Bioinformatic Characterization of Sulfotransferase Provides New Insights for the Exploitation of Sulfated Polysaccharides in Caulerpa
Abstract
:1. Introduction
2. Results
2.1. Caulerpa Showed an Unconventional Number of Sulfotransferase
2.2. Phylogenetic Characterization of Caulerpa Sulfotransferase
2.3. Caulerpa Sulfotransferase Structures: Peculiarities and Similarities vs. Algae and Plants
2.4. Expression Analysis Revealed Tissue Specificity for Sulfotransferases from Caulerpa
2.5. Reconstruction of the Sulfated Polysaccharides Pathway
3. Materials and Methods
3.1. Algae Genome Scan
3.2. Phylogenetic Analysis
3.3. Structures and Localization Prediction
3.4. BLAST Approaches and Expression Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Specie | Proposed Beneficial Effects | Bio-Compounds | References |
---|---|---|---|
Caulerpa cupressoides | Antinociceptive and anti-inflammatory effects | Lectin | [35] |
Antioxidant and antiurolithic effects | Sulfated polysaccharides | [20] | |
Immunostimulatory activity | Sulfated polysaccharides | [34] | |
Possible anticoagulant and antioxidant effects | Sulfated polysaccharides | [31] | |
Caulerpa cylindracea | Antioxidant and antimicrobial activity | Fatty acid derived products | [4] |
Anxiolytic effect in Diplodus sargus | Caulerpin | [38] | |
Regulation of oxidative phosphorylation and of AMPKα1 pathway in cancer cells | Caulerpin | [39] | |
Caulerpa lentillifera | Anti-inflammatory activity | Sulfated polysaccharides | [19] |
Anticoagulant properties | Not specified | [40] | |
Antimicoytic activity | Not specified | [41] | |
Possible immunomodulator roles | Sulfated polysaccharides | [33] | |
Caulerpa mexicana | Gastroprotective effects (reduction of ethanol damage) | Sulfated polysaccharides | [36] |
Caulerpa okamurae | Anti-inflammatory; increases of insulin sensitivity in adipocytes and macrophages | Not specified | [26] |
Caulerpa prolifera | Osteogenic potential | Sulfated polysaccharides | [37] |
Caulerpa racemosa | Antinociceptive and anti-inflammatory effects | Sulfated polysaccharides | [30] |
Antioxidant and antibacterial activity | Different compounds | [27] | |
Immunostimulatory activity (increased of macrophages, no cytokines induction) | Polysaccharides | [32] | |
Positive effects on murine colon damages | Caulerpin | [42] | |
Radical scavenging activities | Not specified | [29] | |
Reduction of pain in the rat temporomandibular joint | Sulfated polysaccharides | [18] | |
Therapeutic role in breast cancer | Racemosin | [43] | |
Caulerpa scalpelliformis | Non-specific immunity and disease resistance in fish (Nile tilapia) | Not specified | [44] |
Caulerpa sertularioides | Antibacteric activity vs. V. parahaemolyticus and V. alginolyticus | Not specified | [45] |
