Detailed information of regulator


Summary

Regulator ID REG0112 experimental
Regulator type protein
Regulatory pathway (from literatures) QS regulatory pathway
KEGG pathway (determined by BlastKOALA) Two-component system (map02020); Quorum sensing (map02024); Biofilm formation - Vibrio cholerae (map05111)
Related T6SS T6SS00043 experimental (Type i1); T6SS00044 experimental (Type i5)
Strain Vibrio parahaemolyticus RIMD 2210633
Replicon chromosome
Sequence Protein sequence (205 a.a.); Nucleotide sequence (615 bp)
Description OpaR was previously suggested to directly bind to promoter regions of V. parahaemolyticus T6SS1 operons, including the promoter of the operon encoding the positive downstream regulator, VP1407.; OpaR represses the transcription of VP1388-1390, VP1400-1406, and VP1409-1407 in a direct manner and expression and secretion of Hcp1 were up-regulated in the POR1ΔopaR and down-regulated when opaR was overexpressed from a plasmid.; Deletion of opaR down-regulated the secretion of Hcp2, but only marginally affected Hcp2 expression levels .In agreement with this result, over-expression of opaR up-regulated both the expression and the secretion levels of Hcp2.; EMSA and DNase I footprinting result that OpaR can bind to the promoter regions of VPA1027-1024, VPA1043-1028, and VPA1044-1046 to stimulate their transcription.
Reference
[1] Ben-Yaakov R, Salomon D. The regulatory network of Vibrio parahaemolyticus type VI secretion system 1. Environ Microbiol. 2019 Jul;21(7):2248-2260. doi: 10.1111/1462-2920.14594. Epub 2019 Apr 2. PMID: 30882997
[2] Zhang Y, Gao H, Osei-Adjei G, et al. Transcriptional Regulation of the Type VI Secretion System 1 Genes by Quorum Sensing and ToxR in Vibrio parahaemolyticus. Front Microbiol. 2017 Oct 16;8:2005. doi: 10.3389/fmicb.2017.02005. eCollection 2017. PMID: 29085350
[3] Salomon D, Gonzalez H, Updegraff BL, et al. Vibrio parahaemolyticus type VI secretion system 1 is activated in marine conditions to target bacteria, and is differentially regulated from system 2. PLoS One. 2013 Apr 16;8(4):e61086. doi: 10.1371/journal.pone.0061086. Print 2013. PMID: 23613791
[4] Ma L, Zhang Y, Yan X, et al. Expression of the type VI secretion system 1 component Hcp1 is indirectly repressed by OpaR in Vibrio parahaemolyticus. ScientificWorldJournal. 2012;2012:982140. doi: 10.1100/2012/982140. Epub 2012 Jul 31. PMID: 22924031
[5] Qiu Y, Hu L, Yang W, et al. The type VI secretion system 2 of Vibrio parahaemolyticus is regulated by QsvR. Microb Pathog. 2020 Dec;149:104579. doi: 10.1016/j.micpath.2020.104579. Epub 2020 Oct 19. PMID: 33091577
[6] Wang L, Zhou D, Mao P, et al. Cell density- and quorum sensing-dependent expression of type VI secretion system 2 in Vibrio parahaemolyticus. PLoS One. 2013 Aug 15;8(8):e73363. doi: 10.1371/journal.pone.0073363. eCollection 2013. PMID: 23977385
External database links

Locus tag (Gene) VP2516 (opaR)
Coordinates (Strand) 2653215..2653829 (+)
NCBI ID 28899290
RefSeq NC_004603
Uniprot ID Q79YV4_VIBPA
KEGG ID vpa:VP2516
KEGG pathway (determined by BlastKOALA) map02020; map02024; map05111
PDB ID -
  Target
Target Regulation (↓/↑) Target sequence
vp1407 ↑ 28898181
VP1388 promotor ↑ -
VP1400 promotor ↑ cgtaagtcaaagagtctaataacttagtaattataactaaaataataggcttactgttcgttttaaatactacccttgaaacaagg
VP1409 promotor ↑ ctgagttgataataaaataataaagatagatttttttattgtattcgcctgctatgccaaatgacatgcaatgcattttttctgattttatagataaaaaaagatttttagacaataaaaagccgataaatctaattaaaatccattttgtgtgatctttgttcctaatattaatatcaattggctaatttgcgtgtaggaaaaa
T6SS2 (Hcp2) expression and secretion ↓ -
VPA1027-1024 transcript ↓ TAATGACATTGTAGACAATA
Predicted OpaR box-like sequences
VPA1027-1024 transcript ↓ TTTTGATACATCAATCATTA
Predicted OpaR box-like sequences
VPA1027-1024 transcript ↓ TTCAGATAATTTAATTAATA
Predicted OpaR box-like sequences
VPA1043-1028 transcript ↓ TATTTATAGATTTGTCTTTA
Predicted OpaR box-like sequences
VPA1044-1046 transcript ↓ TATTAACATTAAGATTAATA
Predicted OpaR box-like sequences
Pfam domain hit(s) of regulator

