Table 3 List of 61 proteins with significant differential abundance (see text) or unique expression when comparing biofilm grown and planktonic cells.

From: An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1

Locus tag	Gene	Product	log2 FC	p_adj	Comment, reference
Biofilm only
MPAO1_19985	napA	Nitrate reductase catalytic subunit NapA	5.02	0.05
MPAO1_04195		SH3 domain-containing protein	5.02	0.05
MPAO1_10705		Methyl-accepting chemotaxis protein	5.11	0.03
MPAO1_17160		EscC/YscC/HrcC family-type III secretion system outer membrane ring protein	5.11	0.03
MPAO1_21585		Itaconyl-CoA hydratase	5.19	0.04
MPAO1_17195		Translocator outer membrane protein PopD	5.19	0.02
MPAO1_17200		Hypothetical protein	5.34	0.01
MPAO1_00520	vgrG1b*	Type VI secretion system tip protein VgrG1b⁵²	5.41	0.01	H1-T6SS⁴⁴
MPAO1_20935		Beta-keto-ACP synthase	5.61	0.04
MPAO1_24325		Cytochrome c551 peroxidase	6.11	0.00
Diff. Abundant
MPAO1_07815		Osmoprotectant NAGGN system M42 family peptidase	4.70	0.02
MPAO1_19625	aprX	Hypothetical protein	5.45	0.00	⁴⁵
MPAO1_24535	*cdrA**	Filamentous hemagglutinin N-terminal domain-containing protein	6.54	0.00	⁵⁰
MPAO1_02725	nirF	Protein NirF	4.30	0.01
MPAO1_24530	cdrB*	ShlB/FhaC/HecB family hemolysin secretion/activation protein	4.35	0.01	⁵⁰
MPAO1_25250		BON domain-containing protein	3.28	0.05
MPAO1_19595		Serralysin	3.75	0.01
MPAO1_22090	putA	Bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA	3.00	0.01
MPAO1_18330	muiA*	Mucoidy inhibitor MuiA	2.69	0.01	⁴⁶
MPAO1_21730	cbpD*	Chitin-binding protein CbpD	2.79	0.00	⁴⁷
MPAO1_06120		Copper chaperone PCu(A)C	1.98	0.03
MPAO1_14990		NAD(P)-dependent alcohol dehydrogenase	2.22	0.01
MPAO1_02740	nirS	Nitrite reductase	2.52	0.00
MPAO1_25230		DUF748 domain-containing protein	1.85	0.02
MPAO1_18000	ccoP	Cytochrome-c oxidase, cbb3-type subunit III	1.60	0.05
MPAO1_28880	adhP	Alcohol dehydrogenase AdhP	2.52	0.00
MPAO1_07010		Phosphoketolase	2.07	0.00
MPAO1_00100		LysM peptidoglycan-binding domain-containing protein	1.44	0.03
MPAO1_02290		TonB-dependent receptor	1.66	0.01
MPAO1_27435		Amino acid ABC transporter substrate-binding protein	−3.09	0.03
MPAO1_05385		DUF1302 domain-containing protein	−2.80	0.03
MPAO1_17965	acnA*	Aconitate hydratase	1.49	0.01	⁴⁸
MPAO1_24155	pilY1*	Type 4a pilus biogenesis protein PilY1	1.54	0.01	⁴⁹
MPAO1_05375		Fatty acid--CoA ligase	−5.06	0.01
MPAO1_04650		OmpW family protein	1.49	0.01
MPAO1_00495	tssH	Type VI secretion system ATPase TssH	1.27	0.03	H1-T6SS⁴⁴
MPAO1_14010		Non-ribosomal peptide synthetase (NRPS)	1.90	0.02
MPAO1_26210	azu	Azurin	2.45	0
MPAO1_13620		Xanthine dehydrogenase family protein molybdopterin-binding subunit	−4.33	0.01
MPAO1_03800	pchA	Salicylate biosynthesis isochorismate synthase	−3.04	0.01
MPAO1_06095		TonB-dependent copper receptor	1.74	0.00
MPAO1_03775		Catalase	1.67	0.00
MPAO1_02430	clpG	AAA family protein disaggregase ClpG	2.31	0.00
MPAO1_26945		Poly(3-hydroxyalkanoate) granule-associated protein PhaF	1.22	0.03
MPAO1_23990		Prepilin-type cleavage/methylation domain-containing protein	3.01	0.00
MPAO1_02180		Response regulator	1.13	0.00
MPAO1_05390		DUF1329 domain-containing protein	−2.62	0.00
MPAO1_13900		NADP-dependent glyceraldehyde-3-phosphate dehydrogenase	−1.11	0.05
MPAO1_13035		Multidrug efflux RND transporter periplasmic adaptor subunit MexE	−1.92	0.00
MPAO1_25100		TonB-dependent hemoglobin/transferrin/lactoferrin family receptor	−1.17	0.02
MPAO1_09260		Carbohydrate ABC transporter substrate-binding protein	−0.99	0.02
MPAO1_16835		Porin	1.34	0.00
MPAO1_09280		Porin	−1.54	0.00
Planktonic only
MPAO1_23930	puiA**	TonB-dependent siderophore receptor	−6.91	0.00
MPAO1_22860	pctC	Methyl-accepting chemotaxis protein PctC	−6.78	0.00
MPAO1_07425	argF	Ornithine carbamoyltransferase	−5.51	0.01
MPAO1_21260		Chain-length determining protein	−5.22	0.02
MPAO1_15475		Siderophore-interacting protein	−5.09	0.02
MPAO1_29055		Class I SAM-dependent methyltransferase	−5.08	0.03
MPAO1_22680		Biliverdin-producing heme oxygenase	−5.02	0.03
MPAO1_09305	pgl	6-phosphogluconolactonase	−5.01	0.03

Publications linking the genes/proteins with various roles in biofilms are listed for proteins highlighted in Fig. 6. Two genes missed in MPAO1/P1 are shown in bold. Gene names stem from the National Center for Biotechnology Information (NCBI) annotation or were deduced from the eggNOG annotation or the respective PAO1 homolog (*) or the Pseudomonas genome database (**); see also Supplementary Data 1.

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Table 3 List of 61 proteins with significant differential abundance (see text) or unique expression when comparing biofilm grown and planktonic cells.

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