Caulerpa Sp | Antiaeging and UV protection action on mice | Not specified | [28] |
PF00685 (1) | PF00685 (2) | PF03567 | PF06990 | PF00884 | |||||
---|---|---|---|---|---|---|---|---|---|
Sulfotransferase | Sulfotransferase | Sulfotransferase | Sulfotransferase | Sulfatase | |||||
Proteins ID | Best BLASTp Hit | Proteins ID | Best BLASTp Hit | Protein ID | Best BLASTp Hit | Proteins ID | Best BLASTp Hit | Proteins ID | Best BLASTp Hit |
g1228.t1 | Sulfotransferase | g5063.t1 | Sulfotransferase | g395.t1 | ABC transporter | No hit | g5709.t1 | Sulf-hydrolase/transferase | |
g1262.t1 | Glutamyl endopeptidase | g5901.t1 | Sulfotransferase | g579.t1 | Sulfotransferase | g6993.t1 | Sulf-hydrolase/transferase | ||
g1631.t1 | Sulfotransferase like | g5902.t1 | Sulfotransferase | g635.t1 | Sulfotransferase | ||||
g1631.t2 | Sulfotransferase like | g5902.t2 | Sulfotransferase | g725.t1 | Sulfotransferase | ||||
g2821.t1 | Sulfotransferase | g5903.t1 | Sulfotransferase | g2127.t1 | Sulfotransferase | ||||
g3147.t1 | Peptidyl-prolyl cis-trans isomerase | g5904.t1 | Sulfotransferase | g2161.t1 | Sulfotransferase | ||||
g3179.t1 | Sulfotransferase | g5905.t1 | Sulfotransferase | g3703.t1 | Acetyl-CoA carboxylase | ||||
g4176.t1 | Sulfotransferase | g6293.t1 | Sulfotransferase | g3783.t1 | Serine acetyltransferase | ||||
g5047.t1 | Sulfotransferase | g6301.t1 | Sulfotransferase | g4170.t1 | Cytochrome p450 | ||||
g5048.t1 | Sulfotransferase | g7623.t1 | Sulfotransferase | g4173.t1 | Sulfotransferase | ||||
g5054.t1 | Sulfotransferase | g8270.t1 | Sulfotransferase | g4271.t1 | Sulfotransferase | ||||
g5055.t1 | Sulfotransferase | g8456.t1 | Sulfotransferase | g4272.t1 | Sulfotransferase | ||||
g5056.t1 | Sulfotransferase | g8457.t1 | Sulfotransferase | g4272.t2 | Sulfotransferase | ||||
g5057.t1 | Sulfotransferase | g8467.t1 | Sulfotransferase | g4896.t1 | Sulfotransferase | ||||
g5060.t1 | Sulfotransferase | ||||||||
g5062.t1 | Sulfotransferase |
Predicted Structures Similarity | C. lentillifera Proteins |
---|---|
Heparan sulfate glucosamine 3-o-sulfotransferase | g1228.t1 (Co = 56%; Cf = 100%); g4176.t1 (Co = 31%; Cf = 100%) |
Protein-tyrosine sulfotransferase 2; | g1631.t1 (Co = 50%; Cf = 100%) |
Heparan sulfate n-deacetylase/n-sulfotransferase | g2821.t1 (Co = 47%; Cf = 100%); g3179.t1 (Co = 39%; Cf = 100%) |
Sulphotransferase-18 from Arabidopsis | g5047.t1; g5048.t1; g5054.t1; g5055.t1; g5056.t1; g5057.t1; g5060.t1; g5062.t1; g5063.t1; g5901.t1; g5902.t1; g5903.t1; g5904.t1; g5905.t1; g6293.t1; g6301.t1; g7623.t1; g8467.t1 (Co = 81–87%; Cf = 100%) |
Haparan sulfate n-deacetylase/n-2 sulfotransferase | g8270.t1 (Co = 56%; Cf = 100%). |
Human sulfotranferase sult1c3 in complex with pap | g8456.t1 (Co = 82%; Cf = 100%); g8457.t1 (Co = 82%; Cf = 100%) |
