PangenomeCOLN315NCTC8325NewmanUSA300_FPR375704-0298108BA0217611819-97685071193ECT-R 2ED133ED98HO 5096 0412JH1JH9JKD6008JKD6159JSNZLGA251M013MRSA252MSHR1132MSSA476MW2Mu3Mu50RF122ST398T0131TCH60TW20USA300_TCH1516VC40

⊟Summary[edit | edit source]

pan ID^?: SAUPAN001380000
symbol^?: —
synonym:
description^?: phage transcriptional activator
- phage transcriptional activator
- phi77 ORF026-like protein phage transcriptional activator
- phage protein
- phage transcriptional regulator, RinA family protein
- putative phage transcriptional activator
- RinA family phage transcriptional regulator
strand^?: +
coordinates^?: 1673740..1674156
synteny block^?: BlockID0008590
occurrence^?: in 35% of 34 strains

rinA (ltrF) : prophage φ77-like late-gene transcriptional activator ^[1]

Prophage late-gene transcriptional activators bind upstream of the terS gene and enable transcription of phage structural genes. These regulators belong to the RinA-Ltr family of phage transcriptional activators. As with other prophage regulators, there is strong evolutionary pressure to diversify binding sites to preserve autonomous regulation when multiple prophage are present. This version is LtrF, the paralogue from prophage φ77. Currently six paralogues are recognized in staphylococcal prophage:


Prophage Prototype	Accession Number	late-gene activator protein	Gene Synonym	Percent Identity / Similarity to RinA	Operator	Crystal Structure	References
φ11	AF424781	AAL82256.1	rinA	100% / 100%	TGRCAGT-n₄-TGRCAGT	n.a.	^[2]
φ12	AF424782	AAL82308.1	ltrD	24% / 42%	ATTGTGCAAA-n-ATTGTGCAAA	n.a.	^[3]
φ13	AF424783	AAL82356.1	ltrG	16% / 33%	GACAATG-n₁₄-GACAAAG	n.a.	^[3]
φ55	AY954963	AAX91676.1	ltrC	17% / 36%	AAATGAC-n₂-AAATGAC-n₂-AAATGAC-n₂-AAATGAC	n.a.	^[4]
φ69	AY954951	AAX90782.1	ltrE	37% / 56%	TGGAAAAA-n₃-TGGAAAAA	n.a.	^[4]
φ77	AY508486	AAR87896.1	ltrF	19% / 39%	GRTCAAAA-n₁₅-GRTCAAAA	n.a.	^[4]

For annotation of individual genomes, a recommended naming convention would be to use "rinA" as the gene name and the prophage prototype in the description, as in "prophage φ77-like late-gene transcriptional activator" for SAUSA300_1944 from strain USA300_FPR3757.

⊟Orthologs[edit | edit source]

COL:

—

N315:

—

NCTC8325:

—

Newman:

NWMN_1902

USA300_FPR3757:

SAUSA300_1944

04-02981:

—

08BA02176:

—

11819-97:

—

6850:

—

71193:

ST398NM01_2934

ECT-R 2:

—

ED133:

SAOV_1098

ED98:

SAAV_2035

HO 5096 0412:

—

JH1:

—

JH9:

—

JKD6008:

SAA6008_02025

JKD6159:

SAA6159_01901

JSNZ:

—

LGA251:

—

M013:

M013TW_1461

MRSA252:

—

MSHR1132:

SAMSHR1132_18100

MSSA476:

—

Mu3:

—

Mu50:

—

MW2:

—

RF122:

—

ST398:

—

T0131:

SAT0131_02104

TCH60:

—

TW20:

SATW20_19630

USA300_TCH1516:

USA300HOU_1974

VC40:

—

⊟Genome Viewer[edit | edit source]

⊟Alignments[edit | edit source]

alignment of orthologues:
CLUSTAL format alignment by MAFFT L-INS-i (v7.307)

Newman          MIKIEKHDIKKLEEYIQHIDNYRRELKMREYELLESHEPDNAGAGKSNLPGNPIERCAIK
USA300_FPR3757  ---------------------------MREYELLESHEPDNAGAGKSNLPGNPIERCAIK
                                           *********************************

Newman          KFSDNRYNTLRNIVNGVDRLIDESDEDTLELLRFRYWDCPIGCYEWEDIAHYFGTSKTSI
USA300_FPR3757  KFSDNRYNTLRNIVNGVDRLIDESDEDTLELLRFRYWDCPIGCYEWEDIAHYFGTSKTSI
                ************************************************************

