Supplemental material
Analytical methods. For Chla analyses, duplicate volumes of 500 ml of whole
seawater were filtered through GF/F filters (Whatman). Chla was extracted overnight at 4
C° in 90% acetone and concentration was measured by fluorescence using a 10-AU
Fluorometer (Turner Designs; Yentsch and Menzel, 1963). Dissolved DMSP (DMSPd)
was measured following the procedure described by Kiene and Slezak (2006). Briefly,
the first 3.5 ml of seawater filtered by gravity through a 47 mm-diameter GF/F filter
(Whatman) were acidified with addition of 15 µl of 50% H2SO4 (v:v) to preserve
DMSP. During analysis, DMSPd was converted to DMS by alkaline hydrolysis,
cryotrapped and detected by sulfur-specific gas chromatography. Total DMSP (DMSPt)
concentration was determined similarly in a 1 ml subsample of acidified seawater (50 ml
of whole seawater in 175 µl of 50% H2SO4). Bacterial production was measured by 3Hleucine incorporation into trichloroacetic acid-insoluble material (Kirchman, 1993).
Incubations were carried out in triplicate in the dark at in situ temperature with additions
of 20 nM of 3H-leucine for 4 hours, starting immediately after water collection. One
TCA-killed sample was used as a control. Samples were processed by the
microcentrifugation method (Smith and Azam, 1992).
RNA preparation . RNA was extracted using the RNeasy kit (Qiagen) with a
modified protocol. Trace amounts of DNA were removed from samples by treating with
the TURBO DNA-free kit (Ambion, Austin, TX), producing 1.4 g of total RNA per
filter. Ribosomal RNA was subsequently removed using two methods: an enzymatic
treatment using the mRNA-ONLY Prokaryotic mRNA Isolation kit (Epicentre
Biotechnologies, Madison, WI) and magnetic subtractive hybridization of rRNA using
the MICROBEnrich kit (Ambion) and MICROBExpress kit (Ambion) (2 rounds of each).
Approximately 50-75 ng of sample was then amplified using the MessageAmp IIBacteria kit (Ambion). Amplified RNA was converted to double-stranded cDNA using
the Universal RiboClone cDNA Synthesis System (Promega). Final cDNA was purified
with the Wizard DNA Clean-up System (Promega). The cDNA concentration was
estimated using spectrophotometric quantification (Nanodrop). A total of 3.5 µg of
cDNA per treatment were obtained.
Supplementary Table S1. Annotation of Control and DMSP transcriptomes.
________________________________________________________________________
Number of reads
Percentage
Control
DMSP
Control DMSP
________________________________________________________________________
Total reads (raw)
Total unique reads
301179
266771
305107
274579
100
89
100
90
Ribosomal RNA reads
153930
145947
51
48
Possible protein-encoding sequences
147249
159160
49
52
RefSeq Identified
66804
81173
22
27
GOS (non-RefSeq) Identified
25599
27343
8
9
nr Identified
787
874
0.3
0.3
Unidentified in RefSeq, GOS and nr
54059
49770
18
16
KEGG-assigned Reads
60100
73289
20
24
COG-assigned Reads
38469
51644
13
17
________________________________________________________________________
Supplementary Table S2. Selected reference genes for BLAST analysis.
