1 Supplementary Information for
1
Max-Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
2
Institute for Geology, Center for Earth System Research and Sustainability, University of Hamburg, 20146 Hamburg, Germany
3
GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology and Christian- Albrechts University of Kiel, Düsternbrooker Weg 20, D-24105 Kiel, Germany
4
Department of Medicinal Chemistry, Pharmacognosy, BioMedical Centre, Husargatan 3, Uppsala University, 751 23 Uppsala, Sweden
5
Florida State University, POB 3064326, Tallahassee, FL 32306, USA
6
Wegener Institute Helmholtz Centre for Polar and Marine Research, HGF-MPG Group for Deep Sea Ecology and Technology, Am Handelshafen 12, 27570 Bremerhaven, Germany
7
MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
8
Israel Limnology and Oceanography Research, Tel Shikmona, 3108000, Haifa, Israel
9
Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
*Corresponding authors
Maxim Rubin-Blum Nicole Dubilier
Phone: 0049 (0)421 2028 905 Phone: 0049 (0)421 2028 9032 E-mail: mrubin@mpi-bremen.de E-mail: ndubilier@mpi-bremen.de
Contents:
1. Supplementary Notes
2. Supplementary Methods
3. Supplementary Tables
4. Supplementary Figures
2
3
4
± ±
5
6
7
8
9
µ µ
10
11
Supplementary Figures
5 10 20 50 100 200 500 1000 2000
0.11101001000
Branching sponge library 1 coverage
Branching sponge library 2 coverage
5 10 20 50 100 200 500 1000 2000 5000
11010010005000
Branching sponge library 2 coverage
Branching sponge library 1 coverage
5 10 20 50 100 200 500 1000 2000
0.0110100
Encrusting sponge Mictlan coverage
Encrusting sponge Chapopote coverage
2 5 10 20 50 100 200 500 1000 2000
0.0010.1101000Encrusting sponge Mictlan coverage
Encrusting sponge Chapopote coverage
2030 4050 60
% GC mitochondria
mitochondria
mitochondria
mitochondria MOX
MOX
MOX
MOX Cycloclasticus
Cycloclasticus
Cycloclasticus
Bdellovibrio
Cycloclasticus
SOX
SOX SOX/JTB23 overlap
SOX/JTB23 overlap
Branchiomonas
Branchiomonas Ekhidna
Ekhidna OCS116 clade
OCS116 clade
SAR324 clade
SAR324 clade
host
host host
host KI89A clade/Turneriella/
Cytophagales sp. overlap Bdellovibrio
KI89A clade/Turneriella/
Cytophagales sp. overlap Nitrosopumilus
Nitrosopumilus
Pseudoxanthomonas sp.
Nitrosopumilus E01-9C-26 clade
E01-9C-26 clade JTB23 clade
JTB23 clade
BD7-8 clade
BD7-8 clade KI89A clade
KI89A clade
Supplementary Figure S1 Differential sequencing coverage of > 2000 bp scaffolds from the sponge metagenomic libraries. Each circle represents a metagenomic scaffold. The circles are colored according to their GC content, the diameter of these circles is proportional to scaffold length. ‘x’ symbols represent scaffolds that contain tRNAs, crossed circles represent scaffolds that contain 16S rRNA genes. Ellipses show examples of bins chosen for reassembly of sponge MOX symbionts. The sizes of the complete bins shown here (all contigs included in the ellipse) are 2.44 Mbp for the branching sponge and 2.29 Mbp for the encrusting sponge.
12
1 m
empty mussel shells
sponges
inactive zone inactive zone
colony of vestimentiferans soft oil-soaked sediments,
gas and oil efusion, mussels
mussels sponges
sponges sponges
sponges
Supplementary Figure S2 A photomosaic of the Chapopote ‘bubble’ site where the sponges were collected (photos taken from 2.5 m above the seafloor). Areas dominated by sponges (green), mussels (red) and tubeworms (yellow) are highlighted.
13
Methylomicrobium/Methylobacter/Methylosarcina/Methylovulum/Methylosoma spp.
Methylomarinum vadi (NR 112675.1) Methylomonas spp.
