SecReT6
I. Summary
SecReT6 ID16 experimental
StrainAgrobacterium tumefaciens str. C58
Repliconchromosome linear [Browse all T6SS(s) in this replicon]
AccessionNC_003063
Location1460756..1488734
CommentDeletion of hcp results in reduced tumorigenesis on potato tuber slices; Agrobacterium tumefaciens Deploys a Superfamily of Type VI Secretion DNase Effectors as Weapons for Interbacterial Competition In Planta; the Tde DNase toxins may be pivotal antibacterial toxins that A. tumefaciens uses against competitors during in planta colonization
Functionanti-eukaryotic and anti-bacterial; effector translocation
T6SS TypeType i; subtype i5
experimental Experimental investigation has been performed on this T6SS.

II. T6SS components
ComponentTssHTssDTssLTssITssATssBTssCTssETssF
Number111111211
ComponentTssGTssJTssKTssM
Number1011
III. genome coordinates of the T6SS gene cluster
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProductNote
1ATU_RS202651456660..1456956 [-], 297493359424PRC-barrel domain-containing protein 
2ATU_RS202701457221..1458357 [+], 1137737274034polysaccharide export protein 
3ATU_RS202751458366..1459271 [-], 906737274050protein kinase 
4ATU_RS20280 (tagF)1459258..1460673 [-], 1416499280693type VI secretion system-associated protein TagF 
5ATU_RS20285 (tssM)1460756..1464235 [-], 3480499280694type VI secretion system membrane subunit TssM 
6ATU_RS20290 (tssL)1464232..1465737 [-], 1506499280695type VI secretion system protein TssL, long form 
7ATU_RS20295 (tssK)1465734..1467074 [-], 1341499280696type VI secretion system baseplate subunit TssK 
8ATU_RS203001467064..1468263 [-], 1200499280697FHA domain-containing protein 
9ATU_RS20305 (tssG)1468274..1469278 [-], 1005499280698type VI secretion system baseplate subunit TssG 
10ATU_RS20310 (tssF)1469288..1471069 [-], 1782499280699type VI secretion system baseplate subunit TssF 
11ATU_RS20315 (tssE)1471062..1471571 [-], 510493359411type VI secretion system baseplate subunit TssE 
12ATU_RS203201471564..1472388 [-], 825493359410hypothetical protein 
13ATU_RS20325 (tssC)1472385..1473779 [-], 1395493359409type VI secretion system contractile sheath large subunit 
14ATU_RS20330 (tssC)1473834..1475315 [-], 1482493359408type VI secretion system contractile sheath large subunit 
15ATU_RS20335 (tssB)1475409..1475918 [-], 510499280700type VI secretion system contractile sheath small subunit 
16ATU_RS20340 (tssA)1475984..1476982 [-], 9991805892852type VI secretion system protein TssA 
17ATU_RS20345 (tssH)1477260..1479938 [+], 2679499280702type VI secretion system ATPase TssH 
18ATU_RS203501479996..1480472 [+], 477489600119type VI secretion system tube protein Hcp  TssD
19ATU_RS203551480579..1480968 [+], 390499280703hypothetical protein 
20ATU_RS203601480980..1481480 [+], 501493359403type VI secretion system amidase effector protein Tae4 
21ATU_RS203651481495..1483945 [+], 2451499280704type VI secretion system tip protein VgrG 
22ATU_RS203701483897..1484904 [+], 1008737273750DUF4123 domain-containing protein 
23ATU_RS203751484901..1485737 [+], 837499280706hypothetical protein 
24ATU_RS203801485765..1486439 [+], 675499280707DUF1851 domain-containing protein 
25ATU_RS203851486452..1486757 [+], 306499280708PAAR domain-containing protein 
26ATU_RS203901486896..1488842 [-], 1947737273753bifunctional diguanylate cyclase/phosphodiesterase 
27ATU_RS203951489103..1490773 [+], 1671499280710metallophosphoesterase 
28ATU_RS204001490777..1492333 [-], 1557499280711TerC family protein 
29ATU_RS204051492710..1493726 [-], 1017499280712DUF1402 family protein 
 
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
Atu4350 (Tde1) , Atu4345, Atu3640 (Tde2), RbsB, Atu4347 (Tae4)

