Pseudomonas aeruginosa modulates alginate biosynthesis and type VI secretion system in two critically ill COVID-19 patients

Qu, Jiuxin; Cai, Zhao; Duan, Xiangke; Zhang, Han; Cheng, Hang; Han, Shuhong; Yu, Kaiwei; Jiang, Zhaofang; Zhang, Yingdan; Liu, Yang; Bai, Fang; Liu, Yingxia; Liu, Lei; Yang, Liang

doi:10.1186/s13578-022-00748-z

Table 3 Selected DEGs in LYSZa6 compared to LYSZa5 related to alginate biosynthesis and type VI secretion system

From: Pseudomonas aeruginosa modulates alginate biosynthesis and type VI secretion system in two critically ill COVID-19 patients

Gene	Product name	Base mean	Fold change	Adj p-value	LYSZa2 Mean	LYSZa3 Mean
algD	GDP-mannose 6-dehydrogenase AlgD	2956.90	138.79	2.47E–170	39.33	6375.00
algX	Alginate biosynthesis protein AlgX	271.80	45.97	1.05E–75	10.67	585.67
algL	Poly(beta-d-mannuronate) lyase precursor AlgL	283.61	44.85	1.98E–74	11.33	609.00
algJ	Alginate o-acetyltransferase AlgJ	118.03	32.97	3.93E–33	6.33	248.67
algE	Alginate production outer membrane protein AlgE precursor	254.48	25.19	1.11E–61	18.33	535.33
algA	Phosphomannose isomerase/guanosine 5'-diphospho-d-mannose pyrophosphorylase	481.88	21.52	9.22E–64	39.00	1000.67
algF	Alginate o-acetyltransferase AlgF	152.00	18.68	7.50E–42	14.33	314.67
alg8	Alginate biosynthesis protein Alg8	292.51	14.91	1.09E–59	34.67	599.33
alg44	Alginate biosynthesis protein Alg44	195.56	14.43	3.38E–61	23.67	403.00
algK	Alginate biosynthetic protein AlgK precursor	135.65	10.35	6.37E–39	21.67	272.67
algI	Alginate o-acetyltransferase AlgI	218.14	8.40	7.47E–47	43.00	427.33
algG	Alginate-c5-mannuronan-epimerase AlgG	356.62	4.45	4.15E–53	121.33	644.33
clpV1	ClpV1	5315.67	− 4.08	7.48E–33	7854.33	2309.33
PA3904	PAAR4	1457.06	− 4.17	3.79E–33	2178.00	631.67
PA2702	Tse2	280.90	− 4.35	2.50E–29	419.33	117.33
PA2774	Tse4	296.61	− 4.37	4.85E–26	461.67	122.33
PA2775	Tsi4	133.81	− 4.71	7.24E–19	212.67	52.33
vgrG1	VgrG1	2637.35	− 4.74	1.56E–50	3969.33	1016.67
PA0093	Tse6	947.79	− 4.91	3.88E-–46	1469.00	360.00
PA3905	Type VI effector chaperone for Tox-Rease, TecT	1073.56	− 4.95	1.10E–53	1671.00	403.00
PA0082	TssA1	1449.46	− 5.32	1.76E–55	2265.00	515.00
PA2703	Tsi2	98.26	− 5.56	5.99E–24	156.67	33.00
PA0094	EagT6	251.06	− 5.79	1.43E–38	401.67	82.00
PA3484	Tse3	544.56	− 5.86	1.50E–54	869.33	174.33
stk1	Stk1	263.85	− 5.90	1.38E–56	423.00	84.67
PA5266	VgrG6	396.48	− 6.81	6.50E–47	654.33	113.33
PA1667	HsiJ2	678.54	− 6.99	2.41E–100	1119.67	188.67
PA1656	HsiA2	3257.03	− 7.01	4.84E–80	5349.67	911.33
PA1662	clpV2	2538.08	− 8.98	3.88E–108	4332.33	564.33
PA1661	HsiH2	693.51	− 9.91	1.55E–110	1186.67	142.00
PA1666	Lip2	340.97	− 10.48	2.48E–72	589.00	65.67
stp1	Stp1	327.95	− 10.61	1.67E–70	562.67	62.67
hcpA	Secreted protein Hcp	72.34	− 10.75	7.25E–26	125.33	13.67
PA1665	Fha2	840.73	− 10.96	1.12E–108	1456.67	155.33
PA1660	HsiG2	907.03	− 11.05	1.78E–125	1551.67	167.33
PA1669	IcmF2	2052.74	− 11.08	6.20E–107	3547.33	375.67
hcpB	Secreted protein Hcp	204.27	− 11.30	8.81E–47	358.00	36.67
PA1668	DotU2	487.58	− 11.30	1.39E–105	836.33	88.00
PA1663	Sfa2	883.17	− 12.92	4.47E–74	1556.67	139.33
PA3334	Acp3	236.04	− 13.79	1.82E–73	415.67	35.33
PA1657	HsiB2	2539.11	− 14.39	1.32E–112	4445.00	366.00
PA1659	HsiF2	480.65	− 17.06	4.25E–89	843.33	59.00
PA1658	HsiC2	5746.91	− 17.11	4.82E–66	10,179.00	695.67

Filtering criteria are fold change ≧ 4, adjusted p-value < 0.05 and base mean ≧ 20. Full list of DEGs is included in Additional file 9: Table S7

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ISSN: 2045-3701

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