SUPPLEMENTARY INFORMATION

LC-MS/MS Proteomic Analysis of Starved Bacillus subtilis Cells Overexpressing Ribonucleotide Reductase (nrdEF): Implications in Stress-Associated Mutagenesis

Karla Viridiana Castro-Cerritosa&, Adolfo Lopez-Torresb&, Armando Obregón-Herreraa, Katarzyna Wrobelc, Kazimierz Wrobelc, Mario Pedraza-Reyesa*.

aDepartment of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico; bInstitute of Applied Chemistry, University of Papaloapan, Tuxtepec, Oaxaca, Mexico; cChemistry Department, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico

Key words

Bacillus subtilis, Ribonucleotide Reductase, Amino Acid Starvation, Stress-Associated Mutagenesis.

*Corresponding author: Mario Pedraza-Reyes,

Inventory

Supplemental Table S1

Table S1. Full list of differential proteins detected in strains B. subtilis ∆nrdR and YB955

Proteins upregulated / Proteins downregulated / Fold of change / Protein / Functionc / Transcriptional Regulation
Nucleotide Metabolism
1 / 1 / 14,6 / NrdE / Ribonucleotide reductase Ib (alfa subunit) / NrdR , ResD
2 / 2 / 2,2 / PurK / Phosphoribosylaminoimidazole carboxylase / G-box, PurR
3 / -2,5 / Prs / Phosphoribosylpyrophosphate synthetase / Stringent response
4 / -2,7 / PurE / Phosphoribosylaminoimidazole carboxylase / G-box, PurR regulon
NDa / NrdF / Ribonucleotide reductase Ib (beta subunit) / NrdR , ResD
NDb / PyrH / Uridylate kinase / Stringent response
NDb / Gmk / Guanylate kinase
NDb / Cmk / Cytidylate kinase
NDb / PurT / Phosphoribosylglycinamide formyltransferase
mRNA degradation
3 / 5 / 14,7 / YhaM / 3'-5' exoribonuclease / LexA
NDa / YugI / Putative polyribonucleotide phosphorylase / Stringent response
Amino acid biosynthesis
NDa / HisH / Imidazole glycerol phosphato synthase
6 / -6,7 / ArgH / Argininosuccinate lyase / AhrC
7 / -2,9 / ArgF / Ornithine carbamoyltransferase / CodY, AhrC
8 / -2,7 / SerC / 3-phosphoserine aminotransferase
9 / -2,5 / IlvD / Dihydroxy-acid dehydratase / CodY
10 / -4,2 / YwaA / Branched-chain amino acid aminotransferase / CodY
NDb / CysI / sulfite reductase (NADPH2) / CysL
NDb / LeuA / 2-isopropylmalate synthase / CcpA, CodY , T-box, TnrA
NDb / YitJ / Methionine synthase / S-box
NDb / ThrB / Homoserine kinase / CodY. ThrR
NDb / AspB / Aspartate transaminase
Degradation of amino acids, proteins and other nitrogen sources
4 / 11 / 2,0 / IspA / intracellular serine protease / CodY
5 / 12 / 2,1 / UreA / Urease (gamma subunit) / CodY, GlnR, PucR, SigH, TnrA
6 / 13 / 2,1 / Vpr / minor extracellular serine protease / CodY, DnaA, LexA , PhoP, SigH
14 / -2,1 / RocD / Ornithine transaminase / AhrC, CodY, RocR , SigL, Spo0A
15 / -2,2 / RocF / Arginase / AhrC, CodY , RocR , SigL, Spo0A
16 / -2,3 / RocA / 3-hydroxy-1-pyrroline-5-carboxylate dehydrogenase / AbrB, AhrC , CodY , RocR , SigL
17 / -2,3 / ClpY / Two-component ATP-dependent protease / CodY
7 / 18 / 2,8 / UreC / Urease (alpha subunit) / CodY, GlnR, PucR, SigH, TnrA
Translation
