as higher amounts of [[Phage_lambda_N:Gene_Product(s)\|N]], [[Phage_lambda_cIII:Gene_Product(s)\|cIII]] and products needed for recombination and integration from ''p''<sub>L</sub>, the phage produce [[Phage_lambda_cro:Gene_Product(s)\|cro]], [[Phage_lambda_cII:Gene_Product(s)\|cII]], [[Phage_lambda_O:Gene_Product(s)\|O]],and [[Phage_lambda_P:Gene_Product(s)\|P]] from ''p''<sub>R</sub>.<ref name='LIB:Lambda_II'/> Transcription to ''t''<sub>R3</sub>, which is unaffected by by the action of [[Phage_lambda_N:Gene_Product(s)\|N]], produces another antiterminator, [[Phage_lambda_Q:Gene_Product(s)\|Q]].<ref name='LIB:BofV'/> Another early gene product, [[Phage_lambda_cro:Gene_Product(s)\|cro]], works against [[Phage_lambda_N:Gene_Product(s)\|N]] by binding at he repressing transcription from ''p''<sub>L</sub> and, at a slightly higher concentration, from ''p''<sub>R</sub>, thereby blocking transcription of all early and middle genes.<ref name="Basic Virology"/>		The middle phase of gene expression occurs about 3-9 minutes after host infection.<ref name='LIB:BofV'/> The early gene product [[Phage_lambda_N:Gene_Product(s)\|N]] behaves like an antiterminator by working in tandem with host [[nusA:Gene_Product(s)\|nusA]] and causes RNA polymerase to read past ''t''<sub>L1</sub> and ''t''<sub>R1</sub><ref name='LIB:BofV'/>; as well as higher amounts of [[Phage_lambda_N:Gene_Product(s)\|N]], [[Phage_lambda_cIII:Gene_Product(s)\|cIII]] and products needed for recombination and integration from ''p''<sub>L</sub>, the phage produce [[Phage_lambda_cro:Gene_Product(s)\|cro]], [[Phage_lambda_cII:Gene_Product(s)\|cII]], [[Phage_lambda_O:Gene_Product(s)\|O]],and [[Phage_lambda_P:Gene_Product(s)\|P]] from ''p''<sub>R</sub>.<ref name='LIB:Lambda_II'/> Transcription to ''t''<sub>R3</sub>, which is unaffected by by the action of [[Phage_lambda_N:Gene_Product(s)\|N]], produces another antiterminator, [[Phage_lambda_Q:Gene_Product(s)\|Q]].<ref name='LIB:BofV'/> Another early gene product, [[Phage_lambda_cro:Gene_Product(s)\|cro]], works against [[Phage_lambda_N:Gene_Product(s)\|N]] by binding at he repressing transcription from ''p''<sub>L</sub> and, at a slightly higher concentration, from ''p''<sub>R</sub>, thereby blocking transcription of all early and middle genes.<ref name="Basic Virology"/>



	~~[[Phage_lambda_cII:Gene_Product(s)\|cII]] and [[Phage_lambda_cIII:Gene_Product(s)\|cIII]] are delayed-early gene products. <ref name='PMID:7770059'/><ref name='LIB:CampbellPhage'/><ref name='LIB:BofV'~~/>