H. (S.) methanophila Mictlan MOX (this study) H. (S.) methanophila Chapopote MOX (this study)
H. (S.) methanophila Chapopote MOX (HE814582.1) H. (S.) methanophila Chapopote MOX (HE814575.1) H. (S.) methanophila Chapopote MOX (HE814569.1)
MMG2 bacterium, Haakon Mosby Mud Volcano (AJ704662.1)
MMG2 genome E33, North Sea sediment enrichment (Vekeman et al. 2016)
MMG2 bacterium, hydrocarbon seep, New Zealand (JF268393.1) MMG2 bacterium, hydrocarbon seep, New Zealand (JF268387.1) MMG2 bacterium, hydrate ridge, Cascadia Margin (AJ535221.1)
MMG2 bacterium, poecilosclerid sponge, Gulf of Mexico (AB453739.1) MMG2 bacterium, hydrocarbon seep, New Zealand (JF268343.1)
MMG1 - Methyloprofundus sedimenti and the symbiotic MOX of Bathymodiolus spp.
Cycloclasticus spp.
Methylosphaera hansonii (NR_026033.1)
MMG3 Methylophaga spp.
0.02
I. methanophila Chapopote MOX (this study)
MMG2 symbiont of squat lobster Shinkaia crosnieri (AB476240.1)
> 90%
> 50%
Bootstrap support
MMG2 symbiont of folliculinid ciliate, Guaymas Basin (KU896787.1)*
MMG2 symbiont of Siboglinum cf. poseidoni (FR729025-7)*
MMG2 symbiont of Cladorhiza methanophila (SRA:SRR4269900.185564.1)*
MMG2 symbiont of Cladorhiza methanophila (SRA:SRR4269900.36609.1)*
MMG2 symbionts
MMG2 free-living/
not reported as symbiont
‘Methylomonadaceae’ I (Methylococcaceae)
‘Methylomonadaceae’ II (Methylococcaceae)
MMG1
Supplementary Figure S3 Phylogeny of the 16S rRNA genes from the symbiotic MOX of sponges collected at the Campeche and Mictlan seeps. The dataset included metagenomic 16S rRNA gene
sequences from this study and sequences from the NCBI database (94 sequences total). Bootstrap values below 50% are not shown. The tree is drawn to scale, with branch lengths representing the number of substitutions per site. The analysis included 1,262 positions. The genome of the North Sea sediment enrichment genome D14 lacked the fully assembled 16S rRNA gene sequence. Star marks the 16S rRNA gene sequences which were excluded from the tree calculation due to its short length, which would have hindered the phylogeny resolution, and whose position in the tree was estimated based on a phylogeny of separately aligned truncated sequences. MMG is Marine Methylotrophic Group.
14
Gulf of Mexico, oil spill clone P192-3 (HQ738557.1) Gulf of Mexico, oil spill clone P230-1 (HQ738566.1)
Jaco Scarp , water column above methane seep, clone Jaco 0.2 27 (FJ858349.1)
Costa Rica oxygen minimum zone, hydrothermal seep clone CR-OMZwc A9 (JX569111.1) Gulf of Mexico, oil spill clone wcpmoA OC242 30 (KJ543506.1)
Gulf of Mexico, oil spill clone wcpmoA OC102 3 17 (KJ543512.1) Gulf of Mexico, oil spill clone wcpmoA OC103 003 (KJ543509.1 ) Gulf of Mexico, oil spill clone P222-1 (HQ738561.1)
Rainbow vent field on the Mid-Atlantic Ridge clone PMO-I (AY354047.1 ) I. methanophila Chapopote 2 (BSC2) MOX
I. methanophila Chapopote 1 (BSC1) MOX H. (S.) methanophila Mictlan (ESM) MOX H. (S.) methanophila Mictlan (ESM) MOX
Republic of the Congo, organic-rich lobe sediments 492CT5 pmoA B8 (KY351428.1) Guaymas Basin, Folliculinid ciliate symbiont clone GY DR399 (KX021876.1)
USA, Del Mar Seep, Folliculinid ciliate symbiont clone SD DR470 7274 (KX021877.1) Hydrate Ridge methane seep clone HR AT18-10 FA (KX021875.1)
New Zealand, methane seep, clone NZ 45 pmoA 68 (KC751370.1) Kuroshima Knoll, southern Ryukyu Arc, methane seep clone:Kuro-pmoA-17 (AB176938.1)
