Detailed information of T6SS

Note: only experimentally validated proteins are displayed in the graph.


Summary

T6SS ID T6SS00016 experimental
T6SS type Type i5
Strain Agrobacterium fabrum str. C58
Replicon (RefSeq) chromosome linear (NC_003063)
Location 1460756..1488734
Function anti-eukaryotic; anti-bacterial; effector translocation
Comment Deletion 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.
References
[1] 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]
[2] 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]
[3] 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]
[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]
[5] 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]
[6] 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]
[7] 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]
[8] 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]
[9] 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 Experimental investigation has been performed.

T6SS components and genome coordinates

ComponentFHAPAARPpkATagF-PppATagJTssATssBTssCTssDTssETssFTssGTssHTssITssKTssLTssM
Number11111112111112111


Component ID Component Locus tag (Gene) Coordinate Strand Size (bp) NCBI ID Product
ATU_RS20265 1456660..1456956 - 297 WP_006315910.1 PRC-barrel domain-containing protein
ATU_RS20270 1457221..1458357 + 1137 WP_035257912.1 polysaccharide export protein
T6CP012426 PpkA ATU_RS20275 1458366..1459271 - 906 WP_035257928.1 protein kinase
T6CP012427 TagF-PppA ATU_RS20280 (tagF) 1459258..1460673 - 1416 WP_010973754.1 type VI secretion system-associated protein TagF
T6CP000114 TssM ATU_RS20285 (tssM) 1460756..1464235 - 3480 WP_010973755.1 type VI secretion system membrane subunit TssM
T6CP000115 TssL ATU_RS20290 (tssL) 1464232..1465737 - 1506 WP_010973756.1 type VI secretion system protein TssL, long form
T6CP000116 TssK ATU_RS20295 (tssK) 1465734..1467074 - 1341 WP_010973757.1 type VI secretion system baseplate subunit TssK
T6CP011404 FHA ATU_RS20300 1467064..1468263 - 1200 WP_010973758.1 type VI secretion system-associated FHA domain protein
T6CP000117 TssG ATU_RS20305 (tssG) 1468274..1469278 - 1005 WP_010973759.1 type VI secretion system baseplate subunit TssG
T6CP000118 TssF ATU_RS20310 (tssF) 1469288..1471069 - 1782 WP_010973760.1 type VI secretion system baseplate subunit TssF
T6CP008386 TssE ATU_RS20315 (tssE) 1471062..1471571 - 510 WP_006315898.1 type VI secretion system baseplate subunit TssE
T6CP012697 TagJ ATU_RS20320 1471564..1472388 - 825 WP_006315897.1 hypothetical protein
T6CP000119 TssC ATU_RS20325 (tssC) 1472385..1473779 - 1395 WP_006315896.1 type VI secretion system contractile sheath large subunit
T6CP000120 TssC ATU_RS20330 (tssC) 1473834..1475315 - 1482 WP_006315895.1 type VI secretion system contractile sheath large subunit
T6CP000121 TssB ATU_RS20335 (tssB) 1475409..1475918 - 510 WP_010973761.1 type VI secretion system contractile sheath small subunit
T6CP009351 TssA ATU_RS20340 (tssA) 1475984..1477039 - 1056 WP_010973762.1 type VI secretion system protein TssA
T6CP000122 TssH ATU_RS20345 (tssH) 1477260..1479938 + 2679 WP_010973763.1 type VI secretion system ATPase TssH
T6CP000123 TssD ATU_RS20350 1479996..1480472 + 477 WP_003504561.1 type VI secretion system tube protein Hcp
ATU_RS20355 1480579..1480968 + 390 WP_010973764.1 hypothetical protein
ATU_RS20360 1480980..1481480 + 501 WP_006315890.1 type VI secretion system amidase effector protein Tae4
T6CP000124 TssI ATU_RS20365 1481495..1483945 + 2451 WP_010973765.1 type VI secretion system tip protein VgrG
ATU_RS20370 1483948..1484904 + 957 WP_010973766.1 DUF4123 domain-containing protein
ATU_RS20375 1484901..1485737 + 837 WP_010973767.1 hypothetical protein
ATU_RS20380 1485765..1486439 + 675 WP_010973768.1 DUF1851 domain-containing protein
T6CP011354 PAAR ATU_RS20385 1486452..1486757 + 306 WP_010973769.1 PAAR domain-containing protein
ATU_RS20390 1486896..1488842 - 1947 WP_035257634.1 bifunctional diguanylate cyclase/phosphodiesterase
ATU_RS20395 1489103..1490773 + 1671 WP_010973771.1 metallophosphoesterase
ATU_RS20400 1490777..1492333 - 1557 WP_010973772.1 TerC family protein
ATU_RS20405 1492710..1493726 - 1017 WP_010973773.1 DUF1402 family protein
flank Genes in the 5-Kb flanking regions if available, or non-core components encoded by the T6SS gene cluster if any.
Download FASTA format files

