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. 2015 Feb 27;14(5):1301–1322. doi: 10.1074/mcp.M114.043166

Table II. Proteins identified by LCMS/MS from various fractions of the soybean symbiosome. A minimum of two peptides were identified in one or more biological samples for all proteins indicated. Proteins are grouped according to functional classification by MapMan. Information about protein function is compiled from the genome annotation (www.phytozome.net) and from the top matches in NCBI (www.ncbi.nlm.nih.gov). Protein names are as annotated in Phytozome (www.phytozome.net) and data are compiled from the August 2012 release of the G. max genome (except peribacteroid space (PBS) which is from the previous genome release). An asterisk (*) indicates that the protein, or a close homologue, has been identified in a previous symbiosome membrane (SM) or PBS proteomic study. The presence of a predicted GPI-anchor sequence (56) within the protein is indicated by G. The presence of a predicted signal peptide (55) on the protein is indicated by SP. Sample/s in which the protein was present are denoted by the total number of spectral counts for each sample in columns corresponding to (SM) (bicarbonate stripped and chloroform-methanol extractions pooled), SM peripheral (SMP) and PBS. Percentage coverage (%C) is the maximum percentage of a protein to which peptides have been mapped in a biological sample and #P indicates the number of unique peptides assigned to the protein match. Membrane topology was predicted by three bioinformatic suites: (i) SOSUI (http://harrier.nagahama-i-bio.ac.jp/sosui/), (ii) TMHMM (http://www.cbs.dtu.dk/services/TMHMM/) and (iii) TopPred2 (http://bioweb.pasteur.fr/seqanal/interfaces/toppred.html), with the number of predicted transmembrane domains indicated. Predicted localisation (L) is a composite result of several sub-cellular localization prediction algorithms (TARGETP, PREDOTAR, Plant mpLOC and MulitLOC) and proteins were classified as either Chloroplastic (C), Endoplasmic Reticulium/Secretory Pathway (ER/SP), Mitochondrial (M), Peroxisomal (P), or Unknown (U). Gene expression, expressed as normalized reads/Kb/Million, in nodule tissue (N) is indicated for each gene and the expression profile across other soybean tissues (E) is denoted significant (S; summed transcript number > 40 across non-nodule tissues), low (L; summed transcript number < 40 across non-nodule tissues), or ns where expression is nodule-specific (66).

Potential function Protein name SM SMP PBS %C #P i ii iii L N E
C and CHO Metabolism
    Serine hydroxymethyl-transferase 3 Glyma13g29410.1 46 63 21 17 6 0 0 1 C 460 S
    Sucrose synthase 4 Glyma17g05067.1* 18 2 5 4 0 0 1 U
    Triosephosphate isomerase Glyma03g34300.1 7 15 3 0 0 0 C 129 S
    Transketolase Glyma03g03200.1 6 4 2 0 0 1 C 35 S
    Trehalase 1 Glyma05g36580.1SP 10 7 3 0 1 1 ER/SP 43 S
Glycolysis