Maltose-binding periplasmic protein, heparan sulfate 2-o | g579.t1 (Co = 99%; Cf = 43%); g725.t1 (Co = 99%; Cf = 51%); g4271.t1 (Co = 98%; Cf = 41%); g4896.t1 (Co = 98%; Cf = 62%). |
Maltose binding protein - heparan sulfate 6-o | g635.t1 (Co = 99%; Cf = 33%); g4173.t1 (Co = 58%; Cf = 99.3%); g4272.t1 (Co = 99%; Cf = 37%) |
Human pregnenolone sulfotransferase | g2127.t1 (Co = 54%; Cf = 99%); g2161.t1 (Co = 43%; Cf = 99%) |
N-acetylgalactosamine-6-sulfatase | g5709.t1 (Co = 70%; Cf = 100%); g6993.t1 (Co = 69%; Cf = 100%) |
Gene Id | TM | Number TM | TM Position (aa) | TP | TP Position (aa) |
---|---|---|---|---|---|
g579.t1 | No | 0 | - | Yes | 5–24 (P = 100%) |
g635.t1 | No | 0 | - | Yes | 7–27 (P = 100%) |
g1228.t1 | Yes | 1 | 415–434 (P = 100%) | Yes | 1–23 (P = 40%) |
g2161.t1 | Yes | 1 | 7–26 | Yes | 6–26 (P = 100%) |
g2821.t1 | Yes | 1 | 476–498 (P = 100%) | Yes | 1–31 (P = 20%) |
g3179.t1 | Yes | 2 | 7–29; 581–603 (P = 100%) | Yes | 1–23 (P = 100%) |
g4173.t1 | Yes | 1 | 13–41 (P = 100%) | No | - |
g4176.t1 | Yes | 2 | 309–329 (P = 40%); 765–787 (P = 100%) | No | - |
g4271.t1 | No | 0 | - | Yes | 1–26 (P = 100%) |
g4272.t1 | Yes | 1 | 13–33 (P = 100%) | No | - |
g8270.t1 | Yes | 1 | 418–440 (P = 100%) | Yes | 1–22 (P = 20%) |
RSEM Read Counts | ||||||
---|---|---|---|---|---|---|
C. taxifolia Transcripts | Frond Apex | Frond Base | Holdfast | Pinnae | Rachis | Stolon |
Ctaxi_contig_10628|comp31456_c3_seq1 | 44.4 | 22.0 | 16.0 | 28.3 | 42.2 | 22.5 |
Ctaxi_contig_10917|comp31547_c2_seq1 | 107.0 | 40.0 | 30.9 | 83.2 | 90.1 | 61.0 |
Ctaxi_contig_10918|comp31547_c2_seq2 | 44.6 | 14.5 | 49.0 | 34.8 | 46.7 | 49.4 |
Ctaxi_contig_15098|comp32496_c3_seq2 | 61.0 | 68.0 | 41.0 | 115.4 | 145.6 | 45.6 |
Ctaxi_contig_15401|comp32550_c1_seq1 | 54.2 | 46.0 | 47.6 | 54.0 | 73.7 | 57.4 |
Ctaxi_contig_15402|comp32550_c1_seq2 | 1.4 | 3.4 | 2.7 | 5.4 | 5.9 | 7.0 |
Ctaxi_contig_16178|comp32679_c5_seq7 | 23.7 | 15.2 | 8.0 | 41.2 | 44.5 | 16.1 |
Ctaxi_contig_16179|comp32679_c5_seq8 | 56.4 | 35.9 | 40.0 | 68.2 | 55.0 | 70.5 |
Ctaxi_contig_16180|comp32679_c5_seq9 | 20.6 | 15.6 | 18.8 | 38.0 | 33.5 | 18.3 |
Ctaxi_contig_16182|comp32679_c5_seq11 | 77.1 | 23.9 | 23.4 | 17.8 | 70.8 | 38.5 |
Ctaxi_contig_16717|comp32777_c2_seq1 | 5.2 | 3.4 | 2.5 | 10.1 | 12.4 | 1.8 |
Ctaxi_contig_18258|comp33042_c0_seq1 | 92.7 | 60.1 | 64.5 | 97.9 | 76.9 | 108.4 |
Ctaxi_contig_18292|comp33050_c1_seq1 | 1879.0 | 1765.0 | 595.6 | 5246.9 | 4964.1 | 907.1 |
Ctaxi_contig_23234|comp33768_c0_seq2 | 62.2 | 70.8 | 57.5 | 113.9 | 125.6 | 55.4 |
Ctaxi_contig_23235|comp33768_c1_seq1 | 86.2 | 64.4 | 57.6 | 136.1 | 147.3 | 41.0 |
Ctaxi_contig_24623|comp33959_c2_seq1 | 237.4 | 157.8 | 241.0 | 247.0 | 230.9 | 242.5 |
