TABLE 1 

Transcriptomic and differential proteomic analyses of T6SS and VgrG clusters in T6+ and T6 A. baumannii ATCC 17978

Gene locusT6SS geneT6+ TPMaT6 TPMaLog2-fold differenceb (P value)cRNA-seq transcript fold differencebCorresponding gene in A. baylyi ADP1TMT-based protein log2-fold differenceb (P value)cNo. of peptides identified (Andromeda identification score)
T6SS cluster
    ACX60_11600tagX37.2 (3.2)3.4 (1.0)3.1 (3.3E-28)8.3ACIAD2699NaNdNaN
    ACX60_11605Hypothetical63.0 (17.0)2.7 (0.5)4.0 (2.8E-32)15.5ACIAD26981.8 (0.00041)3 (22.204)
    ACX60_11610tssL91.3 (18.4)4.5 (2.1)3.9 (6.5E-46)14.7ACIAD26971.2 (0.028232)1 (2.4722)
    ACX60_11615tssK259.6 (14.1)10.8 (1.6)4.3 (7.8E-158)19.8ACIAD26961.7 (0.011007)6 (76.533)
    ACX60_11620tssA221.9 (26.5)5.2 (0.8)5.0 (3.8E-134)32.8ACIAD26952.6 (0.001157)5 (21.411)
    ACX60_11625clpV258.7 (8.6)23.1 (2.0)3.3 (4.8E-1449.5ACIAD26942.5 (0.002065)35 (323.31)
    ACX60_11630PAAR39.2 (15.7)5.0 (0.9)2.3 (8.0E-08)5.1ACIAD26810.9 (0.066403)1 (12.532)
    ACX60_11635tagN99.4 (9.3)8.9 (1.5)3.2 (1.9E-48)9.0ACIAD26821.5 (0.004644)6 (54.441)
    ACX60_11640tagF44.4 (12.6)3.3 (0.8)3.3 (2.6E-28)9.9ACIAD26831.7 (0.005088)4 (22.213)
    ACX60_11645tssM320.3 (16.8)23.3 (0.8)3.5 (3.2E-194)11.7ACIAD26841.8 (0.029757)35 (323.31)
    ACX60_11650Hypothetical89.3 (13.9)4.1 (1.2)4.1 (6.8E-72)17.1ACIAD26851.2 (0.000429)2 (28.15)
    ACX60_11655tssG179.8 (32.2)4.5 (0.3)4.9 (3.2E-99)30.1ACIAD26861.4 (0.000083)2 (4.6976)
    ACX60_11660tssF134.9 (28.3)4.5 (0.5)4.6 (1.1E-103)23.5ACIAD26872.7 (0.018475)4 (23.9)
    ACX60_11665tssE1078.5 (165.7)30.2 (2.3)4.8 (3.2E-167)28.7ACIAD2688NaNNaN
    ACX60_11670hcp11801.2 (588.2)198.8 (18.9)5.6 (0)49.4ACIAD26892.8 (0.000359)11 (139.41)
    ACX60_11675tssC1823.6 (258.4)30.5 (1.6)5.6 (0)49.0ACIAD26902.7 (0.000598)23 (323.31)
    ACX60_11680tssB1516.7 (145.5)34.7 (7.8)5.1 (3.3E-206)35.2ACIAD26913.1 (0.000546)14 (253.32)
    ACX60_11685Hypothetical545.2 (6.2)9.3 (0.6)5.5 (8.2E-202)46.3ACIAD26932.7 (0.001271)9 (235.49)
    ACX60_11690Hypothetical600.3 (50.0)125.4 (19.9)2.0 (8.7E-43)4.0ACIAD3112/31131.1 (0.002987)18 (321.94)
    ACX60_11695tse3 effector167.0 (37.0)14.6 (0.2)3.2 (2.6E-77)9.5ACIAD3114NaNNaN
    ACX60_11700vgrG396.3 (10.7)47.8 (1.4)0.8 (1.2E-08)1.8ACIAD31151.2 (0.013778)13 (1.2162)
    ACX60_11705Hypothetical6.0 (2.3)2.7 (0.6)0.7 (3.0E-01)1.6None0.1 (0.646629)1 (1.8381)
VgrG1 cluster
    ACX60_17640Hypothetical16.2 (3.2)3.4 (2.3)1.7 (2.8E-4)3.2NoneNaNNaN
    ACX60_17645Hypothetical9.6 (40)0.4 (0.4)2.6 (7.9E-6)6.0NoneNaNNaN
    ACX60_17650Hypothetical34.8 (12.5)1.5 (1.0)3.5 (4.8E-15)11.6NoneNaNNaN
    ACX60_17655Hypothetical37.6 (5.3)2.0 (1.2)3.5 (3.8E-19)11.1None1.7 (0.010153)7 (67.368)
    ACX60_17660tse1328.8 (53.3)12.0 (1.7)4.4 (2.0E-117)21.6None2.3 (0.003947)1 (1.6312)
    ACX60_17665vgrG1203.4 (27.4)36.5 (1.0)2.2 (9.11E-59)4.8Multiple vgrG genes2.4 (0.011138)16 (222.15)
    ACX60_17670Hypothetical6.7 (2.9)1.4 (0.3)1.6 (2.7E-3)3.0NoneNaNNaN
VgrG2 cluster
    ACX60_15360tsi2 (tdi)192.3 (17.0)103.2 (2.9)0.7 (2.3E-7)1.6None0.1 (0.350265)9 (114.72)
    ACX60_15365tse2 (tde)158.9 (17.2)64.0 (3.3)1.1 (1.8E-15)2.1None0.4 (0.135599)8 (65.825)
    ACX60_15370vgrG2143.1 (15.3)200.4 (13.8)−0.7 (2.7E-7)−1.6Multiple vgrG genes1.0 (0.049891)12 (33.815)
VgrG4 cluster
    ACX60_00585vgrG465.5 (9.4)23.2 (2.6)1.32.4Multiple vgrG genesNaNNaN
    ACX60_00590Hypothetical1.3 (0.2)3.9 (0.1)−0.7−1.6NoneNaNNaN
    ACX60_00595Hypothetical1.8 (1.8)6.2 (4.1)−0.3−1.2NoneNaNNaN
    ACX60_00600Hypothetical0.4 (0.7)0.0 (0.0)0.21.1NoneNaNNaN
    ACX60_00605tse4 (tae)13.0 (1.6)8.2 (2.1)0.51.4NoneNaNNaN
    ACX60_00610tsi419.2 (8.6)8.8 (3.1)0.81.8None0.2 (0.283492)10 (105.54)
    ACX60_00615Hypothetical5.4 (0.7)3.2 (1.4)0.51.4NoneNaNNaN
  • a Data shown are mean values (standard deviations) of three biological replicate samples.

  • b Between T6+ and T6−.

  • c Statistical significance was tested by using DESEq2.

  • d NaN, not detected.