Domain Pfam ID E-value Aligned region
TetR_N PF00440.25 1.8e-09 22..67
Transmembrane helices

  • Transmembrane helices are predicted using TMHMM 2.0 software.

Prediction                 Region     Sequence
Outside 1-204 MDSIAKRPRTRLSPLKRKQQLMEIALEVFARRGIGRGGHADIAEIAQVSVATVFNYFPTREDLVDEVLNHVVRQFSNFLSDNIDLDIHARENIANITNAMIELVSQDCHWLKVWFEWSASTRDEVWPLFVSTNRTNQLLVQNMFIKAIERGEVCDQHDSEHLANLFHGICYSLFVQANRFKGEAELKELVSAYLDMLCIYNREH


Signal peptides
  • Sec/SPI: "standard" secretory signal peptides transported by the Sec translocon and cleaved by Signal Peptidase I (Lep).
  • Sec/SPII: lipoprotein signal peptides transported by the Sec translocon and cleaved by Signal Peptidase II (Lsp).
  • Tat/SPI: Tat signal peptides transported by the Tat translocon and cleaved by Signal Peptidase I (Lep).
Prediction        Probability Cleavage site Signal peptide sequence
Other 0.9920 - -


  Protein sequence of regulator: 205 a.a.    .

>REG0112 NC_004603:2653215-2653829 [Vibrio parahaemolyticus RIMD 2210633]
MDSIAKRPRTRLSPLKRKQQLMEIALEVFARRGIGRGGHADIAEIAQVSVATVFNYFPTREDLVDEVLNHVVRQFSNFLS
DNIDLDIHARENIANITNAMIELVSQDCHWLKVWFEWSASTRDEVWPLFVSTNRTNQLLVQNMFIKAIERGEVCDQHDSE
HLANLFHGICYSLFVQANRFKGEAELKELVSAYLDMLCIYNREH*

  Nucleotide sequence of regulator: 615 bp    .

>REG0112 NC_004603:2653215-2653829 [Vibrio parahaemolyticus RIMD 2210633]
ATGGACTCAATTGCAAAGAGACCTAGAACTAGGCTTTCTCCTCTTAAACGTAAGCAACAACTCATGGAAATCGCGTTAGA
AGTATTTGCACGCCGTGGTATTGGCCGTGGTGGTCACGCAGATATTGCTGAAATTGCGCAAGTGTCTGTTGCAACCGTTT
TTAACTACTTCCCAACTCGCGAAGATTTGGTTGATGAAGTTCTCAACCATGTTGTCCGTCAGTTCTCGAATTTCCTTTCG
GACAATATCGACCTAGACATACACGCTCGTGAAAACATCGCAAACATCACCAATGCGATGATCGAGCTTGTAAGCCAAGA
TTGTCACTGGCTGAAAGTTTGGTTCGAGTGGAGCGCATCAACTCGTGATGAAGTTTGGCCTCTATTTGTGTCTACCAACC
GCACTAACCAATTATTGGTTCAAAACATGTTCATTAAAGCGATTGAACGCGGTGAAGTGTGTGATCAACACGATTCAGAA
CACTTGGCAAACCTATTCCACGGTATTTGTTACTCGCTGTTCGTACAAGCAAACCGCTTCAAAGGTGAAGCCGAGTTGAA
AGAGCTCGTGAGCGCTTACCTAGATATGCTTTGCATCTACAATCGCGAACACTAA