    Glyceraldehyde-3-phosphate dehydrogenase Glyma18g01330.1 6 8 2 0 0 0 U 291 S
    Glyceraldehyde-3-phosphate dehydrogenase of plastid 2 Glyma16g09020.1 12 7 2 0 0 0 C 70 S
Fermentation
    Aldehyde dehydrogenase (NAD+) Glyma14g24140.1 62 8 4 1 0 1 C 11 S
Mitochondrial
    ADP/ATP carrier 2 Glyma15g42900.1* 40 17 8 0 3 3 U 171 S
    F0F1-type ATP synthase, beta subunit Glyma10g41330.1* 49 22 9 4 0 0 0 M 93 S
    Lactate/malate dehydrogenase family protein Glyma12g19520.1* 27 35 5 0 0 3 M 171 S
    Lactate/malate dehydrogenase family protein Glyma06g34190.1* 18 26 1 0 0 3 M 197 S
    Malate dehydrogenase Glyma05g01010.1* 2 6 2 0 0 3 C 24 S
    Mitochondrial carrier protein Glyma08g16420.1* 37 17 1 0 3 4 U 63 S
    Mitochondrial substrate carrier family protein Glyma05g29050.1 4 9 2 0 0 3 U 51 S
    Mitochondrial substrate carrier family protein Glyma06g07310.1 17 6 2 0 0 4 U 126 L
    Mitochondrial substrate carrier family protein Glyma08g24070.1 6 6 2 0 3 3 U 44 L
    Ubiquinol–cytochrome c reductase. Glyma05g07020.1 5 16 3 1 0 2 M 8 S
Cell wall
    Cellulose synthase Glyma08g44310.1 13 7 4 7 8 7 U 82 S
    Cellulose synthase-like B3 Glyma12g31800.1 5 4 3 2 5 6 U 58 L
    FASCICLIN-like arabinogalactan protein 17 precursor Glyma12g31691.1G, SP 24 9 2 0 1 1 U
    FASCICLIN-like arabinogalactan-protein 10 Glyma09g40420.1 G, SP 23 9 3 3 0 3 ER/SP 82 S
    Glycosyl hydrolase family 3 protein Glyma15g13620.1 G, SP 19 21 11 5 2 1 2 ER/SP 14 L
    Pectin lyase-like superfamily protein Glyma07g07290.1SP 28 18 5 1 0 1 ER/SP 90 ns
    Xyloglucan:-xyloglucosyl transferase Glyma13g01140.1SP 95 15 3 1 1 1 ER/SP 3 L
Lipid metabolism
    Favodoxin-like quinone reductase 1 Glyma07g30750.1 26 19 3 0 0 1 U 14 S
    Neutral/alkaline non-lysosomal ceramidase Glyma18g07680.2G, SP 51 9 5 3 1 0 3 U 10 L
    Neutral/alkaline non-lysosomal ceramidase Glyma02g47420.1 G, SP 21 3 2 3 0 5 U 6 S
    Phospholipase D1 Glyma01g36680.1 18 8 5 0 0 0 U 11 S
    Quinone reductase family protein Glyma01g38400.1 9 10 2 0 0 1 U 16 S
    UDP-Glycosyltransfer-ase superfamily protein Glyma03g19751.1 5 5 3 0 0 0 U
Nitrogen metabolism
    Glutamate dehydrogenase 3 Glyma02g07940.1 9 6 2 0 0 1 U 0 L
    Glutamine synthetase; nodulin 61 Glyma10g06810.1 SP 35 8 6 13 4 1 0 2 ER/SP 417 L
    NADH-dependent glutamate synthase 1 Glyma06g13280.2 3 1 3 0 0 5 U 54 S
Amino acid metabolism
    d-3-phosphoglycerate dehydrogenase Glyma10g40750.1 55 9 4 0 0 0 C 184 S
    d-3-phosphoglycerate dehydrogenase Glyma13g44970.1 15 5 2 0 0 0 C 634 L
    Glycine dehydrogenase (decarboxylating) Glyma14g10820.1 7 3 1 0 0 3 M 10 S
    Glycine dehydrogenase (decarboxylating) Glyma17g34690.1 10 3 3 0 0 3 M 103 S
Hormone metabolism
    Auxin Conjugate Hydrolase M20/M25/M40 family protein Glyma08g21040.1 81 64 35 25 6 0 1 3 ER/SP 345 ns
    Carotenoid cleavage dioxygenase 1 Glyma13g27220.1 21 9 4 1 1 1 U 11 S
    Lipoxygease l-4 Glyma13g42330.1 38 6 5 1 0 1 U 164 S
