Skip to main content
SpringerLink
Log in

Standard Candles for Dating Microbial Lineages

  • Protocol
  • First Online:
Environmental Microbial Evolution

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2569))

Abstract

Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as “standard candles” for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Marshall CR (2019) Using the fossil record to evaluate timetree timescales. Front Genet 10:1049. https://doi.org/10.3389/fgene.2019.01049

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Xu J (2006) Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances: microbial ecological genomics. Mol Ecol 15:1713–1731. https://doi.org/10.1111/j.1365-294X.2006.02882.x

    Article  CAS  PubMed  Google Scholar 

  3. Golubic S, Seong-Joo L (1999) Early cyanobacterial fossil record: preservation, palaeoenvironments and identification. Eur J Phycol 34:339–348. https://doi.org/10.1080/09670269910001736402

    Article  Google Scholar 

  4. Hofmann HJ (1976) Precambrian microflora, Belcher Islands, Canada: significance and systematics. J Paleontol 50:1040–1073

    Google Scholar 

  5. Bosak T, Knoll AH, Petroff AP (2013) The meaning of stromatolites. Annu Rev Earth Planet Sci 41:21–44. https://doi.org/10.1146/annurev-earth-042711-105327

    Article  CAS  Google Scholar 

  6. Brocks JJ, Schaeffer P (2008) Okenane, a biomarker for purple sulfur bacteria (Chromatiaceae), and other new carotenoid derivatives from the 1640Ma Barney Creek Formation. Geochimica et Cosmochimica Acta 72:1396–1414. https://doi.org/10.1016/j.gca.2007.12.006

    Article  CAS  Google Scholar 

  7. Alleon J, Summons RE (2019) Organic geochemical approaches to understanding early life. Free Radic Biol Med 140:103–112. https://doi.org/10.1016/j.freeradbiomed.2019.03.005

    Article  CAS  PubMed  Google Scholar 

  8. Fernie JD (1969) The period-luminosity relation: a historical review. Publ Astron Soc Pac 81:707. https://doi.org/10.1086/128847

    Article  Google Scholar 

  9. Madore BF, Freedman WL (1991) The Cepheid distance scale. Publ Astron Soc Pac 103:933. https://doi.org/10.1086/132911

    Article  Google Scholar 

  10. Hillebrandt W, Niemeyer JC (2000) Type ia supernova explosion models. Annu Rev Astron Astrophys 38:191–230. https://doi.org/10.1146/annurev.astro.38.1.191

    Article  CAS  Google Scholar 

  11. Kinene T, Wainaina J, Maina S, Boykin LM (2016) Rooting trees, methods for. In: Encyclopedia of evolutionary biology. Elsevier, pp 489–493

    Chapter  Google Scholar 

  12. Foote M, Sepkoski JJ (1999) Absolute measures of the completeness of the fossil record. Nature 398:415–417. https://doi.org/10.1038/18872

    Article  CAS  PubMed  Google Scholar 

  13. dos Reis M, Thawornwattana Y, Angelis K et al (2015) Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales. Curr Biol 25:2939–2950. https://doi.org/10.1016/j.cub.2015.09.066

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Dunning Hotopp JC (2011) Horizontal gene transfer between bacteria and animals. Trends Genet 27:157–163. https://doi.org/10.1016/j.tig.2011.01.005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Chriki-Adeeb R, Chriki A (2016) Estimating divergence times and substitution rates in Rhizobia. Evolutionary Bioinformatics 12:EBO.S39070. https://doi.org/10.4137/EBO.S39070

    Article  Google Scholar 

  16. (1993) A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts. Proc R Soc Lond B 253:167–171. https://doi.org/10.1098/rspb.1993.0098

  17. McFall-Ngai M, Hadfield MG, Bosch TCG et al (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci USA 110:3229–3236. https://doi.org/10.1073/pnas.1218525110

    Article  PubMed  PubMed Central  Google Scholar 

  18. Watanabe F, Bito T (2018) Vitamin B 12 sources and microbial interaction. Exp Biol Med (Maywood) 243:148–158. https://doi.org/10.1177/1535370217746612

    Article  CAS  PubMed  Google Scholar 

  19. Hall C, Camilli S, Dwaah H et al (2021) Freshwater sponge hosts and their green algae symbionts: a tractable model to understand intracellular symbiosis. PeerJ 9:e10654. https://doi.org/10.7717/peerj.10654