________________________________________________________________________________________________________________________________________________
Functional
Category
Acrylate
degradation
Label
C3
Gene
or Locus Tag
Annotation
Accession
Number
Strain
Group
Source
# Hits
CONTROL DMSP
SPO1094
Propionyl-CoA carboxylase
AAV94394.1
Ruegeria DSS3
Alpha
Gifford et al. in prep 12
25
MGP11163 Propionyl-CoA carboxylase
ZP_01625303 HTCC2080
Gamma
3
11
SPO1097
conserved hypothetical
AAV94397.1
Ruegeria DSS3
Alpha
1
6
SPO1100
lipoprotein, putative
AAV94400.1
Ruegeria DSS3
Alpha
20
18
SPO1101
pccA_propionyl-CoA carboxylase
AAV94401.1
Ruegeria DSS3
Alpha
0
0
SPO1102
lipoprotein, putative
AAV94402.1
Ruegeria DSS3
Alpha
0
0
SPO1104
hypothetical protein
AAV94404.1
Ruegeria DSS3
Alpha
0
6
SPO2934
propionate--CoA ligase
AAV96175.1
Ruegeria DSS3
Alpha
12
30
prpE
hypthetical protein
YP_266048
SAR11_HTCC0624 Alpha
14
19
________________________________________________________________________________________________________________________________________________
DMS production dddD
dddD
DMSP acyl CoA transferase
ABR72937
MWYL1
Gamma Todd et al. 2007
2
6
ZP_01746034 SS E-37
Alpha
0
2
ZP01224900
HTCC2207
Gamma
1
0
dddL
dddL
DMSP lyase
ZP_00955343 Sulfitobact. EE-36
Alpha
Curson et al. 2008 0
0
YP_351475.1 Rhodobct sph. 2.4.1 Alpha
0
0
dddP
dddP
metallopeptidase, family M24
AAV95561.1
Ruegeria DSS3
Alpha
Todd et al.2009
3
4
________________________________________________________________________________________________________________________________________________
DMSP
dmdA
dmdA
putative aminomethyltransferase
ZP_01625100 HTCC2080
Gamma Howard et al 08
0
2
demethylation
dmdA
putative DMSP demethylase
YP_265671
SAR11_HTCC0246 Alpha
Howard et al 06
6
9
dmdA
putative aminomethyltransferase
EDZ61098
SAR11_HTCC1062 Alpha
Howard et al 08
6
11
SPO1913
putative DMSP demethylase
AAV95190.1
Ruegeria DSS-3
Alpha
Howard et al 06
11
16
________________________________________________________________________________________________________________________________________________
DMS oxidation
DMSox xoxF
putative PQQ dehydrogenase protein
YP_352636.1 Rhodobct sph. 2.4.1 Alpha
9
22
MDMS009 PQQ-dependent dehydrogenase
YP_002669821 Methylophaga
Gamma Schäfer, 2007
7
9
SS37_03200 putative methanol dehydrogenase
jcventer
SS E-37
Alpha
9
13
jcventer:1101159001453
________________________________________________________________________________________________________________________________________________
MeSH incorp.
MeSH
metB
cystathionine gamma-synthase
BAE77371
E. coli K12
Gamma Kiene et al 1999
7
17
________________________________________________________________________________________________________________________________________________
DMSP uptake
TRANS opuAA
GBT/proline ABC transporter
AAV97366.1
Ruegeria DSS3
Alpha
Moran et al 2004
33
40
system
proV
GBT/L-proline transport ATP-bind.
YP_266219.1 SAR11_HTCC1062 Alpha
Moran et al 2004
16
21
opuD
GBT transporter
AAV96421.1
Ruegeria DSS3
Alpha
Moran et al 2004
1
3
opuAA
GBT/l-proline transport ATP-bind.
YP_266705.1
SAR11_HTCC1062 Alpha
Moran et al 2004
0
0
________________________________________________________________________________________________________________________________________________
DMSO reductase DMSOrd SPO3557
dimethyl sulfoxide reductase
AAV96782.1
Ruegeria DSS3
Alpha
Moran et al 2004
8
2
________________________________________________________________________________________________________________________________________________
Inorg. S oxid.