8 / 19 / 2,2 / RplU / Ribosomal protein L21 / Stringent response
9 / 20 / 2,4 / RpmE / Ribosomal protein L31 / Stringent response
10 / 21 / 2,5 / InfA / Translation initiation factor IF-1 / Stringent response
11 / 22 / 2,5 / RplF / Ribosomal protein L6 / Stringent response
23 / -2,8 / TyrZ / Alternative tyrosyl-tRNA synthetase / DtrR T-box
24 / -3,0 / GltX / Glutamyl-tRNA synthetase
12 / 25 / 3,2 / AsnS / Asparagyl-tRNA synthetase
26 / -3,2 / GatB / Glutamyl-tRNA(Gln)
27 / -7,2 / InfB / Translation initiation factor IF-2 / Stringent response
NDb / PheT / Phenylalanyl-tRNA synthetase (beta subunit) / T-box
NDb / LeuS / Leu-tRNA synthetase / T-box
NDb / Obg / GTP-binding protein
NDb / YaaA / Ribosome assembly factor
NDb / RplJ / Ribosomal protein L10 / Stringent response
Transcription factors
28 / -2,3 / CodY / Transcriptional pleiotropic repressor / CodY
29 / -2,7 / GreA / Transcription elongation factor
Cell lifestyles
13 / 30 / 14,7 / SinI / Antagonist of SinR / SinR, Spo0A, AbrB, Scoc
14 / 31 / 2,4 / YfmS / Soluble chemotaxis receptor / SigD
15 / 32 / 2,5 / ComZ / competence protein / Spo0A
16 / 33 / 2,6 / SpeD / S-adenosylmethionine decarboxylase / CcpN
17 / 34 / 2,9 / Hag / Flagellin protein / CodY, CsrA, ScoC, SigD
18 / 35 / 2,9 / SpoVG / Negative effector of asymetric septation / AbrB, SigH, SinR
19 / 36 / 3,2 / Rok / Repressor of comK / AbrB, Rok, SinR, Spo0A
20 / 37 / 3,7 / BslA / Bacterial hydrophobin / AbrB, DegU
21 / 38 / 4,2 / YvcA / Lipoprotein / AbrB, DegU
22 / 39 / 4,9 / Oppb / Oligopeptide ABC transporter / CodY, TnrA, ScoC
NDb / YvyC / Similar to flagellar protein / SigD
NDb / FliF / flagellar basal-body M-ring protein / CodY , DegU, SigD, Spo0A
c-di-AMP interacting proteins
23 / 40 / 2,6 / CdaR / effector protein controlling CdaA diadenylate cyclase activity
41 / -3,4 / DisA / DNA integrity scanning protein / CtsR, SigB, SigM
24 / 42 / 3,9 / DarA / c-di-AMP-binding PII-like protein
25 / 43 / 4,3 / YfkN / c-di-AMP phosphodiesterase / CcpA, PhoP
DNA repair
44 / -2,4 / RecA / multifunctional protein / ComK, LexA
45 / -2,2 / Nfo / type IV apurinic/apyrimidinic endonuclease / SigG
NDb / SbcC / DNA exonuclease / ComK
46 / -8,9 / DinB / nuclease inhibitor
Biosynthesis of cofactors
26 / 47 / 9,3 / RibH / Riboflavin synthase (beta subunit) / FMN box
48 / -3,9 / MenB / naphthoate synthase
49 / -3,9 / HemQ / heme-binding protein
50 / -2,1 / NadA / quinolinate synthetase
51 / -2,1 / YumC / ferredoxin/flavodoxin-NAD(P) oxidoreductase
NDb / PanC / pantothenate synthase
Other proteins
27 / 52 / 4,8 / YuiA / unknown
28 / 53 / 2,9 / YwlF / Ribose-5-phosphate isomerase / TnrA
29 / 54 / 2,9 / CspC / Cold shock protein
30 / 55 / 4,7 / YuiA / unknown / CodY, TnrA
31 / 56 / 3,8 / YtmB / unknown
32 / 57 / 4,7 / YqkB / unknown
33 / 58 / 9,2 / YhdX / unknown
34 / 59 / 6,4 / SknR / Transcriptional repressor
35 / 60 / 4,6 / YwqI / unknown
36 / 61 / 6,3 / RbsB / Ribose ABC transporter (binding protein) / AbrB, CcpA
37 / 62 / 2,7 / SipT / Signal peptidase I / DegU