Stress
    Adenine nucleotide alpha hydrolases-like superfamily protein Glyma02g17470.3 24 22 2 0 0 1 U 1278 S
    Chaperone protein htpG family protein Glyma14g40320.1 SP 6 2 2 1 0 1 ER/SP 16 S
    Chitinase A Glyma20g30450.1G, SP 47 4 21 20 3 0 1 2 ER/SP 72 L
    Domain of unknown function (DUF221) Glyma02g43910.1 11 6 4 10 9 10 U 6 S
    Domain of unknown function (DUF221) Glyma07g39320.1 15 4 3 9 10 10 ER/SP 13 S
    Heat shock protein 70 (Hsp 70) family protein Glyma05g36600.1* 19 4 3 0 1 1 U 4 S
    Heat shock protein 70 (Hsp 70) family protein Glyma18g52650.2* 12 5 2 0 0 2 U 14 L
    Respiratory burst NADPH oxidase Glyma10g29280.1 78 11 9 4 4 6 U 4 L
    Respiratory burst NADPH oxidase Glyma20g38000.2 56 8 2 4 4 6 U 5 L
Redox
    Catalase 2 Glyma04g01920.1 7 5 2 0 0 0 U 89 S
    Cytochrome B5 Glyma04g41010.1 33 39 1 1 1 1 M 122 S
    Cytochrome B5 isoform E Glyma06g13840.5 29 28 3 1 1 1 M 117 S
    Leghemoglobin Glyma10g34280.1* 25 29 40 2 0 0 0 U 12309 L
    Leghemoglobin Glyma20g33290.1* 51 10 25 40 2 0 0 0 U 7046 ns
    Leghemoglobin Glyma10g34260.1* 51 10 34 40 4 0 0 0 U 6913 ns
    Leghemoglobin Glyma10g34290.1* 74 59 43 50 5 0 0 0 U 55714 L
    Protein disulfide isomerase-like 1–2 Glyma04g42690.1* SP 18 10 4 1 1 1 ER/SP 48 S
    Protein disulfide isomerase A1 Glyma06g12090.1* SP 17 8 2 1 0 1 ER/SP 13 S
Nucleotide metabolism
    Adenylosuccin-ate lyase Glyma02g42130.1 25 5 4 1 0 0 C 31 L
    Adenylosuccin-ate lyase Glyma14g06780.1 24 8 5 4 1 0 0 C 62 S
    Glutamine phosphoribosyl-pyrophosphate amidotransferase Glyma04g00930.1 19 4 2 0 0 0 C 932 L
    Phosphoribosyl-amidoimidazole-succinocarbox-amide synthase Glyma14g35690.1 4 8 2 0 0 0 U 183 L
    Phosphoribosyl-amine–glycine ligase Glyma10g29780.1 3 7 2 0 0 1 U 163 S
    Phosphoribosyl-aminoimidazole carboxylase Glyma20g36934.1 18 7 3 0 0 1 C
    Phosphoribosyl-aminoimidazole carboxylase Glyma10g30611.1 20 16 7 1 0 0 2 C
    Phosphoribosy-lformylglycin-amidine synthase Glyma18g04070.1 14 4 1 0 0 2 C 76 S
    Phosphoribosyl-formylglycin-amidine synthase Glyma11g34241.1 34 22 5 6 0 0 1 C
    Uricase (nodulin 35) Glyma10g23790.1 167 107 32 66 15 0 0 0 P 2632 S
RNA regulation
    Remorin family protein Glyma08g01590.1 53 20 4 0 0 0 U 323 ns
    Remorin family protein Glyma05g37990.2 32 15 1 0 0 0 U 243 ns
DNA synthesis
    Histone superfamily protein Glyma02g38921.1 6 15 2 0 0 0 U
Protein synthesis
    GTP binding elongation factor Tu family protein Glyma05g11630.2 30 7 2 0 0 0 U 113 S
    Large subunit ribosomal protein L12e Glyma10g06040.1 24 22 3 0 0 0 U 30 S
    Ribosomal protein L5 B Glyma07g06580.3 4 11 2 0 0 1 U 25 S
Protein targeting
    Insulinase (Peptidase family M16) protein Glyma05g36040.1 4 4 2 0 0 2 M 5 S
    Insulinase (Peptidase family M16) protein Glyma07g01720.1 4 4 2 0 0 2 M 19 S
    Insulinase (Peptidase family M16) protein Glyma08g46020.1 3 4 2 0 0 1 M 98 S
