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
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III. genome coordinates of the T6SS gene cluster
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProductNote
1Atu43271456654..1457076 [+], 423159186118hypothetical protein 
2Atu43281457193..1457393 [-], 20117938017hypothetical protein 
3Atu4329 (bexD)1457455..1458357 [+], 90315890654polysaccharide export protein 
4Atu4330 (impN)1458366..1459178 [-], 813159186119serine/threonine protein kinase  PpkA
5Atu4331 (impM)1459258..1460673 [-], 1416159186120serine/threonine phosphoprotein phosphatase  TagF-PppA
6Atu4332 (impL)1460756..1464235 [-], 348015890651IcmF family protein  TssM
7Atu4333 (impK)1464232..1465737 [-], 1506159186121OmpA-like porin  TssL
8Atu4334 (impJ)1465734..1467074 [-], 134115890649hypothetical protein  TssK
9Atu4335 (impI)1467064..1468263 [-], 120015890648forkhead-type phosphopeptide-binding protein  Fha
10Atu4336 (impH)1468274..1469278 [-], 100515890647hypothetical protein  TssG
11Atu4337 (impG)1469288..1471069 [-], 178215890646hypothetical protein  TssF
12Atu4338 (impF)1471062..1471571 [-], 510159186122hypothetical protein  TssE
13Atu4339 (impE)1471564..1472388 [-], 82515890644hypothetical protein  TagJ
14Atu4340 (impD)1472385..1473779 [-], 1395159186123hypothetical protein  TssC
15Atu4341 (impC)1473834..1475315 [-], 148215890642hypothetical protein  TssC
16Atu4342 (impB)1475409..1475918 [-], 510159186124hypothetical protein  TssB
17Atu4343 (impA)1475984..1477039 [-], 105615890640hypothetical protein  TssA
18Atu4344 (clpB)1477260..1479938 [+], 2679159186125ATP-dependent Clp protease, ATP-binding subunit  TssH
19Atu43451479996..1480472 [+], 47715890638hypothetical protein  TssD
20Atu43461480579..1480968 [+], 390159186126hypothetical protein  Tai (i)
21Atu43471480980..1481480 [+], 501159186127hypothetical protein  Tae (e)
22Atu4348 (vgrG)1481495..1483945 [+], 245115890635VgrG protein  TssI
23Atu43491483948..1484904 [+], 957159186128hypothetical protein 
24Atu43501484901..1485737 [+], 83715890633hypothetical protein  Tde1 (e)
25Atu43511485765..1486439 [+], 67515890632hypothetical protein  Tdi1 (i)
26Atu43521486452..1486757 [+], 30615890631hypothetical protein  PAAR
27Atu43531486896..1488734 [-], 1839159186129hypothetical protein 
28Atu43541489103..1490773 [+], 1671159186130hypothetical protein 
29Atu43551490777..1492333 [-], 155715890628hypothetical protein 
30Atu43561492710..1493726 [-], 101715890627hypothetical 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
1Atu43501484901..1485737 [+], 83715890633hypothetical protein (Tde1)Atu4350 (Tde1)
2Atu43451479996..1480472 [+], 47715890638hypothetical protein Atu4345
3Atu3640692241..693821 [-], 158115891300hypothetical protein (Tde2)Atu3640 (Tde2)
4Atu1899(rbsB)1875825..1876754 [-], 930159184970ABC transporter substrate-binding protein (ribose) RbsB
5Atu43471480980..1481480 [+], 501159186127hypothetical protein (Tae4)Atu4347 (Tae4)
Data from experimental literature

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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
1Atu43511485765..1486439 [+], 67515890632hypothetical protein (Tdi1)Atu4351 (Tdi1)
2Atu3639691507..692238 [-], 732159185838hypothetical protein (Tdi2)Atu3639 (Tdi2)
3Atu43461480579..1480968 [+], 390159186126hypothetical protein (Tai4)Atu4346 (Tai4)
Data from experimental literature

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Proteins        Genes
Regulatory element identified
ChvG-ChvI
RegulatorDescriptionReference
ChvG (Atu0033)ActivatorPMID: 23028331
ChvI (Atu0034)ActivatorPMID: 23028331

ExoR
RegulatorDescriptionReference
ExoR (Atu1715)Indirect repressorPMID: 23028331

PpkA
RegulatorDescriptionReference
PpkA (Atu4330)ActivatorPMID: 24626341

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

Fha
RegulatorDescriptionReference
Fha (Atu4335)ActivatorPMID: 24626341

(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