38 / 63 / 3,6 / Ptsh / Phosphocarrier protein / Stringent response, GltC
39 / 64 / 2,7 / YfhC / unknown
40 / 65 / 5,3 / Acca / Acetyl-CoA carboxylase (alpha subunit) / Spo0A
41 / 66 / 2,5 / SppA / Signal peptide peptidase / SigW
42 / 67 / 2,5 / BmrU / General stress protein, / SigB
43 / 68 / 4,2 / YvcA / Lipoprotein / AbrB, DegU
44 / 69 / 2,4 / YabA / Inhibitor of DnaA oligomerization
45 / 70 / 2,4 / Fer / Ferredoxin
46 / 71 / 2,4 / YdjO / Unknown / SigW
47 / 72 / 2,4 / YndB / unknown
48 / 73 / 3,1 / YuzD / unknown
49 / 74 / 2,1 / AtpC / ATP synthase / Stringent response
50 / 75 / 2,1 / YqeY / Unknown
51 / 76 / 2,0 / PpiB / Peptidyl-prolyl isomerase
NDa / Lgt / Prolipoprotein diacylglyceryl transferase
NDb / YbfA / unknown
NDb / YrvC / unknown
NDb / MelA / alpha-galactosidase / CcpA
NDb / YtpA / phospholipase / SigM
NDb / TagD / glycerol-3-phosphate cytidylyltransferase / PhoP , WalR
NDb / YwfO / unknown
NDb / YtxG / general stress protein / SigB, SigH
NDb / GsaB / glutamate-1-semialdehyde aminotransferase
NDb / MinC / cell-division inhibitor / SigH, SigM, ComK
NDb / Dps / mini-ferritin / SigB
NDb / YwtF / phosphotransferase / SigM
77 / -8,9 / YceC / similar to tellurium resistance protein / SigB, SigM, SigW, SigX
78 / -6,7 / YqhY / Unknown / LexA
79 / -4,6 / DegV / fatty acid binding protein
80 / -4,1 / YfmJ / similar to predicted oxidoreductase / Spo0A
81 / -3,9 / YtoP / similar to endo-1,4-beta-glucanase
82 / -3,6 / Dat / D-alanine aminotransferase
83 / -3,4 / TagC / possibly involved in polyglycerol phosphate teichoic acid biosynthesis / LexA
84 / -3,3 / CotE / spore coat morphogenetic protein / SigE, SigK, GerE
85 / -2,8 / YcsN / similar to aryl-alcohol dehydrogenase
86 / -2,8 / YhfK / general stress protein / SigB, SigW
87 / -2,7 / YmfH / similar to peptidase / Mta
88 / -2,5 / Hmob / heme monooxygenase
89 / -2,5 / YtjP / imilar to succinyl-diaminopimelate disuccinylase
90 / -2,4 / YjcH / unknown
91 / -2,3 / PepF / oligoendopeptidase
92 / -2,3 / YtvA / blue light sensor / Spx
93 / -2,3 / GpmI / phosphoglycerate mutase / CggR
94 / -2,2 / RbsD / ribose ABC transporter (membrane protein) / AbrB, CcpA
95 / -2,2 / MurB / UDP-N-acetylenolpyruvoylglucosamine reductase / SigE, SigM, SpoIIID
96 / -2,2 / SufB / FeS scaffold
97 / -2,2 / BshA / L-malic acid glycosyltransferase / Spx
98 / -2,1 / YwpJ / unknown
99 / -2,1 / YxdD / formation of 5-deoxy-D-glucuronic acid (3rd reaction) / CcpA , IolR
100 / -2,1 / YtpR / similar to Phe-tRNA synthetase (beta subunit) / spx
101 / -2,1 / PtsI / Enzyme I, general component of the HPr / GlcT , stringent response
102 / -2,1 / MtnD / 1,2,-dihydroxy-3-keto-5-methylthiopentene dioxygenase / S-box

aND. Protein not detected in soluble extracts of strain B. subtilis YB955

bND. Protein not in soluble extracts of strain B. subtilis DNrdR

cThe function was assigned based on the description of the database Subtiwiki (http://www.subtiwiki.uni-goettingen.de)

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