Protein postranslational modification
    Protein kinase superfamily protein Glyma05g02080.1 6 5 1 0 0 1 U 16 S
    Protein kinase superfamily protein Glyma10g44212.1 23 27 6 0 0 0 U
    Protein phosphatase 2C Glyma05g24410.1 64 18 1 0 0 0 U 10 S
    Protein phosphatase 2C Glyma08g19090.1 87 30 7 0 0 0 U 11 S
    Protein phosphatase 2C family protein Glyma06g10820.1 9 11 2 0 0 0 U 6 L
    Serine/threonine protein kinase Glyma19g27110.1 29 8 2 0 0 0 U 23 L
Protein degradation
    Aspartyl protease Glyma15g41420.1 SP 140 49 66 31 7 0 0 4 ER/SP 278 ns
    Eukaryotic aspartyl protease family protein Glyma08g17680.1 SP 13 27 20 4 0 0 2 ER/SP 108 ns
    Matrix metalloproteinase Glyma01g04370.1G, SP 19 9 3 2 1 1 ER/SP 5 ns
    Membrane-anchored ubiquitin-fold protein 2 Glyma08g26430.1 5 18 2 0 0 0 U 3 S
    Prolyl oligopeptidase family protein Glyma20g23350.1 3 3 1 1 1 1 U 17 S
    Saposin-like aspartyl protease family protein Glyma10g28370.1 SP 10 5 2 1 1 1 ER/SP 21 S
    Serine carboxypeptid-ase-like 50 Glyma07g34300.1 SP 5 7 2 0 1 3 ER/SP 21 L
    Subtilase family protein Glyma17g14270.1 SP 35 15 5 0 0 5 ER/SP 95 ns
    Subtilisin/kexin-related serine protease Glyma05g03760.1 49 102 98 30 13 1 1 4 U 310 ns
    Subtilisin/kexin-related serine protease Glyma14g06970.1 SP 6 43 21 7 1 0 5 ER/SP 315 L
    Subtilisin/kexin-related serine protease Glyma19g44060.1 73 14 8 1 1 4 ER/SP 429 L
    Ubiquitin family protein Glyma01g03570.1 51 30 4 0 0 0 U 71 S
    Ubiquitin family protein Glyma05g38330.2 20 26 3 0 0 0 U 14 S
Protein folding
    Chaperonin precursor Glyma08g18760.1 43 11 10 4 0 0 0 C 57 S
    Chaperonin-60alpha Glyma11g20180.1 35 12 6 0 0 0 U 27 S
    Heat shock protein 60 Glyma10g25630.1 41 7 4 0 0 1 M 6 S
Protein glycosylation
    Oligosaccharyl-transferase Glyma11g12800.1 6 6 2 1 1 2 U 11 S
Signalling
    ATP-binding protein Glyma14g39550.1 SP 60 11 2 2 2 2 ER/SP 44 S
    Autoinhibited Ca2+ -ATPase, isoform 8 Glyma09g06890.2 11 4 3 10 9 7 U 3 S
    BCL-2-associated athanogene 7 Glyma09g36560.1 18 12 4 0 0 0 U 91 S
    Calcium-dependent lipid-binding (CaLB domain) family protein Glyma03g02370.1 11 4 2 3 3 4 ER/SP 9 S
    Calcium-dependent lipid-binding (CaLB domain) family protein Glyma10g35410.1 5 6 3 1 1 2 ER/SP 82 L
    Calcium-dependent lipid-binding (CaLB domain) family protein Glyma11g11470.1 6 7 3 1 1 1 ER/SP 14 S
    Calnexin Glyma04g38000.1 SP 17 11 1 3 3 3 ER/SP 28 S
    Calnexin Glyma06g17060.1 SP 20 11 4 3 3 3 ER/SP 32 S
    Calreticulin 1b Glyma10g28890.2 SP 20 2 4 0 0 1 ER/SP 107 S
    Endomembrane-type CA-ATPase 4 Glyma03g33240.1 62 8 2 8 8 9 U 29 S
    Endomembrane-type CA-ATPase 4 Glyma19g35960.1 57 10 8 8 8 10 U 37 S
    GTPase Rab homolog G3D (Rab7) Glyma07g00660.1* 11 10 2 0 0 0 U 5 S
Glyma08g21940 6 S
Glyma11g12630 9 S
Glyma12g04830* 30 S
    GTPase Rab2, small G protein superfamily Glyma09g01950.1 18 17 3 0 0 0 U 5 S
Glyma15g12880.1 5 S
Glyma02g10450.1 9 S