Ctaxi_contig_24659|comp33966_c1_seq3 | 86.4 | 55.6 | 65.9 | 122.3 | 115.2 | 80.2 |
Ctaxi_contig_24664|comp33966_c1_seq8 | 27.6 | 27.2 | 19.6 | 39.7 | 42.0 | 23.6 |
Ctaxi_contig_24669|comp33966_c1_seq13 | 29.8 | 21.0 | 20.5 | 42.5 | 38.1 | 20.4 |
Ctaxi_contig_26858|comp34188_c2_seq1 | 20.6 | 19.1 | 18.6 | 49.4 | 34.5 | 22.3 |
Ctaxi_contig_26859|comp34188_c2_seq2 | 84.7 | 66.2 | 90.9 | 124.0 | 119.3 | 97.2 |
Ctaxi_contig_27564|comp34267_c0_seq1 | 202.3 | 136.6 | 106.5 | 428.3 | 310.6 | 136.4 |
Ctaxi_contig_27571|comp34267_c3_seq1 | 47.7 | 40.2 | 12.0 | 130.6 | 85.4 | 19.0 |
Ctaxi_contig_40054|comp35467_c2_seq1 | 715.5 | 595.7 | 444.6 | 1266.3 | 1549.7 | 549.7 |
Ctaxi_contig_40059|comp35467_c3_seq1 | 172.8 | 107.2 | 117.2 | 197.4 | 167.2 | 86.5 |
Ctaxi_contig_47488|comp35975_c4_seq1 | 62.8 | 30.4 | 36.5 | 56.4 | 40.9 | 26.9 |
Ctaxi_contig_47489|comp35975_c4_seq2 | 360.6 | 209.4 | 251.1 | 452.0 | 455.4 | 211.7 |
Ctaxi_contig_47490|comp35975_c4_seq3 | 0.0 | 0.0 | 1.0 | 0.2 | 0.0 | 0.0 |
Ctaxi_contig_47491|comp35975_c4_seq4 | 3.6 | 0.0 | 2.6 | 3.4 | 3.1 | 0.4 |
Ctaxi_contig_47493|comp35975_c4_seq6 | 9.6 | 3.4 | 2.9 | 4.9 | 2.8 | 2.2 |
Ctaxi_contig_47494|comp35975_c4_seq7 | 0.1 | 0.0 | 0.1 | 0.2 | 0.1 | 0.1 |
Ctaxi_contig_47495|comp35975_c4_seq8 | 143.8 | 68.9 | 66.5 | 142.1 | 144.5 | 64.6 |
Ctaxi_contig_47496|comp35975_c4_seq9 | 1.7 | 2.0 | 3.1 | 8.0 | 4.4 | 3.4 |
Ctaxi_contig_47497|comp35975_c4_seq10 | 468.7 | 442.3 | 308.2 | 632.8 | 643.2 | 499.7 |
Ctaxi_contig_47499|comp35975_c4_seq12 | 121.7 | 93.5 | 77.8 | 161.7 | 174.7 | 87.6 |
Ctaxi_contig_47500|comp35975_c4_seq13 | 46.4 | 35.1 | 30.5 | 49.8 | 61.4 | 38.7 |
Ctaxi_contig_56778|comp36555_c3_seq5 | 141.0 | 49.2 | 47.5 | 84.9 | 79.4 | 62.6 |
Ctaxi_contig_70773|comp37223_c1_seq6 | 97.2 | 81.5 | 59.5 | 181.2 | 128.2 | 73.0 |
Ctaxi_contig_9279|comp31033_c1_seq1 | 13.8 | 7.1 | 4.8 | 10.0 | 11.2 | 8.9 |
Ctaxi_contig_9848|comp31227_c0_seq3 | 25.7 | 24.6 | 16.3 | 45.7 | 41.9 | 22.6 |
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Share and Cite
Landi, S.; Esposito, S. Bioinformatic Characterization of Sulfotransferase Provides New Insights for the Exploitation of Sulfated Polysaccharides in Caulerpa. Int. J. Mol. Sci. 2020, 21, 6681. https://doi.org/10.3390/ijms21186681
Landi S, Esposito S. Bioinformatic Characterization of Sulfotransferase Provides New Insights for the Exploitation of Sulfated Polysaccharides in Caulerpa. International Journal of Molecular Sciences. 2020; 21(18):6681. https://doi.org/10.3390/ijms21186681
Chicago/Turabian StyleLandi, Simone, and Sergio Esposito. 2020. "Bioinformatic Characterization of Sulfotransferase Provides New Insights for the Exploitation of Sulfated Polysaccharides in Caulerpa" International Journal of Molecular Sciences 21, no. 18: 6681. https://doi.org/10.3390/ijms21186681