New Zealand, methane seep, clone NZ 45 pmoA 68 (KC751370.1) Escarpment cold seep site, clone BR1pmoA30 (EU982958.1)
Siboglinum cf. poseidoni symbiont, clone W10 M11 (FR729005.1)
Republic of the Congo, organic-rich lobe sediments clone 492CT5 pmoA A8 (KY351416.1) Republic of the Congo, organic-rich lobe sediments 491CT12 pmoA C6 (KY351183.1) Escarpment cold seep site, clone BR1pmoA11 (EU983006.1)
Methylococcaceae bacterium SF-BR (AB453965.1 )
Republic of the Congo, organic-rich lobe sediments clone 486CT9 pmoA G10 (KY351033.1) Republic of the Congo, organic-rich lobe sediments clone 486CT9 pmoA E5 (KY351009.1) North Sea MMG2 isolate D14 (LT555367.1 )
North Sea MMG2 isolate E33 (LT555366.1)
North American continental margin methane sep clone Bubsed 2H (EU444857.1) Shinkaia crosnieri epibiont, clone ihePR661 145 (AB794867.1)
MMG1 - Methyloprofundus sedimenti and Bathymodiolus spp. MOX Methylomarinum vadi strain IT-4(AB302947.2 )
Methylomarinum vadi strain: T2-1 (AB453964.1) Methylomarinum sp. SSMP1 (KU740209.1)
Methylobacter sp. BB5.1 (AF016982.1)
Methylobacter tundripaludum (AJ414658.1) Methylomicrobium sp. 5B (AF307139.1 )
Methylomicrobium japanense (AB253367.1) Methylomicrobium alcaliphilum (FO082060.1) Methylovulum psychrotolerans (CP022129.1)
Methylovulum miyakonense (AB501285.1) Methylosoma sp. TFB (KX282487.1) 0.050
Methylomonas spp.
Branch bootstrap support:
> 90%
> 80%
> 50%
MMG2 symbionts
MMG1 MMG2 free-living/ not reported as symbiont
‘Methylomonadaceae’ I
‘Methylomonadaceae’ II (Methylococcaceae)
(Methylococcaceae)
Supplementary Figure S4a Phylogeny of pmoA genes from the symbiotic MOX of sponges collected at the Campeche and Mictlan seeps. The dataset included pmoA sequences from this study and from the NCBI database (54 nucleotide sequences total). The tree is drawn to scale, with branch lengths
representing the number of substitutions per site. The analysis included 344 positions.
15
Methylmonas denitrificans Methylomo
nas ko yamae
Methylomonas met hanica
Methylmo nas lenta
Methylomarinum vadi North S
ea MM G2 g
enome E33
North Sea MM
G2 genome D14
Bathymodiolus sp. SMAR MOX Methyloprofundus sedimenti
Bathymodiolus azoricus MOX Bathymodiolus platifrons MOX I. methanophila MOX H. (S.)
methanophila Chapop ote MOX H. (S.) met
hanophila Mictlan MO X Methylobacter l
uteus Methy
lobacter w hitten
buryi Methylom
icrob ium
alcali philum Meth
ylom icrob
ium bur
yatense
etM
lovhy
ulum
iy m
onak
ense
luvulohyetM
m p
sychrotolerans
Methylosarcina fi bra ta
Methylosarcina lac
us
Methylomicrobium agile
Nitrosococcus halophilus Nitrosococcus oceani Nitrosococcus watsonii Methyloglobulus morosus Methylocystis rosea Methylocystis bryophila
Beijerinckiaceae sp.
Methylomicrobium agile Methylobacter tun
dripaludum Methylobacter l
uteus Methylov
ulum miyakonense Methylmo
nas d enitrifica
ns Methylomo
nas met hanica Candida
tus N itros
pira ni trific
ans Can
dida tus N
itros pira ni
trosa
0.20
Methylobacter tundripaludum
AmoCAB Am
oCAB
PxmABC PmoCAB Branch bootstrap support:
> 95%
> 80%
> 50%
‘Methylomonadaceae’ I
‘Methylomonadaceae’ II
MMG1 MMG2 free-living
MMG2 symbionts
‘Methylomonadaceae’ II and I
Supplementary Figure S4b Phylogeny of concatenated PmoCAB and PxmABC proteins (39 amino acid sequences total). Sequences were first aligned for each subunit, following concatenation of individual alignments in the ABC order. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis included 886 positions.