soxB
SoxB
sulfur oxidation B protein
YP_166249.1 Ruegeria DSS3
Alpha
Moran et al 2004
4
7
________________________________________________________________________________________________________________________________________________
Assimilatory
Sulfate
cysD
sulfate adenylyltransferase
NP_417232.1 E.coli K12
Gamma Tripp et al. 2008
53
53
sulfate
cysN
sulfate adenylyltransferase
NP_417231.1 E.coli K12
Gamma Tripp et al. 2008
0
0
reduction
cysH
phosphoadenosine phosphosulfate red
NP_417242.1 E.coli K12
Gamma Tripp et al. 2008
0
0
cysI
sulfite reductase
NP_417243.1 E.coli K12
Gamma Tripp et al. 2008
0
0
cysJ
sulfite reductase, alpha subunit
NP_417244.1 E.coli K12
Gamma Tripp et al. 2008
0
0
SPO0900
sulfate adenylyltransferase
YP_166153.1 Ruegeria DSS3
Alpha
Moran et al 2004
5
20
SPO2634
sulfite reductase
YP_167844.1 Ruegeria DSS3
Alpha
Moran et al 2004
9
7
SPO2635
phosophoadenylyl-sulfate reductase
YP_167845.1 Ruegeria DSS3
Alpha
Moran et al 2004
6
0
________________________________________________________________________________________________________________________________________________
MSA
MSA
msmA
hydroxylase alpha subunit 2
AAK84308
Marinosulf. methyl. Alpha
Baxter et al 2002
4
11
Monooxygenase
msmB
hydroxylase beta subunit
AAK84302
Marinosulf. methyl. Alpha
1
1
msmC
ferredoxin
AAK84303
Marinosulf. methyl. Alpha
0
2
msmD
putative LysR transcriptional
AAK84304
Marinosulf. methyl. Alpha
1
2
msmA
MSA monooxygenase hydroxylase
ABK97404
Sargasso-2218644
Leitao et al. 2009
8
10
msmB
MSA monooxygenase hydroxylase
ABK97405
Sargasso-2218645
1
2
msmC
MSA monooxygenase ferredoxin
ABK97406
Sargasso-2218646
0
1
msmD
MSA monooxygenase reductase
ABK97407
Sargasso-2218647
1
1
________________________________________________________________________________________________________________________________________________
Upregulated
MICRO SPOA0268 transcriptional regulator, IclR family
AAV97402.1
Ruegeria DSS3
Alpha
Gifford et al.prep
0
0
genes in
SPOA0269 conserved hypothetical protein
AAV97403.1
Ruegeria DSS3
Alpha
6
1
Roseo- microarray
MGP 08771 selenium-binding protein
ZP_01626818 HTCC2080
Gamma
7
4
after DMSP
SPOA0270 conserved hypothetical protein
AAV97404.1
Ruegeria DSS3
Alpha
0
0
addition
SPOA0271 methylamine utilization protein MauG
AAV97405.1
Ruegeria DSS3
Alpha
0
1
MGP 08766 methylamine utilization protein MauG
ZP_01626817 HTCC2080
Gamma
0
1
SPOA0272 glutathione-dpnt formaldehyde dehydr. AAV97406.1
Ruegeria DSS3
Alpha
9
6
MGP 12693 Zn-containing alcohol dehydrogenase
ZP_01626542 HTCC2080
Gamma
9
10
SPOA0273 DNA-binding protein, putative
AAV97407.1
Ruegeria DSS3
Alpha
0
0
SPO0453
conserved hypothetical protein
AAV93771.1
Ruegeria DSS3
Alpha
0
0
________________________________________________________________________________________________________________________________________________
Glycine betaine
GBT
SPO2134
trimethylamine methyltransferase
AAV95403.1
Ruegeria DSS3
Alpha
Moran et al 2004
5
2
degradation
MttB
trimethylamine methyltransferase
ZP_01626141 HTCC2080
Gamma
0
3
SPO0565
trimethylamine methyltransferase
YP_165825.1 Ruegeria DSS3
Alpha
Moran et al 2004
7
9
soxB
sarcosine oxidase
AAZ21869
SAR11_HTCC1062 Alpha
Moran et al 2004
43
55
________________________________________________________________________________________________________________________________________________
Proteorhodopsin
PROT
EF640904
proteorhodopsin
ABR27795
SAR11_HTCC1013 Alpha
NCBI
463
249
OM2255
bacteriorhodopsin
ZP_01447408 Roseo_HTCC2255 Alpha
NCBI
245
229
EF182737.1 proteorho dopsin
ABO88140
HTCC2207
Gamma NCBI
71
58
________________________________________________________________________________________________________________________________________________
ATP synthase
ATP
atpC
ATP synthase F1
AAV96396.1
Ruegeria DSS3
Alpha
Moran et al 2004
6
4
atpC
ATP synthase epsilon chain
YP_265653.1 SAR11_HTCC1062 Alpha
Giovannoni et al 05 1
5
MGP 03410 ATP synthase subunit beta
ZP_01625638
HTCC2080
Gamma
154
273
________________________________________________________________________________________________________________________________________________
Strain abbreviations are as follows: Ruegeria DSS3: Ruegeria pomeroyi DSS-3. HTCC2080: Marine gammaproteobacterium HTCC2080. SAR11_HTCC#:
Candidatus Pelagibacter ubique HTCC#. Roseo_HTCC2255: Rhodobacterales bacterium HTCC2255. MWYL1: Marinomonas MWYL1. SS E-37: Sagitulla
stellata E-37. Rhodobct sph. 2.4.1: Rhodobacter sphaeroides 2.4.1. HTCC2207: Marine gammaproteobacterium HTCC2207. Marinosulf. methyl.:
Marinosulfonomonas methylotropha. Sargasso_#: uncultured bacterium Sargasso-# retrieved from the Sargasso Sea metagenome (Venter et al 2004). Locus tag
abbreviation: MGP#: MGP2080_#.
Supplementary Table S3. KEGG pathways significantly depleted or enriched in the Sargasso Sea transcriptome after DMSP