Effector identified
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProduct  Homolog
4Atu1899(rbsB)1875825..1876754 [-], 930159184970ABC transporter substrate-binding protein (ribose) RbsB

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Proteins        Genes

Homology Immunity protein list
Atu4351 (Tdi1), Atu3639 (Tdi2), Atu4346 (Tai4)

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

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Proteins        Genes
Regulatory element identified
ExoR
RegulatorDescriptionReference
ExoR (Atu1715)Indirect repressorPMID: 23028331

ChvG-ChvI
RegulatorDescriptionReference
ChvG (Atu0033)ActivatorPMID: 23028331
ChvI (Atu0034)ActivatorPMID: 23028331

PpkA
RegulatorDescriptionReference
PpkA (Atu4330)ActivatorPMID: 24626341

TagF-PppA
RegulatorDescriptionReference
TagF-PppA (Atu4331)RepressorPMID: 24626341

Fha
RegulatorDescriptionReference
Fha (Atu4335)ActivatorPMID: 24626341


Adaptors list
Atu3641, Atu4349

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

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Proteins        Genes
The information on regulator interaction.

#homolog effector locus tagRegulator wayFunctionRegulate targetDescription
1Atu4331 (TagF-PppA)TPP-Fha (Atu4335)The TagF-Fha interaction has a different impact in different bacteria but ultimately prevents successful T6SS assembly.
2Atu2091 C-di-GMP-the levels of c-di-GMPHigh levels of c-di-GMP are capable of down-regulating the T6SS, as seen by monitoring Hcp, ClpV and TssB production.
3Atu5372C-di-GMP-the levels of c-di-GMPHigh levels of c-di-GMP are capable of down-regulating the T7SS, as seen by monitoring Hcp, ClpV and TssB production.
4Atu1257 (DgcA)C-di-GMP-the levels of c-di-GMPHigh levels of c-di-GMP are capable of down-regulating the T8SS, as seen by monitoring Hcp, ClpV and TssB production.
5Atu2179 (DgcC)C-di-GMP-the levels of c-di-GMPHigh levels of c-di-GMP are capable of down-regulating the T9SS, as seen by monitoring Hcp, ClpV and TssB production.
(1) Heckel BC et al. (2014). Agrobacterium tumefaciens ExoR Controls Acid Response Genes and Impacts Exopolysaccharide Synthesis, Horizontal Gene Transfer and Virulence Gene Expression. J Bacteriol. 196(18):3221-33. [PudMed:24982308] experimental
(2) Ma LS et al. (2014). Agrobacterium tumefaciens Deploys a Superfamily of Type VI Secretion DNase Effectors as Weapons for Interbacterial Competition In Planta. Cell Host Microbe. 16(1):94-104. [PudMed:24981331] experimental
(3) Lin JS et al. (2014). Fha Interaction with Phosphothreonine of TssL Activates Type VI Secretion in Agrobacterium tumefaciens. PLoS Pathog. 10(3):e1003991. [PudMed:24626341] experimental
(4) Lin JS et al. (2013). Systematic Dissection of the Agrobacterium Type VI Secretion System Reveals Machinery and Secreted Components for Subcomplex Formation. PLoS One. 8(7):e67647. [PudMed:23861778] experimental
(5) Wu CF et al. (2012). Acid-Induced Type VI Secretion System Is Regulated by ExoR-ChvG/ChvI Signaling Cascade in Agrobacterium tumefaciens. PLoS Pathog. 8(9):e1002938. [PudMed:23028331] experimental
(6) Ma LS et al. (2012). IcmF family protein TssM exhibits ATPase activity and energizes type VI secretion. J Biol Chem. 287(19):15610-21. [PudMed:22393043] experimental
(7) Ma LS et al. (2009). An IcmF family protein, ImpLM, is an integral inner membrane protein interacting with ImpKL, and its walker a motif is required for type VI secretion system-mediated Hcp secretion in Agrobacterium tumefaciens. J Bacteriol. 191(13):4316-29. [PudMed:19395482] experimental
(8) Wu HY et al. (2008). Secretome analysis uncovers an Hcp-family protein secreted via a type VI secretion system in Agrobacterium tumefaciens. J Bacteriol. 190(8):2841-50. [PudMed:18263727] experimental
 
experimental This literature contains experimental investigation