Table 2 List of cysteine residues identified to be differentially S-nitrosylated in aerobically grown biofilm vs planktonic E. coli cultures by using the biotin-switch SILAC method.

Protein	Function	COG cat^a	Cysteine position	Aerobic BFO₂ vs PKO₂
Biofilm-specific
GldA	Glycerol dehydrogenase	C	C85	BF only
GltD^b	Glutamate synthase (NADPH) small chain	E, R	C108	BF only
Planktonic-specific
ArcA^b	Aerobic respiration control protein	T, K	C173	PK only
PurC	Phosphoribosylaminoimidazole-succinocarboxamide synthase	F	C79	PK only
YtfE	Iron–sulfur cluster repair protein	O	C184	PK only
Aph	Aminoglycoside 3′-phosphotransferase	R	C31	PK only
GuaB	Inosine-5′-monophosphate dehydrogenase	R	C441	PK only
HisG	ATP phosphoribosyltransferase	E	C149	PK only
IleS	Isoleucine–tRNA ligase	J	C463	PK only
IleS	Isoleucine–tRNA ligase	J	C924	PK only
OxyR^b	DNA-binding transcriptional dual regulator	K	C25	PK only
Pgl	6-phosphogluconolactonase	G	C152	PK only
PyrI	Aspartate carbamoyltransferase regulatory chain	F	C141	PK only
Rnr	Ribonuclease R	K	C118	PK only
RpsK	30S ribosomal protein S11	J	C70	PK only
LeuC	3-Isopropylmalate dehydratase large subunit	E	C75	−3.00
GlmS	Glutamine--fructose-6-phosphate aminotransferase	M	C2	−2.12
Ndk	Nucleoside diphosphate kinase	F	C139	−1.78
KatG^b	Catalase hydroperoxidase I	P	C16	−1.75

Posttranslationally modified peptides that were detected only in one type of sample are listed as “BF only” (biofilm) or “PK only” (planktonic). Peptides with significant changes in S-NO profile with adjusted p values < 0.05 are shown (n = 5); data indicate fold changes in modified peptide normalized to total peptide count for biofilm compared to planktonic samples. Negative values indicate PKO₂ vs BFO₂ fold change.
PKO₂ planktonic with O₂, BFO₂ biofilm with O₂.
^aCOG categories⁷³: C, energy production and conversion; D, cell cycle control, cell division, chromosome partitioning; E, amino acid metabolism and transport; F, nucleotide transport and metabolism; G, carbohydrate metabolism and transport; H, coenzyme transport and metabolism; J, translation, ribosomal structure, and biogenesis; K, transcription; L, cell wall/membrane/envelope biogenesis; M, cell wall/membrane/envelop biogenesis; O, posttranslational modification, protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary structure; R, general function prediction only; T, signal transduction; V, defense mechanisms.
^bProteins for which the S-nitrosylated cysteine was selected for cysteine-to-serine point mutation.

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