16
bc
f cf cf
f e f
embryo
embryo
5 μm
n
n n
bc cf
cf cf
f
f sp
sp
sp
sp sp
sp
n f
f cf
cf
cf bcbc sp
bc bc
sp bc sp
sp
5 μm 20 μm
a b c
d
ma mi
5 μm bl
li
1 μm li
li li
5 μm
n
he ho co
MOX
Supplementary Figure S5 TEM images of H. (S.) methanophila embryo tissue a, Overview of an embryo.
mi=micromere cells, ma=macromere. b, electron-dense blastomeres (bl) with lipid droplet inclusions (li).
c, Lipid droplet inclusions in blastomeres. d, nucleolated larval cells with homogeneous (ho) and heterogeneous yolk (he), n = nucleus, co = collagen fibers. e and f, methane-oxidizing symbionts accumulated between follicle-like cells (f) and embryo, and on the periphery of follicle-like cells.
bc=bacteria in bacteriocytes; cf= collagen fibrils; n=nucleus; sp=sponge cell.
17
1290 618 823*(97)
608* 7819*
2385*
(1361)***
11 522 733 70
10 31
117 118 44
Sponge MOX symbionts
(4 genomes) MMG1 MOX
(3 genomes) North Sea
enrichment MMG2 (2 genomes)
Methylomonadaceae isolates (18 genomes) 1402
119 13
15 14
298 45
344 2
109
137 8
2 111 7
I. met hano
phila C hapop
ote 1 M OX
I. methanophila Chapopote 2 MOX H. (S.) methanophila Mictlan MOX
H. (S.) met
hanophila Chapopote MOX
a
b
**
Supplementary Figure S6 Pangenome analysis of methane-oxidizing bacteria (MOX). Orthologous gene counts are shown. a, Comparison of the sponge MOX symbiont genomes assembled in this study. b, Comparison between the genomes of the sponge MOX symbionts and related free-living and symbiotic MOX. “Sponge MOX symbionts” group includes the genomes of MOX from the four sponge individuals analyzed in this study. “North Sea enrichment MMG2” group includes the two genomes of the Marine Methylotrophic Group 2 bacteria enriched from the North Sea sediments. “Methylomonadaceae isolates”
group comprises the 18 representative genomes of Methylomonadaceae (main text, Figure 4), which were downloaded from NCBI. “MMG1” group comprises genomes of Methyloprofundus sedimenti, as well as those of MOX hosted by mussels Bathymodiolus sp. SMAR and B. platifrons. * clade-specific genes; **
unique to the sponge MOX symbiont core genome; *** mussel symbionts only (not including M.
sedimenti).
18
H. (S.) methanophila
BGC0000837: Arylpolyene Vf biosynthetic gene cluster Vibrio fischeri (40% of genes show similarity) BGC0000836: Arylpolyene Ec biosynthetic gene cluster Escherichia coli (25% of genes show similarity)
halogenase
VF0841
c1204
beta-ketoacyl synthase beta-ketoacyl synthase short-chain dehydrogenase
acyl carrier protein (ACP1) acyl carrier protein (ACP2) acyl transferase
histidine ammonia-lyase
VF0860
c1186
1 2 3 4 5 log(TPM+1)
Supplementary Figure S7: Aryl polyene synthesis cluster in H. (S.) methanophila MOX symbiont genome. Vibrio fischeri and Escherichia coli Vf and Ec aryl polyene synthesis domains are shown as references. Homologs are shown in the same color. The second alignment is colored according to the average expression values of respective genes (color legend is shown in figure on bottom right).
