SecReT6
I. Summary
SecReT6 ID43 experimental
StrainVibrio parahaemolyticus RIMD 2210633
Repliconchromosome I [Browse all T6SS(s) in this replicon]
AccessionNC_004603
Location1486402..1526996
CommentAdhesion to cultured cell monolayers; V. parahaemolyticus T6SS1 effectors mediate its antibacterial activity
Functionanti-eukaryotic and anti-bacterial;effector translocation;adherence;virulence
T6SS TypeType i; subtype i1
experimental Experimental investigation has been performed on this T6SS.

II. T6SS components
ComponentTssHTssDTssLTssITssATssBTssCTssETssF
Number111121111
ComponentTssGTssJTssKTssM
Number1111
III. genome coordinates of the T6SS gene cluster
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProductNote
1VP_RS067451483454..1485205 [+], 1752658932605hypothetical protein 
2VP_RS067501485278..1486405 [+], 1128491623207hypothetical protein  VP1389 (i)
3VP_RS067551486402..1491144 [+], 4743491623077OmpA family protein  TagL
4VP_RS067601491226..1492857 [-], 1632491623132sigma-54-dependent Fis family transcriptional regulator 
5VP_RS06765 (tssH)1492844..1495516 [-], 2673491623235type VI secretion system ATPase TssH  TssH
6VP_RS067701495971..1496489 [+], 519491623110Hcp family type VI secretion system effector  TssD
7VP_RS06775 (tssI)1496562..1498640 [+], 2079491623168type VI secretion system tip protein VgrG  TssI
8VP_RS067801498640..1499125 [+], 486491623219hypothetical protein 
9VP_RS067851499195..1500536 [+], 1342pseudogenehypothetical protein 
10VP_RS067901500517..1501509 [+], 993491623051DUF2169 domain-containing protein 
11VP_RS067951501502..1502446 [+], 945491623166hypothetical protein 
12VP_RS068001502681..1504684 [+], 2004491623092protein kinase family protein 
13VP_RS06805 (tssA)1504684..1506258 [+], 1575491623195type VI secretion system protein TssA  TssA
14VP_RS06810 (tssB)1506285..1506791 [+], 507491623049type VI secretion system contractile sheath small subunit  TssB
15VP_RS06815 (tssC)1506800..1508275 [+], 1476491623191type VI secretion system contractile sheath large subunit  TssC
16VP_RS06820 (tssE)1508337..1508747 [+], 411491623044type VI secretion system baseplate subunit TssE 
17VP_RS06825 (tssF)1508758..1510506 [+], 1749491623126type VI secretion system baseplate subunit TssF  TssF
18VP_RS06830 (tssG)1510503..1511501 [+], 999491623152type VI secretion system baseplate subunit TssG  TssG
19VP_RS068351511565..1512017 [-], 453491623128Lrp/AsnC family transcriptional regulator 
20VP_RS06840 (tssM)1512050..1515439 [-], 3390491623145type VI secretion system membrane subunit TssM  TssM
21VP_RS068451515461..1516756 [-], 1296491623074type VI secretion system ImpA family N-terminal domain-containing protein 
22VP_RS068501517276..1517875 [+], 600491623205hypothetical protein 
23VP_RS068551517885..1519399 [+], 1515491623043FHA domain-containing protein  Fha
24VP_RS06860 (tssJ)1519392..1519892 [+], 501499418365type VI secretion system lipoprotein TssJ  TssJ
25VP_RS06865 (tssK)1519904..1521229 [+], 1326491623174type VI secretion system baseplate subunit TssK  TssK
26VP_RS068701521226..1522017 [+], 792491591893type IVB secretion system protein IcmH/DotU  TssL
27VP_RS068751522167..1524323 [+], 2157491623108DUF4150 domain-containing protein 
28VP_RS068801524323..1524916 [+], 594491623139hypothetical protein  VP1416 (i)
29VP_RS068851524916..1525467 [+], 552491623242hypothetical protein 
30VP_RS068901525615..1526144 [+], 530pseudogenehypothetical protein 
31VP_RS068951526553..1526996 [+], 444491623062hypothetical protein 
32VP_RS069001527018..1527506 [+], 489491623156hypothetical protein 
33VP_RS069051527691..1527984 [+], 294491623041hypothetical protein 
34VP_RS069101528144..1528746 [+], 6034915973262OG-Fe(II) oxygenase 
35VP_RS069151528811..1530076 [-], 1266491623213HD-GYP domain-containing protein 
36VP_RS069201530652..1531842 [+], 1191491597333iron-containing alcohol dehydrogenase 
 
flank Genes in the 5-kb flanking regions if available, or non-core components encoded by the T6SS gene cluster if any. In the 'Note' column,if available, '(e)' denotes effector while '(i)' for immunity protein

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Proteins        Genes

V. Investigation of the genomic context of the T6SS gene cluster.
1. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against the mobile genetic elements database, ACLAME.
 






2. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against the virulence factor database, VFDB.
 






3. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against against the antibiotic resistance database, ARDB.
 







Homology Effector list
VP1388 , VP1393, VP1415, VPA1263

Effector identified
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog

Download FASTA format files
Proteins        Genes

Homology Immunity protein list
VP1389, VP1416   Vti2

Immunity protein identified
#Locus tag(Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog

Download FASTA format files
Proteins        Genes
Regulatory element identified
OpaR
RegulatorDescriptionReference
OpaR (VP2516)RepressorPMID: 23613791

VP1391
RegulatorDescriptionReference
VP1391ActivatorPMID: 23613791

VP1407
RegulatorDescriptionReference
VP1407ActivatorPMID: 23613791

H-NS
RegulatorDescriptionReference
H-NS (VP1133)RepressorPMID: 24987102

The information on regulator interaction.

#homolog effector locus tagRegulator wayFunctionRegulate targetDescription
1vp2049 (Thymidylate kinase,Tmk) Unknown+T6SS1 (VgrG1) expression and secretionTmk,or one of the downstream products of its enzymatic activity, is critical for activating T6SS1.
2VP1028 (TfoY)c-di-GMP +T6SS1 (VgrG1) expression and secretionTfoY is a positive regulator required and sufficient for T6SS1 activation.
3vp1391Unknown+T6SS1 (VgrG1) expression and secretionTfoY-mediated activation of T6SS1 was dependent on the presence of both vp1391 and vp1407.
4vp1407Unknown+T6SS1 (VgrG1) expression and secretionTfoY-mediated activation of T6SS1 was dependent on the presence of both vp1391 and vp1407.
5VP2516 (opaR)-vp1407OpaR was previously suggested to directly bind to promoter regions of V. parahaemolyticus T6SS1 operons, including the pro- moter of the operon encoding the positive downstream reg- ulator, VP1407.
6VP1133 (hns)Transcriptional-VP1028 (TfoY).
7VP2762 (AphA)Transcription regulator-T6SS1 transcriptAphA appears to negatively regulate the transcription of T6SS2 in an indirect manner.
8VP2516 (opaR)Transcription regulator-VP1388 promotorOpaR represses the transcription of VP1388-1390, VP1400-1406, and VP1409-1407 in a direct manner.
9VP2516 (opaR)VP1400 promotor.
10VP2516 (opaR)VP1409 promotor.
11VP0820 (ToxR)Transcription regulator-VP1400 promotorToxR represses the transcription of VP1400-1406 and VP1409-1407 in a direct manner.
12VP0820 (ToxR)VP1409 promotor.
13VPA1088 (cdpA)c-di-GMP-VP1028 (TfoY)A phosphodiesterase keeps c-di-GMP in low levels.
14VPA0739 (vdcA)c-di-GMP+VP1028 (TfoY)c-di-GMP-producing diguanylate cyclase.
15VP2516 (OpaR)Transcription regulator+T6SS1TfoX-mediated T6SS induction in V. parahaemolyticus requires co-regulation by OpaR.
16VP1028 (TfoY)c-di-GMP+T6SS1TfoY solely led to T6SS1-mediated prey killing .
(1) Salomon D et al. (2014). H-NS regulates the Vibrio parahaemolyticus type VI secretion system 1. Microbiology. 160(Pt 9):1867-73. [PudMed:24987102] experimental
(2) Salomon D et al. (2014). Marker for type VI secretion system effectors. Proc Natl Acad Sci U S A. 111(25):9271-6. [PudMed:24927539] experimental in_silico
(3) Salomon D et al. (2013). Vibrio parahaemolyticus Type VI Secretion System 1 Is Activated in Marine Conditions to Target Bacteria, and Is Differentially Regulated from System 2. PLoS One. 8(4):e61086. [PudMed:23613791] experimental
(4) Ma L et al. (2012). Expression of the Type VI Secretion System 1 Component Hcp1 Is Indirectly Repressed by OpaR in Vibrio parahaemolyticus. Scientific World Journal. 2012:982140. [PudMed:22924031] experimental
(5) Yu Y et al. (2012). Putative type VI secretion systems of Vibrio parahaemolyticus contribute to adhesion to cultured cell monolayers. Arch Microbiol. 194(10):827-35. [PudMed:22535222] experimental
(6) Boyer F et al. (2009). Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources. BMC Genomics. 10:104. [PudMed:19284603] in_silico
 
experimental This literature contains experimental investigation
in_silico This literature contains bioinformatics investigation

Genomics & Bioinformatics Group in MML, SJTU