addition. Pathway number is indicated in parenthesis. Significance levels above 90% are indicated with one (95%) or two (98%)
asterisks.
_________________________________________________________________________________________________________________________________
CATEGORY
DEPLETED
ENRICHED
Nucleotide Metabolism
Pyrimidine metabolism (00240)**
Purine metabolism (00230)*
_________________________________________________________________________________________________________________________________
Transcription
RNA polymerase (03020)**
Ribosome (03010)**
_____________________________________________________________________________________________________________________________ ____
Translation
Aminoacyl-tRNA biosynthesis (00970)*
_____________________________________________________________________________________________________________________________ ____
§
Energy Metabolism
Photosynthesis (00195)**
Reductive carboxylate cycle (CO2 fixation) (00720)
Photosynthesis - antenna proteins (00196)**
_____________________________________________________________________________________________________________________________ ____
Amino Acid Metabolism
Glutamate metabolism (00251)
Valine, leucine and isoleucine degradation (00280)*
Valine, leucine and isoleucine biosynthesis (00290)
_____________________________________________________________________________________________________________________________ ____
Metabolism of Other Amino Acids
Porphyrin and chlorophyll metabolism (00860)*
Beta-alanine metabolism (00410)
D-Glutamine and D-glutamate metabolism (00471)
_____________________________________________________________________________________________________________________________ ____
Carbohydrate Metabolism
Citrate cycle (TCA cycle) (00020)
Nucleotide sugars metabolism (00520)
Propanoate metabolism (00640)
_________________________________________________________________________________________________________________________________
Lipid Metabolism
Fatty acid metabolism (00071)
_____________________________________________________________________________________________________________________________ ____
Glycan Biosynthesis and Metabolism
Peptidoglycan biosynthesis (00550)
Lipopolysaccharide biosynthesis (00540)*
Metabolism of Cofactors and Vitamins
Ubiquinone biosynthesis (00130)
_____________________________________________________________________________________________________________________________ ____
Xenobiotics Biodegradation and Metabolism
Biphenyl degradation (00621)
Geraniol degradation (00281)
Benzoate degradation via CoA ligation (00632)
_________________________________________________________________________________________________________________________________
Biosynthesis of Secondary Metabolites
Limonene and pinene degradation (00903)
_____________________________________________________________________________________________________________________________ ____
Membrane Transport
ABC transporters (02010)**
_____________________________________________________________________________________________________________________________ ____
Signal Transduction
Two-component systems (02020)**
_________________________________________________________________________________________________________________________________
Cell Motility
Flagellar assembly (02040)**
Bacterial chemotaxis (02030)
_________________________________________________________________________________________________________________________________
Folding, Sorting and Degradation
Protein export (03060)**
_____________________________________________________________________________________________________________________________ ____
+
Metabolic Disorders
chaperone [Type I diabetes mellitus (04940)]**
_____________________________________________________________________________________________________________________________ ____
+
Neurodegenerative Disorders
chaperone [Prion disease (05060)]**
_________________________________________________________________________________________________________________________________
+
Immune System
chaperone [Antigen processing (04612)]
_________________________________________________________________________________________________________________________________
+
+
Endocrine System
chaperone (Progesterone-mediated
putative acyl-CoA dehydrogenase
oocyte maturation (04914))
[PPAR signaling pathway (03320)]
_________________________________________________________________________________________________________________________________
§
This pathway has significant overlap with TCA cycle enzymes
+
Annotation based on BLAST analysis of transcript sequences. The KEGG pathway name is given in brackets.