Newman          LRRRNALIDKLAKYIGYV
USA300_FPR3757  LRRRNALIDKLAKYIGYV
                ******************

↑ María Desamparados Ferrer, Nuria Quiles-Puchalt, Michael D Harwich, María Ángeles Tormo-Más, Susana Campoy, Jordi Barbé, Iñigo Lasa, Richard P Novick, Gail E Christie, José R Penadés
RinA controls phage-mediated packaging and transfer of virulence genes in Gram-positive bacteria.
Nucleic Acids Res: 2011, 39(14);5866-78
[PubMed:21450808] [WorldCat.org] [DOI] (I p)Nuria Quiles-Puchalt, María Ángeles Tormo-Más, Susana Campoy, Alejandro Toledo-Arana, Vicente Monedero, Iñigo Lasa, Richard P Novick, Gail E Christie, José R Penadés
A super-family of transcriptional activators regulates bacteriophage packaging and lysis in Gram-positive bacteria.
Nucleic Acids Res: 2013, 41(15);7260-75
[PubMed:23771138] [WorldCat.org] [DOI] (I p)
↑ John J Iandolo, Veronica Worrell, Kajetan H Groicher, Yudong Qian, Runying Tian, Steve Kenton, Angela Dorman, Honggui Ji, Shaoping Lin, Phoebe Loh, Sulan Qi, Hua Zhu, B A Roe
Comparative analysis of the genomes of the temperate bacteriophages phi 11, phi 12 and phi 13 of Staphylococcus aureus 8325.
Gene: 2002, 289(1-2);109-18
[PubMed:12036589] [WorldCat.org] [DOI] (P p)María Desamparados Ferrer, Nuria Quiles-Puchalt, Michael D Harwich, María Ángeles Tormo-Más, Susana Campoy, Jordi Barbé, Iñigo Lasa, Richard P Novick, Gail E Christie, José R Penadés
RinA controls phage-mediated packaging and transfer of virulence genes in Gram-positive bacteria.
Nucleic Acids Res: 2011, 39(14);5866-78
[PubMed:21450808] [WorldCat.org] [DOI] (I p)Nuria Quiles-Puchalt, María Ángeles Tormo-Más, Susana Campoy, Alejandro Toledo-Arana, Vicente Monedero, Iñigo Lasa, Richard P Novick, Gail E Christie, José R Penadés
A super-family of transcriptional activators regulates bacteriophage packaging and lysis in Gram-positive bacteria.
Nucleic Acids Res: 2013, 41(15);7260-75
[PubMed:23771138] [WorldCat.org] [DOI] (I p)
↑ ^3.0 ^3.1 John J Iandolo, Veronica Worrell, Kajetan H Groicher, Yudong Qian, Runying Tian, Steve Kenton, Angela Dorman, Honggui Ji, Shaoping Lin, Phoebe Loh, Sulan Qi, Hua Zhu, B A Roe
Comparative analysis of the genomes of the temperate bacteriophages phi 11, phi 12 and phi 13 of Staphylococcus aureus 8325.
Gene: 2002, 289(1-2);109-18
[PubMed:12036589] [WorldCat.org] [DOI] (P p)Nuria Quiles-Puchalt, María Ángeles Tormo-Más, Susana Campoy, Alejandro Toledo-Arana, Vicente Monedero, Iñigo Lasa, Richard P Novick, Gail E Christie, José R Penadés
A super-family of transcriptional activators regulates bacteriophage packaging and lysis in Gram-positive bacteria.
Nucleic Acids Res: 2013, 41(15);7260-75
[PubMed:23771138] [WorldCat.org] [DOI] (I p)
↑ ^4.0 ^4.1 ^4.2 Nuria Quiles-Puchalt, María Ángeles Tormo-Más, Susana Campoy, Alejandro Toledo-Arana, Vicente Monedero, Iñigo Lasa, Richard P Novick, Gail E Christie, José R Penadés
A super-family of transcriptional activators regulates bacteriophage packaging and lysis in Gram-positive bacteria.
Nucleic Acids Res: 2013, 41(15);7260-75
[PubMed:23771138] [WorldCat.org] [DOI] (I p)Jing Liu, Mohammed Dehbi, Greg Moeck, Francis Arhin, Pascale Bauda, Dominique Bergeron, Mario Callejo, Vincent Ferretti, Nhuan Ha, Tony Kwan, John McCarty, Ramakrishnan Srikumar, Dan Williams, Jinzi J Wu, Philippe Gros, Jerry Pelletier, Michael DuBow
Antimicrobial drug discovery through bacteriophage genomics.
Nat Biotechnol: 2004, 22(2);185-91
[PubMed:14716317] [WorldCat.org] [DOI] (P p)