19
1 2500 5000 7500 10000 12500 14616 bp
1 2500 4603 bp
consensus MPI
consensus MPI query 1 query 1
query 1
H. (S.) methanophila Cycloclasticus
I. methanophila methane-oxidizing symbiont H. (S.) methanophila methane-oxidizing symbiont
Autotransporter beta-domain DUF285: related to leucine rich repeats Cadherin-like beta sandwich domain
Fibronectin type 3 domain PKD domain
consensus MPIquery 2 query 2
a
b
ORU94421.1 (98%) (94%)
(86%)
ORU92747.1 (81%) ORU91689.1 (51%) ORU94544.1 (75%) ORU94587.1 (45%) ORU94767.1 (42%) (87%)
(84%) (84%) (76%) (85%) (46%) (85%) (62%) (46%)
(51%) (57%) (57%) (48%) (43%) (37%) (47%) (43%)
ORU91839.1 (59%)
Supplementary Figure S8 (a,b) Structure of and occurrence of eukaryote-like protein (ELP)-encoding sequences in the genomes of sponge symbionts (a, b) and in sponge metagenomes (c, d). a, The structure of the longest ELP in H. (S.) methanophila MOX symbiont. Eukaryote-like domains (ELDs), which comprised leucine-rich repeats and cadherin-like domains, as well as an autotransporter beta-domain, which encodes a pore-forming element of the type V secretion system are shown. BLAST hits for this sequence (query 1) within the genome of H. (S.) methanophila MOX and Cycloclasticus symbionts are shown below. b, The structure of the longest ELP in I. methanophila MOX symbiont. Eukaryote-like domains (ELDs), which comprised leucine-rich repeats cadherin-like, polycystic kidney disease (PKD) and fibronectin type 3 domains are shown. BLAST hits for this sequence (query 2) within the genome of H. (S.) methanophila MOX are shown below. In panels a and b, identity values at amino acid level
between the query and the sequences identified by BLAST are shown in parentheses. Consensus sequence and the mean pairwise identity (MPI) over all pairs in the column are included (100%, green; 30-99%, yellow; below 30%, red).
20
Supplementary Figure S8 (c, d) Structure of and occurrence of eukaryote-like protein (ELP)-encoding sequences in the genomes of sponge symbionts (a, b) and in sponge metagenomes (c, d). c, d: Scaffolds that contain ELPs (green circles) in the metagenomes of H. (S.) methanophila (c) and I. methanophila (d), revealed by BLAST analysis using the longest assembled ELP genes as queries. In panel c, red circles mark scaffolds that contain the autotransporter beta domains identified by BLAST using the respective partial ELP sequence as a query.
5 10 20 50 100 200 500 1000 2000
5 10 20 50 100 200 500 1000 2000
0.0110100H. (S.) methanophila Chapopote coverage
H. (S.) methanophilaMictlan coverage
0.11101001000
I. methanophila library 2 coverage
mitochondria MOX
Cycloclasticus
host
Nitrosopumilus
E01-9C-26 JTB23
SUP05 BD7-8
KI89A
mitochondria MOX
CycloclasticusAqs2-like SUP05/JTB23 overlap
Ekhidna OCS116
SAR324 host
KI89A/Turneriella/
Cytophagales sp. overlap Bdellovibrio
Nitrosopumilus
2030 4050 60
% GC
2030 4050 60
% GC scaffold with an ELP BLAST hit
scaffold with an autotransporter beta domain BLAST hit
scaffold with an ELP BLAST hit
I. methanophilalibrary 1 coverage
c
d
21
H. (S.) methanophila Mictlan MOX H. (S.) methanophila Chapopote MOX I. methanophila Chapopote MOX
MMG1 - Methyloprofundus sedimenti and Bathymodiolus spp. MOX Thermithiobacillus tepidarius (WP_028989412.1)
Thioalbus denitrificans (WP_114279615.1)
Sedimenticolaceae (free living Sedimenticola sp. + symbionts of tubeworms and bivalves) Candidatus Thioglobus autotrophicus (WP_053951905.1)
Nitrosomonadales bacterium (PWB46437.1) Methylophilaceae spp.
Rhodocyclaceae spp.
Thiohalorhabdus denitrificans (WP_054965502.1) Burkholderia pseudomallei (WP_085538356.1)
Nitrosomonadales spp.
Beijerinckiaceae sp. (WP_009337376.1 ) Thioalkalivibrio paradoxus (WP_006747611.1) Thioalkalivibrio nitratireducens (WP_015258541.1) Methylococcaceae bacterium AMb10-2013 (PZN76546.1)
Methylosarcina fibrata (WP 020564491.1) Methylomonas methanica (WP 064044676.1) Methylobacter tundripaludum (WP_104423249.1)
Rhodobacteraceae spp.
Kordimonadales spp.
Thioglobaceae (SUP05) symbionts of Bathymodiolus spp. and clams Oceanospirillales spp.
0.10
Methylomonas denitrificans (WP_036278592.1) Crenothrix polyspora (WP 087145999.1)
Crenothrix sp. D3 (TE97995.1) Branch bootstrap support:
> 90%
> 50%
‘Methylomonadaceae’
MMG1 MMG2 sponge symbionts
Supplementary Figure S9 Phylogeny of narG genes from the symbiotic MOX of sponges collected at the Campeche and Mictlan seeps (highlighted in green). The dataset included narG sequences from this study and from the NCBI database (73 amino sequences total). The tree is drawn to scale, with branch lengths representing the number of substitutions per site. The analysis included 1167 positions.