Supplementary Table S4. COG categories significantly depleted or enriched in the Sargasso Sea transcriptome after DMSP addition.
Significance levels above 90% are indicated with one (95%) or two (98%) asterisks.
_________________________________________________________________________________________________________________________________
GENERAL
FUNCTIONAL
DEPLETED
ENRICHED
CATEGORY
CATEGORY
_____________________________________________________________________________________________________________________________ ____
Metabolism
Energy production
and conversion
Ribulose bisphosphate carboxylase small subunit**
Na+-transporting NADH:ubiquinone oxidored. **
Formate hydrogenlyase sub6/NADH:ubiquinone *
Inorganic pyrophosphatase*
Rubrerythrin*
F0F1-type ATP synthase, beta subunit*
F0F1-type ATP synthase, subunit c/Archaeal/vacuola* F0F1-type ATP synthase, gamma subunit*
NADH:ubiquinone oxidoreductase subunit 1 (chain H)* NAD-dependent aldehyde dehydrogenases
NADH:ubiquinone oxidoreductase subunit 4 (chain M) Na+/H+-dicarboxylate symporters
Isocitrate lyase
Aerobic-type carbon monoxide dehydrogenase
NADH:ubiquinone oxidoreductase subunit 3 (chain A) Citrate synthase
Aldehyde:ferredoxin oxidoreductase
Rieske Fe-S protein
Ferredoxin
Isocitrate dehydrogenases
NADH:ubiquinone oxidoreductase 24 kD subunit
Pyruvate:ferredoxin oxidoreductase
Aerobic-type carbon monoxide dehydrogenase
NADPH:quinone reductase and related Zn-dependent
________________________________________________________________________________________________________________
Amino acid transport
ABC-type proline/glycine betaine transport systems** Tryptophan synthase beta chain*
and metabolism
Spermidine/putrescine-binding periplasmic protein*
Dipeptide/tripeptide permease*
ABC-type dipeptide transport system
Diaminopimelate decarboxylase
ABC-type amino acid transport system
Cysteine synthase
Urea amidohydrolase (urease) alpha subunit
Isopropylmalate/homocitrate/citramalate synthases
Oligoendopeptidase F
Glycine/D-amino acid oxidases (deaminating)
Gamma-glutamyl phosphate reductase
Tetrahydrodipicolinate N-succinyltransferase
Arginine kinase
O-acetylhomoserine sulfhydrylase
ABC-type amino acid transport/signal transduction
Carbamoylphosphate synthase large subunit
________________________________________________________________________________________________________________
Nucleotide transport
Cytidine deaminase
Thymidine kinase
and metabolism
Xanthine/uracil permeases
Phosphoribosylformylglycinamidine (FGAM) synthase
dGTP triphosphohydrolase
Thymidylate synthase
Phosphoribosylamine-glycine ligase
Aspartate carbamoyltransferase, catalytic chain
Phosphoribosylpyrophosphate synthetase
Cytosine deaminase and related metal-dependent hy
_______________________________________________________________________________________________________________
Carbohydrate transport
Ribulose 1,5-bisphosphate carboxylase, large subunit* 2-keto-3-deoxy-6-phosphogluconate aldolase
and metabolism
ADP-glucose pyrophosphorylase*
Sugar phosphate isomerases/epimerases
ABC-type sugar transport system*
Fructose-1,6-bisphosphate aldolase
Ribulose-5-phosphate 4-epimerase
Fructose-1,6-bisphosphatase
Phosphoheptose isomerase
Beta-galactosidase/beta-glucuronidase
Gluconolactonase
_______________________________________________________________________________________________________________
Coenzyme metabolism