    Article  PubMed  PubMed Central  Google Scholar 

  20. Rowan R, Powers DA (1991) A molecular genetic classification of zooxanthellae and the evolution of animal-algal symbioses. Science 251:1348–1351. https://doi.org/10.1126/science.251.4999.1348

    Article  CAS  PubMed  Google Scholar 

  21. Gehling JG, Droser ML (2018) Ediacaran scavenging as a prelude to predation. Emerg Top Life Sci 2:213–222. https://doi.org/10.1042/ETLS20170166

    Article  CAS  PubMed  Google Scholar 

  22. Dittmann E, Fewer DP, Neilan BA (2013) Cyanobacterial toxins: biosynthetic routes and evolutionary roots. FEMS Microbiol Rev 37:23–43. https://doi.org/10.1111/j.1574-6976.2012.12000.x

    Article  CAS  PubMed  Google Scholar 

  23. Exposito J-Y, Lethias C (2013) Invertebrate and vertebrate collagens. In: Keeley FW, Mecham RP (eds) Evolution of extracellular matrix. Springer, Berlin/Heidelberg, pp 39–72

    Chapter  Google Scholar 

  24. Rasmussen M, Jacobsson M, Björck L (2003) Genome-based identification and analysis of collagen-related structural motifs in bacterial and viral proteins. J Biol Chem 278:32313–32316. https://doi.org/10.1074/jbc.M304709200

    Article  CAS  PubMed  Google Scholar 

  25. Fidler AL, Darris CE, Chetyrkin SV et al (2017) Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues. eLife 6:e24176. https://doi.org/10.7554/eLife.24176

    Article  PubMed  PubMed Central  Google Scholar 

  26. Marino-Puertas L, Goulas T, Gomis-Rüth FX (2017) Matrix metalloproteinases outside vertebrates. Biochimica et Biophysica Acta (BBA) – Mol Cell Res 1864:2026–2035. https://doi.org/10.1016/j.bbamcr.2017.04.003

    Article  CAS  Google Scholar 

  27. Flinn BS (2008) Plant extracellular matrix metalloproteinases. Funct Plant Biol 35:1183. https://doi.org/10.1071/FP08182

    Article  CAS  PubMed  Google Scholar 

  28. Elieh-Ali-Komi D, Hamblin MR (2016) Chitin and chitosan: production and application of versatile biomedical nanomaterials. Int J Adv Res (Indore) 4:411–427

    CAS  PubMed  Google Scholar 

  29. Tang WJ, Fernandez JG, Sohn JJ, Amemiya CT (2015) Chitin is endogenously produced in vertebrates. Curr Biol 25:897–900. https://doi.org/10.1016/j.cub.2015.01.058

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Bar-On YM, Phillips R, Milo R (2018) The biomass distribution on Earth. Proc Natl Acad Sci USA 115:6506–6511. https://doi.org/10.1073/pnas.1711842115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Ehrlich H (2010) Chitin and collagen as universal and alternative templates in biomineralization. Int Geol Rev 52:661–699. https://doi.org/10.1080/00206811003679521

    Article  Google Scholar 

  32. Bo M, Bavestrello G, Kurek D et al (2012) Isolation and identification of chitin in the black coral Parantipathes larix (Anthozoa: Cnidaria). Int J Biol Macromol 51:129–137. https://doi.org/10.1016/j.ijbiomac.2012.04.016

    Article  CAS  PubMed  Google Scholar 

  33. Daley AC, Antcliffe JB, Drage HB, Pates S (2018) Early fossil record of Euarthropoda and the Cambrian Explosion. Proc Natl Acad Sci USA 115:5323–5331. https://doi.org/10.1073/pnas.1719962115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Rota-Stabelli O, Daley AC, Pisani D (2013) Molecular timetrees reveal a Cambrian colonization of land and a new scenario for ecdysozoan evolution. Curr Biol 23:392–398. https://doi.org/10.1016/j.cub.2013.01.026

    Article  CAS  PubMed  Google Scholar 

  35. Lozano-Fernandez J, Carton R, Tanner AR et al (2016) A molecular palaeobiological exploration of arthropod terrestrialization. Philos Trans R Soc B 371:20150133. https://doi.org/10.1098/rstb.2015.0133

    Article  Google Scholar 

  36. Chen W-M, Yang S-H, Huang W-C et al (2012) Chitinivorax tropicus gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater lake. Int J Syst Evol Microbiol 62:1086–1091. https://doi.org/10.1099/ijs.0.031310-0