    Leucine-rich repeat ATP-binding protein kinase Glyma02g41160.2 SP 35 11 5 2 2 2 ER/SP 20 S
    Ras-related small GTP-binding family protein (Rab8, RABE1) Glyma10g43590 19 10 2 0 0 0 U 13 S
Glyma11g15120 7 S
Glyma12g07070 15 S
Glyma18g52450 7 S
Glyma20g23210 10 S
Cell vesicle transport
    SNARE protein Syntaxin 131 Glyma13g38370.1 16 13 3 1 1 1 U 6 L
Transport ATPase
    P-type H+ATPase Glyma19g02270.2* 196 17 14 10 8 9 U 13 L
    P-type H+ATPase Glyma04g34370.1* 120 9 2 10 8 12 U 11 S
    P-type H+ATPase Glyma06g20200.1* 59 9 2 10 8 12 U 3 S
Peptides and oligopeptide transport
    GmNPF8.6 Oligopeptide transport related Glyma02g38970.1* 19 9 4 11 10 11 U 31 ns
    GmNPF5.25 Oligopeptide transport related Glyma11g34600.1* 21 6 5 12 10 11 U 61 ns
    GmNPF1.2 Oligopeptide transport related Glyma08g04160.4 51 9 5 12 10 11 U 155 ns
    GmNPF5.24 Oligopeptide transport related Glyma11g34613.1* 27 5 1 12 10 12 U
    GmNPF5.29 Oligopeptide transport related Glyma18g03790.1* 17 3 1 11 10 11 U 25 L
    GmYSL7A Yellow Stripe Like 7 Glyma11g31870.1 4 4 2 12 14 13 U 160 ns
ABC Transporters
    GmABCA2 ABC transporter subfamily A Glyma04g34140.2 16 3 2 7 6 6 U 52 L
    GmABCA7 ABC transporter subfamily A Glyma04g34130.1 37 7 6 6 7 6 U 205 L
    GmABCB20 ABC transporter subfamily B Glyma02g10530.1 11 2 2 11 13 10 U 2 L
    GmABCG39 ABC transporter subfamily G (PDR) Glyma10g34700.2 16 4 4 10 13 13 U 6 L
    GmABCG11 ABC transporter subfamily G (white-brown complex) Glyma08g07580.1 20 4 2 4 6 6 U 37 L
Sugar Transport
    Voltage-dependent anion channel Glyma08g40800.1* 15 21 1 0 0 1 U 14 S
    Voltage-dependent anion channel Glyma09g37570.1* 4 12 1 0 0 2 U 30 S
    Voltage-dependent anion channel Glyma18g16260.1* 22 21 5 0 0 0 U 25 S
    Voltage-dependent anion channel Glyma18g49070.1* 7 21 4 0 0 0 U 47 S
Amino acid transport
    GmAPC1 Amino acid permease Glyma09g21070.2 22 10 4 14 14 13 U 70 L
Sulfate transport
    Sulfate/bicarbon-ate/oxalate exchanger SAT-1 (SST1 Lotus homologue) Glyma07g09710.1 55 3 1 10 12 10 U 209 S
    Sulfate/bicarbon-ate/oxalate exchanger SAT-1 (SST1 Lotus homologue) Glyma09g32110.3 105 13 6 10 10 10 U 355 ns
Phosphate transport
    Phosphate transporter 1–1, MFS Glyma10g33030.1 9 7 2 9 11 12 U 38 S
    Phosphate transporter 1–4 Glyma10g04230.1 10 5 2 11 11 12 U 13 L
NIP Transport
    Nod26 aquaporin Glyma08g12650.1 929 35 20 5 6 6 6 U 3167 S
Miscellaneous transport
    Nucleotide transporter 1 Glyma15g01420.1 50 10 5 10 9 8 C 29 L
    Secretory carrier membrane protein Glyma06g45160.1 90 10 4 4 4 4 U 190 S
    Secretory carrier membrane protein 3 Glyma12g11820.1 78 10 2 4 4 4 U 63 S
Other
    C2 domain protein binding Glyma09g05100.1 2 7 2 0 1 2 U 67 S
    Cupredoxin superfamily protein Glyma17g14730.1G, SP 12 10 4 2 1 2 ER/SP 7 S
    Cytochrome P450 CYP2 subfamily Glyma07g20430.1* 29 14 6 1 1 1 ER/SP 64 ns
    Domain of unknown function (DUF221) Glyma13g29270.1 6 3 2 10 9 9 U 2 S
