SecReT4
T4SS ID6
StrainAgrobacterium tumefaciens plasmid pTi-SAKURA (NC_002147)
Repliconplasmid pTi-SAKURA [Browse all T4SS(s) in this replicon]
AccessionNC_002147
Location140576..158661
NameVirB
Functioneffector translocation and conjugation
ClassificationType IVA; Type P
sequence This T4SS has been mentioned in a genome sequencing report.

T4SS components
ComponentVirB1VirB2VirB3VirB4VirB5VirB6VirB7VirB8VirB9
Number111111111
ComponentVirB10VirB11VirD4
Number111

The information of T4SS components from NC_002147
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProductComponent
1pTi-SAKURA_p141 (tiorf139)135962..136693 [-], 73210954959hypothetical protein 
2pTi-SAKURA_p142 (tiorf140)137530..140031 [+], 250210954960two-component VirA-like sensor kinase 
3pTi-SAKURA_p143 (tiorf141)140576..141313 [+], 73810954961type IV secretion system lytic transglycosylase VirB1  VirB1
4pTi-SAKURA_p144 (tiorf142)141313..141678 [+], 36610954962type IV secretion system pilin subunit VirB2  VirB2
5pTi-SAKURA_p145 (tiorf143)141678..142004 [+], 32710954963type IV secretion system protein VirB3  VirB3
6pTi-SAKURA_p146 (tiorf144)142004..144373 [+], 237010954964type IV secretion system protein VirB4  VirB4
7pTi-SAKURA_p147 (tiorf145)144390..145052 [+], 66310954965type IV secretion system protein VirB5  VirB5
8pTi-SAKURA_p148 (tiorf146)145153..146040 [+], 88810954966type IV secretion system protein VirB6  VirB6
9pTi-SAKURA_p149 (tiorf147)146076..146243 [+], 16810954967type IV secretion system lipoprotein VirB7  VirB7
10pTi-SAKURA_p150 (tiorf148)146230..146943 [+], 71410954968type IV secretion system protein VirB8  VirB8
11pTi-SAKURA_p151 (tiorf149)146940..147821 [+], 88210954969type IV secretion system protein VirB9  VirB9
12pTi-SAKURA_p152 (tiorf150)147818..148951 [+], 113410954970type IV secretion system protein VirB10  VirB10
13pTi-SAKURA_p153 (tiorf151)148992..150026 [+], 103510954971type IV secretion system protein VirB11  VirB11
14pTi-SAKURA_p154 (tiorf152)150245..151006 [+], 76210954972two-component response regulator VirG 
15pTi-SAKURA_p155 (tiorf153)151148..151756 [-], 60910954973putative crown gall tumor protein VirC2 
16pTi-SAKURA_p156 (tiorf154)151759..152454 [-], 69610954974putative crown gall tumor protein VirC1  accesspry protein
17pTi-SAKURA_p157 (tiorf155)152725..153168 [+], 44410954975type IV secretion system T-DNA border endonuclease VirD1 
18pTi-SAKURA_p158 (tiorf156)153202..154545 [+], 134410954976type IV secretion system T-DNA border endonuclease VirD2 
19pTi-SAKURA_p159 (tiorf157)154560..156581 [+], 202210954977hypothetical protein 
20pTi-SAKURA_p160 (tiorf158)156655..158661 [+], 200710954978type IV secretion system protein VirD4  VirD4
21pTi-SAKURA_p161 (tiorf159)158773..161298 [+], 252610954979hypothetical protein 
22pTi-SAKURA_p162 (tiorf160)161675..162001 [-], 32710954980hypothetical protein 
23pTi-SAKURA_p163 (tiorf161)162387..162638 [+], 25210954981hypothetical protein 
24pTi-SAKURA_p164 (tiorf162)162754..162945 [+], 19210954982type IV secretion system chaperone VirE1  accesspry protein
 
accesspry protein This T4SS contains information of accessory protein.
flank Genes in the 5-Kb flanking regions if available, or non-essential genes in the T4SS gene cluster if any.