	==== DNA Replication ====		==== DNA Replication ====

Saleksander: /* DNA Replication */

2011-11-10T20:50:08Z

DNA Replication

← Older revision		Revision as of 20:50, 10 November 2011
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	Both [[Phage_lambda_O:Gene_Product(s)\|O]] and [[Phage_lambda_P:Gene_Product(s)\|P]], as well as several host enzymes, are needed for replication.<ref name='LIB:Lambda_II'/>There are two phases of replication in λ. Replication first proceeds via θ (theta) replication, which begins during the middle stages of transcription.<ref name="Basic Virology"/> θ replication originates from the [[Phage_lambda_O:Gene_Product(s)\|O]]/[[Phage_lambda_cII:Gene_Product(s)\|cII]] gene region once host gyrase has supercoiled the λ DNA; two daughters, both circular, are produced by each full round of θ replication.<ref name='LIB:Lambda_II'/><ref name="Basic Virology"/>		Both [[Phage_lambda_O:Gene_Product(s)\|O]] and [[Phage_lambda_P:Gene_Product(s)\|P]], as well as several host enzymes, are needed for replication.<ref name='LIB:Lambda_II'/>There are two phases of replication in λ. Replication first proceeds via θ (theta) replication, which begins during the middle stages of transcription.<ref name="Basic Virology"/> θ replication originates from the [[Phage_lambda_O:Gene_Product(s)\|O]]/[[Phage_lambda_cII:Gene_Product(s)\|cII]] gene region once host gyrase has supercoiled the λ DNA; two daughters, both circular, are produced by each full round of θ replication.<ref name='LIB:Lambda_II'/><ref name="Basic Virology"/>

	Replication proceeds in the late stages via rolling circle (σ) replication when entering the lytic cycle, and the resulting concatemers are cut on the (+) strand by phage-encoded endonuclease.<ref name="Basic Virology"/>		Replication proceeds in the late stages, about 15 minutes post infection<ref name='LIB:Lambda_II'/>, via rolling circle (σ) replication when entering the lytic cycle, and the resulting concatemers are cut on the (+) strand by phage-encoded endonuclease.<ref name="Basic Virology"/>

	==== Late Gene Expression ====		==== Late Gene Expression ====

Saleksander: /* Adsorbtion and Injection */

2011-11-08T22:50:32Z

Adsorbtion and Injection

← Older revision		Revision as of 22:50, 8 November 2011
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	==== Adsorbtion and Injection ====		==== Adsorbtion and Injection ====
	The [[Phage_lambda_J:Gene_Product(s)\|J protein]], located at the tip of the tail, attaches to the host maltoporin [[lamB]], which is displayed on the outer membrane.<ref name='LIB:Lambda_II'/> The original isolate was able to infect hosts using [[ompF]] as well as [[lamB]].<ref name='LIB:CampbellPhage'/> The dsDNA is stored in the phage head as a linear strand, then fed through the tail when the phage tail interacts with the inner membrane protein [[ptsM]]; the genome enters "right" end first and recircularizes immediately upon entry into the host due to complementary 12nt long sticky ends. <ref name='LIB:Lambda_II'/> ~~Host DNA ligase is needed to seal the ends together.~~ The sticky ends are each neighbored by packing signals, and the entire site is termed '''co'''hesive end '''s'''ite, or [[Cis_Element:Phage_lambda_cos\|''cos'']].<ref name='LIB:Lambda_II'/>		The [[Phage_lambda_J:Gene_Product(s)\|J protein]], located at the tip of the tail, attaches to the host maltoporin [[lamB]], which is displayed on the outer membrane.<ref name='LIB:Lambda_II'/> The original isolate was able to infect hosts using [[ompF]] as well as [[lamB]].<ref name='LIB:CampbellPhage'/> The dsDNA is stored in the phage head as a linear strand, then fed through the tail when the phage tail interacts with the inner membrane protein [[ptsM]]; the genome enters "right" end first and recircularizes immediately upon entry into the host due to complementary 12nt long sticky ends. <ref name='LIB:Lambda_II'/> The sticky ends are each neighbored by packing signals, and the entire site is termed '''co'''hesive end '''s'''ite, or [[Cis_Element:Phage_lambda_cos\|''cos'']].<ref name='LIB:Lambda_II'/> Host DNA ligase is needed to covalently seal the ends together, and host gyrase is required to catalyze the negative supercoiling of the relaxed genome. <ref name='LIB:Lambda_II'/>