    Domain of unknown function (DUF588) Glyma01g31910.2 42 11 2 4 3 4 U 247 ns
    Domain of unknown function (DUF588) Glyma03g05230.1 11 23 2 0 3 3 U 247 L
    Domain of unknown function (DUF3411) Glyma11g09920.1 23 7 2 0 0 3 C 62 S
    Protein of unknown function (DUF3411) Glyma18g44970.1 8 5 2 0 2 4 C 48 S
    Early nodulin-like protein 10 Glyma02g36580.1G, SP 44 9 2 2 0 2 ER/SP 454 ns
    EKN rich protein Glyma05g25020.1 244 66 7 0 0 0 U 372 L
    EKN rich protein Glyma08g08140.1 317 77 6 0 0 0 U 798 L
    Endomembrane protein 70 Glyma08g20640.1 4 3 2 10 10 10 ER/SP 12 S
    FAD/NAD(P)-binding oxidoreductase family protein Glyma11g18320.1 13 6 2 0 0 0 U 12 S
    Fatty acid amide hydrolase Glyma08g00535.1 37 11 5 0 1 4 U
    Ferretin 1 Glyma18g43650.2 13 10 1 0 0 0 C 44 S
    Glucosidase 1 Glyma05g27890.1 189 114 142 28 21 0 1 4 U 149 L
    Glycosyl hydrolase family 17 protein Glyma14g08200.2G, SP 2 6 2 1 1 2 U 69 S
    Glycosyl hydrolase family 17 protein Glyma14g16830.1G 36 11 4 1 1 1 ER/SP 14 S
    Glycosyl hydrolase family 17 protein Glyma16g04680.1G, SP 12 6 3 2 2 2 ER/SP 4 S
    Glycosyl hydrolase family 31 protein Glyma15g14150.1 7 5 3 1 0 3 U 21 S
    Lipase/lipooxygenase, PLAT/LH2 family protein Glyma11g38220.1 SP 26 10 2 1 0 0 ER/SP 75 S
    LITAF-domain-containing protein Glyma08g47500.1 16 23 2 1 1 1 U 276 S
    Membrane-associated progesterone binding protein 3 Glyma09g25940.1 2 14 2 2 1 1 U 67 S
    Mo25 family protein Glyma17g01180.2 3 5 2 0 0 0 U 330 S
    Nodulin Glyma20g02921.1 SP 21 9 2 1 1 1 ER/SP
    Nucleotide-diphospho-sugar transferase Glyma16g06180.1 5 5 2 1 1 1 U 129 ns
    Oligosaccharyl-transferase subunit Ribophorin II Glyma03g32140.3 SP 9 7 3 4 4 5 ER/SP 3 S
    Outer envelope pore protein 24 Glyma09g18920.1 8 14 3 0 0 0 U 18 S
    Patched family protein Glyma04g01901.1 SP 6 2 2 13 12 12 ER/SP
    Peroxidase Glyma16g27890.1 34 24 22 6 2 1 1 ER/SP 191 ns
    Peroxidase superfamily protein Glyma14g38210.1 SP 33 19 5 0 0 1 ER/SP 14 L
    PLAC8 family protein Glyma05g37590.1 28 13 3 0 1 3 U 482 S
    PLAC8 family protein Glyma08g01990.1 9 7 2 0 1 4 U 31 S
    PLAC8 family protein Glyma08g04830.1 167 5 20 3 0 0 1 U 1146 L
    PLAC8 family protein Glyma09g31910.1 310 21 5 2 1 1 U 1015 ns
    Protein of unknown function (DUF2359) Glyma05g27090.1 2 4 2 0 0 1 U 10 S
    Protein of unknown function (DUFB2219) Glyma13g25150.1 35 10 4 0 0 1 C 3 L
    Proteinase inhibitor, propeptide Glyma02g18320.1 SP 7 12 26 3 1 1 1 ER/SP 133 S
    Purple acid phosphatases superfamily protein Glyma18g17541.1 SP 25 9 4 0 0 0 ER/SP
    SPFH/Band 7/PHB protein family Glyma05g01360.1* 728 9 49 14 0 0 0 U 484 S
    SPFH/Band 7/PHB protein family Glyma13g05120.3* 417 38 1 0 0 1 U 18 S
    SPFH/Band 7/PHB protein family Glyma19g02370.1* 444 38 7 0 0 0 U 37 S
    SPFH/Band 7/PHB protein family Nod53b flotillin Glyma06g06930.1* 475 23 43 18 0 0 0 U 342 L