    

Note: in the 'Target' column, ↓ means the target is positively regulated by the regulator, while ↑ indicates negatively regulation.
experimental Experimental investigation has been performed.
insolico Bioinformatics investigation has been performed.
Regulator ID Locus tag (Gene) Regulator type Regulatory pathway Organism                 Replicon (Accession) Coordinates (Strand) NCBI ID Target (Regulation)
REG0077 experimental Atu4335 (Fha/TagH) protein Tpp Agrobacterium fabrum str. C58 chromosome (NC_003063) 1467064..1468263 (-) 499280697 Unknown (↓)
REG0078 experimental Atu4330 (PpkA) protein Tpp Agrobacterium fabrum str. C58 chromosome (NC_003063) 1458366..1459271 (-) 737274050 Unknown (↓)
REG0079 experimental Atu4331 (TagF-PppA) protein Tpp Agrobacterium fabrum str. C58 chromosome (NC_003063) 1459258..1460673 (-) 159186120 Fha (Atu4335) (↑)
REG0080 experimental Atu2091 protein c-di-GMP regulatory pathway Agrobacterium fabrum str. C58 chromosome (NC_003063) 2054055..2054864 (-) 159185045 the levels of c-di-GMP (↑)
REG0081 experimental Atu5372 protein c-di-GMP regulatory pathway Agrobacterium fabrum str. C58 chromosome (NC_003064) 363293..364387 (+) 1805892863 the levels of c-di-GMP (↑)
REG0082 experimental Atu1257 (DgcA) protein c-di-GMP regulatory pathway Agrobacterium fabrum str. C58 chromosome (NC_003062) 1244567..1245814 (-) 159184686 the levels of c-di-GMP (↑)
REG0083 experimental Atu2179 (DgcC) protein c-di-GMP regulatory pathway Agrobacterium fabrum str. C58 chromosome (NC_003062) 2154605..2155744 (-) 159185090 the levels of c-di-GMP (↑)
REG0084 experimental chvG protein TCS-HK Agrobacterium fabrum str. C58 chromosome (NC_003062) 34679..36469 (-) chvI (↓)
REG0085 experimental chvI protein TCS-RR Agrobacterium fabrum str. C58 chromosome (NC_003062) 36525..37250 (-) The intergenic region of the imp and hcp operons (↓)
REG0086 experimental exoR protein TCS regulatory pathway Agrobacterium fabrum str. C58 chromosome (NC_003062) 1702398..1703192 (-) chvG (↑)

experimental Experimental investigation has been performed.
insolico Bioinformatics investigation has been performed.
Effector ID Locus tag (Gene) Classification Cognate immunity protein Organism                 Replicon (Accession) Coordinates (Strand) NCBI ID
EFF00996 experimental Atu4347 (Tae4) Tae Agrobacterium fabrum str. C58 chromosome (NC_003063) 1480980..1481480 (+) 159186127
EFF01308 experimental Atu4350 (Tde1) Tde - Agrobacterium fabrum str. C58 chromosome (NC_003063) 1484901..1485737 (+) 15890633
EFF01307 experimental Atu3640 (Tde2) Tde IMU00054 experimental Agrobacterium fabrum str. C58 chromosome (NC_003063) 692241..693821 (-) 15891300
EFF00024 experimental ATU_RS20350 - - Agrobacterium fabrum str. C58 chromosome (NC_003063) 1479996..1480472 (+) 15890638

experimental Experimental investigation has been performed.
insolico Bioinformatics investigation has been performed.
Immunity protein ID Locus tag (Gene) Cognate effector Organism                 Replicon (Accession) Coordinates (Strand) NCBI ID
IMU00053 experimental Atu4351 (Tdi1) EFF00996 experimental Agrobacterium fabrum str. C58 chromosome (NC_003063) 1485765..1486439 (+) 15890632
IMU00054 experimental Atu3639 (Tdi2) EFF01307 experimental Agrobacterium fabrum str. C58 chromosome (NC_003063) 691507..692238 (-) 159185838
IMU00192 experimental Atu4346 (Tai4) EFF00996 experimental Agrobacterium fabrum str. C58 chromosome (NC_003063) 1480579..1480968 (+) 159186126

experimental Experimental investigation has been performed.
Accessory protein ID Locus tag (Gene) Type             Organism                 Replicon (Accession) Coordinates (Strand) NCBI ID Related structure protein Related effector
ACP00010 experimental Atu4349 (tap-1) adaptor Agrobacterium fabrum str. C58 chromosome (NC_003063) 1483948..1484904 (+) 737273750 Atu4348 (VgrG1) Atu4350 (Tde1)
ACP00011 experimental Atu3641 adaptor Agrobacterium fabrum str. C58 chromosome (NC_003063) 693818..694927 (-) 499279473 Atu3642 (VgrG2) Atu3640 (Tde2)