	==== Early Gene Expression ====		==== Early Gene Expression ====

Saleksander: /* Early Gene Expression */

2011-11-08T21:45:29Z

Early Gene Expression

← Older revision		Revision as of 21:45, 8 November 2011
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	==== Early Gene Expression ====		==== Early Gene Expression ====
	Transcripton requires host RNA polymerase and occurs almost immediately from ''p''<sub>R</sub> (for '''p'''romoter '''r'''ight) to the ''t''<sub>R1</sub> terminator, producing the [[Phage_lambda_cro:Gene_Product(s)\|cro gene product]], and simultaneously from ''p''<sub>L</sub> to ''t''<sub>L1</sub>, resulting in production of [[Phage_lambda_N:Gene_Product(s)\|N]]. <ref name='PMID: 7669336'/><ref name='LIB:Lambda_II'/><ref name='LIB:BofV'/> Neither termination is completely efficient; about 20% of transcripts continue from ''p''<sub>L</sub> through ''t''<sub>L1</sub> to ''t''<sub>L2</sub> and result in [[Phage_lambda_cIII:Gene_Product(s)\|cIII]].<ref name='LIB:Lambda_II'/> Transcription from ''p''<sub>R</sub> through ''t''<sub>R1</sub> to ''t''<sub>R2</sub>, which occurs with about half the transcripts, produces [[Phage_lambda_cII:Gene_Product(s)\|cII]], [[Phage_lambda_O:Gene_Product(s)\|O]] and [[Phage_lambda_P:Gene_Product(s)\|P]].<ref name='LIB:Lambda_II'/>		Transcripton requires host RNA polymerase and occurs almost immediately from ''p''<sub>R</sub> (for '''p'''romoter '''r'''ight) to the ''t''<sub>R1</sub> terminator, producing the [[Phage_lambda_cro:Gene_Product(s)\|cro gene product]], and simultaneously from ''p''<sub>L</sub> to ''t''<sub>L1</sub>, resulting in production of [[Phage_lambda_N:Gene_Product(s)\|N]]. <ref name='PMID: 7669336'/><ref name='LIB:Lambda_II'/><ref name='LIB:BofV'/> Neither termination is completely efficient; about 20% of transcripts continue from ''p''<sub>L</sub> through ''t''<sub>L1</sub> to ''t''<sub>L2</sub> and result in [[Phage_lambda_cIII:Gene_Product(s)\|cIII]].<ref name='LIB:Lambda_II'/> Transcription from ''p''<sub>R</sub> through ''t''<sub>R1</sub> to ''t''<sub>R2</sub>, which occurs with about half the transcripts, produces [[Phage_lambda_cII:Gene_Product(s)\|cII]], [[Phage_lambda_O:Gene_Product(s)\|O]] and [[Phage_lambda_P:Gene_Product(s)\|P]].<ref name='LIB:Lambda_II'/>
			[[Phage_lambda_gam:Gene_Product(s)\|Gam]] is an early gene product which inhibits host exonuclease V ([[recB:Gene_Product(s)\|recB]]/[[recC:Gene_Product(s)\|recC]]/[[recD:Gene_Product(s)\|recD]]).<ref name='PMID:7770059'/><ref name='LIB:CampbellPhage'/><ref name='LIB:BofV'/>

	==== Middle Gene Expression ====		==== Middle Gene Expression ====

Saleksander: /* Middle Gene Expression */

2011-11-08T21:44:44Z

Middle Gene Expression

← Older revision		Revision as of 21:44, 8 November 2011
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	[[Phage_lambda_gam:Gene_Product(s)\|Gam]] is an early gene product which inhibits host exonuclease V ([[recB:Gene_Product(s)\|recB]]/[[recC:Gene_Product(s)\|recC]]/[[recD:Gene_Product(s)\|recD]]).<ref name='PMID:7770059'/><ref name='LIB:CampbellPhage'/><ref name='LIB:BofV'/>

	[[Phage_lambda_cII:Gene_Product(s)\|cII]] and [[Phage_lambda_cIII:Gene_Product(s)\|cIII]] are delayed-early gene products. <ref name='PMID:7770059'/><ref name='LIB:CampbellPhage'/><ref name='LIB:BofV'/>		[[Phage_lambda_cII:Gene_Product(s)\|cII]] and [[Phage_lambda_cIII:Gene_Product(s)\|cIII]] are delayed-early gene products. <ref name='PMID:7770059'/><ref name='LIB:CampbellPhage'/><ref name='LIB:BofV'/>