Porphobilinogen deaminase
NAD synthase*
Protoheme ferro-lyase (ferrochelatase)
Precorrin-2 methylase
6-pyruvoyl-tetrahydropterin synthase
Gamma-glutamylcysteine synthetase
4-hydroxybenzoate polyprenyltransferase
5,10-methylene-tetrahydrofolate dehydrogenase
Glutamyl-tRNA reductase
GTP cyclohydrolase II
Dinucleotide-utilizing enzymes involved in Mo
_______________________________________________________________________________________________________________
Lipid metabolism
Fatty-acid desaturase*
Acyl-CoA dehydrogenases**
Phosphatidylserine decarboxylase
Enoyl-CoA hydratase/carnithine racemase*
Oligoketide cyclase/lipid transport protein
Acetyl-CoA carboxylase*
Phosphatidylserine synthase
3-oxoacyl-(acyl-carrier-protein) synthase
_______________________________________________________________________________________________________________
Secondary metabolites
Putative multicopper oxidases*
ABC-type transport system
biosynthesis, transport RTX toxins and related Ca2+-binding proteins
Cytochrome P450
and catabolism
Imidazolonepropionase and related amidohydrolases
_________________________________________________________________________________________________________________________________
Information storage Translation, ribosomal
Protein implicated in ribosomal biogenesis, Nop56p* GTPases - translation elongation factors**
and processing
structure and biogenesis Ribosomal protein L27
Ribosomal protein L11**
NAD(FAD)-utilizing enzyme
Ribosomal protein L1**
Ribosomal protein S3**
Ribosomal protein L16/L10E**
Translation elongation factors (GTPases)**
Polyribonucleotide nucleotidyltransferase **
Ribosomal protein S12*
Ribosomal protein S7*
Ribosomal protein L3*
Ribosomal protein L2*
Ribosomal protein L22*
Ribosomal protein L14*
Ribosomal protein L6P/L9E*
Ribosomal protein S5*
Aspartyl-tRNA synthetase*
Ribosomal protein L15*
Ribosomal protein L18*
Prolyl-tRNA synthetase
Translation initiation factor 2 (IF-2; GTPase)*
Ribosomal protein S1*
Ribonucleases G and E*
Predicted GTPase, probable translation factor
Phenylalanyl-tRNA synthetase alpha subunit
Isoleucyl-tRNA synthetase
Phenylalanyl-tRNA synthetase beta subunit
Ribosomal protein L4
Ribosomal protein S8
Ribosomal protein S11
Ribosomal protein S19
Ribosomal protein S14
Ribosomal protein L17
Ribosomal protein S18
RNase PH
________________________________________________________________________________________________________________
Transcription
Cold shock proteins**
DNA-directed RNA polymerase, beta sub/140 kDs**
DNA-directed RNA polymerase, sigma subunit7
DNA-directed RNA polymerase, beta sub/160 kD**
Putative transcriptional regulator, homolog of Bvg
Transcription antiterminator**
DNA-directed RNA polymerase
Transcription elongation factor*
Response regulator consisting of a CheY
NAD-dependent protein deacetylases, SIR2 family
_______________________________________________________________________________________________________________
DNA replication,
Bacterial nucleoid DNA-binding protein**
Recombinational DNA repair protein (RecF pathway)*
recombination
Nucleotidyltransferase/DNA polymerase
ATPase involved in DNA replication initiation*
and repair
Recombinational DNA repair ATPase (RecF pathway) Topoisomerase IA
3 Superfamily II DNA and RNA helicases
Retron-type reverse transcriptase
_________________________________________________________________________________________________________________________________
Cellular processes