[1] María Desamparados Ferrer, Nuria Quiles-Puchalt, Michael D Harwich, María Ángeles Tormo-Más, Susana Campoy, Jordi Barbé, Iñigo Lasa, Richard P Novick, Gail E Christie, José R Penadés
RinA controls phage-mediated packaging and transfer of virulence genes in Gram-positive bacteria.
Nucleic Acids Res: 2011, 39(14);5866-78
[PubMed:21450808] [WorldCat.org] [DOI] (I p)Nuria Quiles-Puchalt, María Ángeles Tormo-Más, Susana Campoy, Alejandro Toledo-Arana, Vicente Monedero, Iñigo Lasa, Richard P Novick, Gail E Christie, José R Penadés
A super-family of transcriptional activators regulates bacteriophage packaging and lysis in Gram-positive bacteria.
Nucleic Acids Res: 2013, 41(15);7260-75
[PubMed:23771138] [WorldCat.org] [DOI] (I p)

[2] John J Iandolo, Veronica Worrell, Kajetan H Groicher, Yudong Qian, Runying Tian, Steve Kenton, Angela Dorman, Honggui Ji, Shaoping Lin, Phoebe Loh, Sulan Qi, Hua Zhu, B A Roe
Comparative analysis of the genomes of the temperate bacteriophages phi 11, phi 12 and phi 13 of Staphylococcus aureus 8325.
Gene: 2002, 289(1-2);109-18
[PubMed:12036589] [WorldCat.org] [DOI] (P p)María Desamparados Ferrer, Nuria Quiles-Puchalt, Michael D Harwich, María Ángeles Tormo-Más, Susana Campoy, Jordi Barbé, Iñigo Lasa, Richard P Novick, Gail E Christie, José R Penadés
RinA controls phage-mediated packaging and transfer of virulence genes in Gram-positive bacteria.
Nucleic Acids Res: 2011, 39(14);5866-78
[PubMed:21450808] [WorldCat.org] [DOI] (I p)Nuria Quiles-Puchalt, María Ángeles Tormo-Más, Susana Campoy, Alejandro Toledo-Arana, Vicente Monedero, Iñigo Lasa, Richard P Novick, Gail E Christie, José R Penadés
A super-family of transcriptional activators regulates bacteriophage packaging and lysis in Gram-positive bacteria.
Nucleic Acids Res: 2013, 41(15);7260-75
[PubMed:23771138] [WorldCat.org] [DOI] (I p)

[:1-3] 3.0 ^3.1 John J Iandolo, Veronica Worrell, Kajetan H Groicher, Yudong Qian, Runying Tian, Steve Kenton, Angela Dorman, Honggui Ji, Shaoping Lin, Phoebe Loh, Sulan Qi, Hua Zhu, B A Roe
Comparative analysis of the genomes of the temperate bacteriophages phi 11, phi 12 and phi 13 of Staphylococcus aureus 8325.
Gene: 2002, 289(1-2);109-18
[PubMed:12036589] [WorldCat.org] [DOI] (P p)Nuria Quiles-Puchalt, María Ángeles Tormo-Más, Susana Campoy, Alejandro Toledo-Arana, Vicente Monedero, Iñigo Lasa, Richard P Novick, Gail E Christie, José R Penadés
A super-family of transcriptional activators regulates bacteriophage packaging and lysis in Gram-positive bacteria.
Nucleic Acids Res: 2013, 41(15);7260-75
[PubMed:23771138] [WorldCat.org] [DOI] (I p)

[:0-4] 4.0 ^4.1 ^4.2 Nuria Quiles-Puchalt, María Ángeles Tormo-Más, Susana Campoy, Alejandro Toledo-Arana, Vicente Monedero, Iñigo Lasa, Richard P Novick, Gail E Christie, José R Penadés
A super-family of transcriptional activators regulates bacteriophage packaging and lysis in Gram-positive bacteria.
Nucleic Acids Res: 2013, 41(15);7260-75
[PubMed:23771138] [WorldCat.org] [DOI] (I p)Jing Liu, Mohammed Dehbi, Greg Moeck, Francis Arhin, Pascale Bauda, Dominique Bergeron, Mario Callejo, Vincent Ferretti, Nhuan Ha, Tony Kwan, John McCarty, Ramakrishnan Srikumar, Dan Williams, Jinzi J Wu, Philippe Gros, Jerry Pelletier, Michael DuBow
Antimicrobial drug discovery through bacteriophage genomics.
Nat Biotechnol: 2004, 22(2);185-91
[PubMed:14716317] [WorldCat.org] [DOI] (P p)

[1]

[2]

[3]

[4]

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⊟Summary[edit | edit source]

⊟Orthologs[edit | edit source]

⊟Genome Viewer[edit | edit source]

⊟Alignments[edit | edit source]

Newman
USA300_FPR3757

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⊟Summary[edit | edit source]

⊟Orthologs[edit | edit source]

⊟Genome Viewer[edit | edit source]

⊟Alignments[edit | edit source]