Download FASTA format files
Proteins        Genes
This system delivers both DNA and proteins into plant cell. The transferred DNA (T-DNA) region: NC_002147: 170935..197050)

Effectors
VirF, VirD2, VirD5, VirE2, VirE3

The information of protein effectors
#Locus tag (Gene)Coordinates [+/-], size (bp)Protein GIProduct  *
1pTi-SAKURA_p135 (tiorf133)129189..130127 [+], 93910954953hypothetical protein  VirF
2pTi-SAKURA_p158 (tiorf156)153202..154545 [+], 134410954976type IV secretion system T-DNA border endonuclease VirD2  VirD2
3pTi-SAKURA_p161 (tiorf159)158773..161298 [+], 252610954979hypothetical protein  VirD5
4pTi-SAKURA_p165 (tiorf163)162959..164629 [+], 167110954983type IV secretion system single-stranded DNA binding protein VirE2  VirE2
5pTi-SAKURA_p166 (tiorf164)164744..166750 [+], 200710954984hypothetical protein  VirE3


Download FASTA format files
Proteins        Genes
The information on requirements for T4SS substrate-channel docking

Certain T4SS substrates require secretion chaperones for translocation. These chaperones often possess physical properties (small size of 15 kDa, acidic pI, and amphipathic helices) resembling those of chaperones associated with the type III secretion systems, a family of macromolecular translocation systems ancestrally related to bacterial flagella.

#Accessory protein(GI)motif(s)Substrate(s)FunctionReference
1VirC1 (10954974)NDVirD2VirC1 pairwise interacts with the processing factors VirD2 relaxase, VirC2, and VirD1 to stimulate generation of multiple copies per cell of the T-DNA substrate. VirC1 promotes conjugative T-DNA transfer.(1) PubMed: 17505518
2VirE1 chaperone (10954982)CT50aa sufficient (interacts with the VirD4 T4CP. CT100aa(VirE2) sufficient for the T4CP interation)VirE2Translocation of the VirE2 effector through the A. tumefaciens VirB/VirD4 T4SS requires VirE1. (2) PubMed: 19946141
Tips:
1.Substrate(s): For the conjugation systems, the listed proteins are relaxases that bind a cognate T4CP and are delivered to recipient cells. For the effector translocator systems, the listed proteins are effectors that play a role in the infection processes of the bacterial pathogen.
2.motif(s):The motifs listed are required for substrate translocation. In some cases, the protein or its C-terminal fragment (CT) is sufficient to mediate translocation to target cells, as shown by fusion to a reporter protein such as Cre recombinase or adenylate cyclase. Amino acids (aa) at positions listed relative to the C-terminal fragment (subscript) are required for translocation, as shown by mutational analysis. ND, not determined. Parentheses indicate that the interaction between a protein substrate and a cognate T4CP has been experimentally shown.
3.Accessory protein: Accessory factors required for T4SS channel docking or translocation. The proposed function in mediating substrate-T4SS channel docking is shown in parentheses.PubMed:19946141

(1) Atmakuri K; Cascales E; Burton OT; Banta LM; Christie PJ (2007). Agrobacterium ParA/MinD-like VirC1 spatially coordinates early conjugative DNA transfer reactions. EMBO J. 26(10):2540-51. [PudMed:17505518] experimental
(2) Alvarez-Martinez CE; Christie PJ (2009). Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev. 73(4):775-808. [PudMed:19946141]
(1) Hattori Y; Iwata K; Suzuki K; Uraji M; Ohta N; Katoh A; Yoshida K (2001). Sequence characterization of the vir region of a nopaline type Ti plasmid, pTi-SAKURA. Genes Genet Syst. 76(2):121-30. [PudMed:11434457]
(2) Suzuki K; Hattori Y; Uraji M; Ohta N; Iwata K; Murata K; Kato A; Yoshida K (2000). Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene. 242(1-2):331-6. [PudMed:10721727]
(3) Suzuki K; Hattori Y; Uraji M; Ohta N; Katoh A; Yoshida K (1997). Genome structure of pTi-SAKURA (II): genetic map constructed by complete DNA sequencing. Nucleic Acids Symp Ser. (37):161-2. [PudMed:9586049]
 

Genomics & Bioinformatics Group in MML, SJTU