22
retention time
intensity
C16:1w8/w7
C16:2D5,9
istd C26:3D5,9,?
C14
C16:1w6/w5
C18:1w8/w7
C20:1w8/w7 C22:1w8/w7C24:1w8/w7
C26:3D5,9,?
C26:2D5,9
C26:1w8/w7
C26:3D5,9,? (brominated)
C26:2D5,9 (brominated)
16:2D5,9 istd
C14
24:1ω9
C28:3D5,9,?
C28
C26
C24 22:1ω9
C22 22:1ω7 20:1ω8
20:1ω7 20:1ω6
C20
24:1ω7 18:1ω7
20:2∆5,9 18:1ω9
18:2∆5,9
C18
C17
C15 16:1ω8 16:1ω7/6/5
a
b
²⁸D⁵,²⁴
retention time
intensity
istd
istd c
c c 27∆5
²⁷D⁵,²⁴
²⁹D⁵,²⁴E
²⁹D⁵,²⁴Zcdiplopterol
²⁸D⁵,²⁴ 27D5
diplopterol
c c c c
c
d
C16
Supplementary Figure S10 Partial gas chromatograms (total ion current) of fatty acid (a, b) and alcohol fractions (c, d) in H. (S.) methanophila (a, c) and I. methanophila (b, d). Istd= internal standard. Symbols and detailed nomenclature; fatty acids (a, b): gray circles= saturated fatty acids, white circles=
monounsaturated fatty acids, black stars= demospongic acids, red stars= brominated demospongic acids, white triangle= iso-fatty acids, black triangle= anteiso-fatty acids, ω= position of double bond counting from the methyl-end of the chain, Δ= position of double bonds counting from the carboxylic acid end.
Nomenclature alcohols (c, d): 27Δ5=cholest-5-en-3β-ol (cholesterol), 27Δ5,24= cholesta-5,24-dien-3β-ol (desmosterol), 28Δ5,24= 24-methylcholesta-5,24-dien-3β-ol, 29Δ5,24= 24-ethylcholesta-5,24E-dien-3β-ol (fucosterol), 28Δ5,24= 24-ethylcholesta-5,24Z-dien-3β-ol (iso-fucosterol), c= contaminants.
23
GADP Pyruvate
dxs 1-deoxy-D-xylulose 5-phosphate synthase
DOXP
ispC 1-deoxy-D-xylulose 5-phosphate reductoisomerase MEP
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase ispD
CDP-ME
4-diphosphocytidyl-2-C-methyl-D-erythritol kinase ispE
CDP-MEP
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase ispF
MEcPP
4-hydroxy-3-methyl-2-(E)-bute- nyl-4-diphosphate synthase ispG
HMB-PP
4-Hydroxy-3-methyl-2-(E)- butenyl-4-diphosphate reductase ispH
Isopentenyl pyrophosphate (IPP) ? Dimethylallyl pyrophosphate (DMAP)
ispA ispB Farnesyl/octaprenyl diphosphate synthase
Farnesyl/octaprenyl diphosphate
Farnesyl-diphosphate farnesyltransferase fdft
Squalene-hopene cyclase Squalene
shc
The non-mevalonate pathway (MEP/DOXP)
Squalene monooxygenase 2,3-oxidosqualene sterol cyclase
Sterol 14-demethylase
4-methylated sterols
1 2 3 4
hpnG Hopanoid-associated phosphorylase
Hopanoid biosynthesis associated radical SAM protein HpnH Present in Bathymodiolus MOX
hpnH
Aminotransferase in hopanoid biosynthesus cluster argD
hpnN Hopanoid biosynthesis associated RND transporter like protein HpnN MOX hopanoid
Hopanoid synthesis
Scale [Log (TPM+1)]
Supplementary Figure S11 Hopanoid synthesis in sponge MOX symbionts. The reconstruction is based on genomes of I. methanophila and H. (S.) methanophila MOX and on transcriptomes of H. (S.)
methanophila MOX. Enzymes and their subunits are abbreviated with the name of the encoding gene.
Boxes are colored according to the expression value of a respective transcript (color legend for expression values is shown on the bottom of figure).
24