Cell envelope biogenesis, UDP-N-acetylmuramyl pentapeptide P-transferase*
Predicted membrane-associated Zn-dpendnt protease*
outer membrane
UDP-N-acetylmuramate-alanine ligase
UDP-3-O-acyl-N-acetylglucosamine deacetylase
Membrane carboxypeptidase
N-acetylglucosamine-1-phosphate uridyltransferase
Periplasmic protease
Periplasmic protein involved in polysaccharide exp
Membrane-fusion protein
3-deoxy-D-manno-octulosonic acid (KDO)8-phosphate
_______________________________________________________________________________________________________________
Cell motility and
Flagellin and related hook-associated proteins**
Flagellar basal-body P-ring protein*
secretion
Chemotaxis protein histidine kinase
Type II secretory pathway, pseudopilin PulG
Flagellar hook-basal body protein
9 Type II secretory pathway
_______________________________________________________________________________________________________________
Posttranslational
Molecular chaperone (small heat shock protein)**
Predicted carbamoyl transferase, NodU family
modification, protein
Co-chaperonin GroES (HSP10)**
Cysteine protease
turnover, chaperones
Trypsin-like serine proteases**
Thiol:disulfide interchange protein
Membrane protease subunits**
Molecular chaperone**
Chaperonin GroEL (HSP60 family)**
ATP-dependent Zn proteases**
ATP-dependent Lon protease, bacterial type**
DnaJ-class molecular chaperone with C-terminal Zn**
ATPases with chaperone activity, ATP-binding**
Peroxiredoxin*
Polyprenyltransferase*
ATPases of the AAA+ class*
Molecular chaperone, HSP90 family*
Molecular chaperone GrpE (heat shock protein)*
Glutaredoxin-related protein
Cytochrome c biogenesis factor
ABC-type transport system involved in cytochrome c
ABC-type transport system involved in Fe-S cluster
ATP-dependent protease HslVU (ClpYQ),ATPase subunit
Glutamine synthetase adenylyltransferase
_______________________________________________________________________________________________________________
Inorganic ion transport Kef-type K+ transport systems, membrane components* Outer membrane receptor proteins**
and metabolism
Heme oxygenase*
Na+/H+ antiporter*
GTPases - Sulfate adenylate transferase subunit 1
Arylsulfatase A and related enzymes
ABC-type phosphate transport system, periplasmic
K+ transport systems, NAD-binding component
ABC-type phosphate transport system
High-affinity Fe2+/Pb2+ permease
Na+/H+ antiporter NhaD
Phosphodiesterase/alkaline phosphatase D
Uncharacterized copper-binding protein
Nitrogenase subunit NifH (ATPase)
ABC-type Fe3+-siderophore transport system
Co/Zn/Cd efflux system component
Cation transport ATPase
Cation transport ATPase
_______________________________________________________________________________________________________________
Cell envelope biogenesis, Outer membrane protein
outer membrane
_________________________________________________________________________________________________________________________________
Poorly characterized General function
Predicted symporter**
Predicted GTPase*
prediction only
Uncharacterized ABC-type transport system**
Dioxygenases related to 2-nitropropane dioxygenase*
Integral membrane protein, interacts with FtsH**
Predicted P-loop-containing kinase
GTPase SAR1 and related small G proteins*
Predicted amidohydrolase
Predicted permeases*
Uncharacterized membrane protein
Predicted Zn-dependent proteases*
Uncharacterized anaerobic dehydrogenase
Predicted transporter component*
MoxR-like ATPases
Predicted nucleotide-utilizing enzyme
Acetyltransferase (isoleucine patch superfamily)
Uncharacterized ABC-type transport system
Isopenicillin N synthase and related dioxygenases
ABC-type uncharacterized transport system
Short-chain dehydrogenases
Protein containing von Willebrand factor type A
Predicted aminopeptidases
Predicted pyrophosphatase
Predicted nucleoside-diphosphate sugar epimerase
RNA-binding proteins (RRM domain)
AT-rich DNA-binding protein
Bacteriorhodopsin
Uncharacter. protein involved in propionate catabolism
Uncharacterized protein
DMSO reductase anchor subunit
Predicted Fe-S oxidoreductases
Pirin-related protein
Predicted dioxygenase of extradiol dioxygenase
Predicted Zn-dependent protease
Predicted PP-loop superfamily ATPase
Zn-dependent hydrolases, including glyoxylases
Predicted phosphatase/phosphohexomutase
Predicted dehydrogenase
_______________________________________________________________________________________________________________
Function unknown
Predicted membrane protein*
Uncharacterized protein conserved in bacteria*
Uncharacterized conserved protein*
FOG: WD40-like repeat
Uncharacterized low-complexity proteins*
_________________________________________________________________________________________________________________________________
Defense Mechanisms
Multidrug resistance efflux pump
ABC-type antimicrobial peptide transport system
ABC-type antimicrobial peptide transport system
_____________________________________________________________________________________________________________________________ ____
Supplementary Table S5. Abundance of transcripts representing propanoate metabolism
(KEGG pathway 00640) and the TCA cycle (KEGG pathway 00020), normalized by total
possible protein-encoding sequences in each library. These ratios are shown in the table
multiplied by 104. Transcripts are labeled based on the enzyme number in the KEGG map.
Transcripts present in both pathways are shown only once. Significant differences between
Control and DMSP treatments are labeled with an asterisk (95% significance level).
_____________________________________________________________________________
Metabolism
Trancript
Control
DMSP
Control
DMSP
abundance abundance
ratio
ratio
______________________________________________________________________________
Propaonate
EC:6.4.1.3
22
42
1.49
2.64
EC:6.4.1.2
57
71
3.87
4.46
EC:6.2.1.5
87
113
5.91
7.10
EC:6.2.1.17
5
11
0.34
0.69
EC:6.2.1.1
51
68
3.46
4.27
EC:5.4.99.2
13
16
0.88
1.01
EC:4.2.1.99
0
1
0.00
0.06
EC:4.2.1.79
7
22
0.48
1.38
*EC:4.2.1.17
57
125
3.87
7.85
EC:2.6.1.18
29
44
1.97
2.76
*EC:2.3.3.5
7
27
0.48
1.70
EC:1.3.99.3
74
146
5.03
9.17
*EC:1.2.7.1
2
15
0.14
0.94
EC:1.2.1.3
73
102
4.96
6.41
EC:1.2.1.27
28
39
1.90
2.45
EC:1.1.99.8
29
34
1.97
2.14
EC:6.4.1.1
13
17
0.88
1.07
TCA cycle
EC:4.1.1.32
17
20
1.15
1.26
EC:4.2.1.2
16
27
1.09
1.70
EC:1.1.1.41
21
29
1.43
1.82
*EC:1.2.7.3
4
29
0.27
1.82
EC:2.3.1.61
25
32
1.70
2.01
EC:1.1.1.42
26
57
1.77
3.58
EC:4.1.1.49
41
59
2.78
3.71
EC:2.3.3.1
36
60
2.44
3.77
EC:1.1.1.37
47
68
3.19
4.27
EC:1.2.4.2
57
78
3.87
4.90
EC:1.8.1.4
58
89
3.94
5.59
EC:1.3.99.1
72
101
4.89
6.35
EC:4.2.1.3
91
130
6.18
8.17
EC:1.3.5.1
EC:1.3.99.13
170
0
252
3
11.55
0.00
15.83
0.19
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