    Article  CAS  PubMed  Google Scholar 

  37. Gruen DS, Wolfe JM, Fournier GP (2019) Paleozoic diversification of terrestrial chitin-degrading bacterial lineages. BMC Evol Biol 19:34. https://doi.org/10.1186/s12862-019-1357-8

    Article  PubMed  PubMed Central  Google Scholar 

  38. Gandhi NS, Mancera RL (2008) The structure of glycosaminoglycans and their interactions with proteins. Chem Biol Drug Des 72:455–482. https://doi.org/10.1111/j.1747-0285.2008.00741.x

    Article  CAS  PubMed  Google Scholar 

  39. Woznica A, Gerdt JP, Hulett RE et al (2017) Mating in the closest living relatives of animals is induced by a bacterial chondroitinase. Cell 170:1175–1183.e11. https://doi.org/10.1016/j.cell.2017.08.005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. DeAngelis PL (2002) Evolution of glycosaminoglycans and their glycosyltransferases: implications for the extracellular matrices of animals and the capsules of pathogenic bacteria. Anat Rec 268:317–326. https://doi.org/10.1002/ar.10163

    Article  CAS  PubMed  Google Scholar 

  41. Yamada S, Sugahara K, Özbek S (2011) Evolution of glycosaminoglycans: comparative biochemical study. Commun Integr Biol 4:150–158. https://doi.org/10.4161/cib.4.2.14547

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Mizumoto S, Yamada S, Sugahara K (2015) Molecular interactions between chondroitin–dermatan sulfate and growth factors/receptors/matrix proteins. Curr Opin Struct Biol 34:35–42. https://doi.org/10.1016/j.sbi.2015.06.004

    Article  CAS  PubMed  Google Scholar 

  43. Csoka AB, Stern R (2013) Hypotheses on the evolution of hyaluronan: a highly ironic acid. Glycobiology 23:398–411. https://doi.org/10.1093/glycob/cws218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Wang W, Wang J, Li F (2016) Hyaluronidase and Chondroitinase. In: Atassi MZ (ed) Protein Rev. Springer, Singapore, pp 75–87

    Chapter  Google Scholar 

  45. Zhang Z, Su H, Wang X et al (2020) Cloning and characterization of a novel chondroitinase ABC categorized into a new subfamily of polysaccharide lyase family 8. Int J Biol Macromol 164:3762–3770. https://doi.org/10.1016/j.ijbiomac.2020.08.210

    Article  CAS  PubMed  Google Scholar 

  46. Tao L, Song F, Xu N et al (2017) New insights into the action of bacterial chondroitinase AC I and hyaluronidase on hyaluronic acid. Carbohydr Polym 158:85–92. https://doi.org/10.1016/j.carbpol.2016.12.010

    Article  CAS  PubMed  Google Scholar 

  47. Singh V, Haque S, Kumari V et al (2019) Isolation, purification, and characterization of heparinase from streptomyces variabilis MTCC 12266. Sci Rep 9:6482. https://doi.org/10.1038/s41598-019-42740-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. DeAngelis PL (2002) Microbial glycosaminoglycan glycosyltransferases. Glycobiology 12:9R–16R. https://doi.org/10.1093/glycob/12.1.9R

    Article  CAS  PubMed  Google Scholar 

  49. Alibardi L (2009) Embryonic keratinization in vertebrates in relation to land colonization. Acta Zoologica 90:1–17. https://doi.org/10.1111/j.1463-6395.2008.00327.x

    Article  Google Scholar 

  50. Wang B, Yang W, McKittrick J, Meyers MA (2016) Keratin: structure, mechanical properties, occurrence in biological organisms, and efforts at bioinspiration. Prog Mater Sci 76:229–318. https://doi.org/10.1016/j.pmatsci.2015.06.001

    Article  CAS  Google Scholar 

  51. Benton M, Donoghue P, Vinther J et al (2015) Constraints on the timescale of animal evolutionary history. Palaeontologia Electronica 18:1–106. 10.26879/424

    Google Scholar 

  52. Schaffeld M, Markl J (2004) Fish Keratins. In: Methods in cell biology, Elsevier, pp 627–671

    Google Scholar 

  53. Vandebergh W, Bossuyt F (2012) Radiation and functional diversification of alpha keratins during early vertebrate evolution. Mol Biol Evol 29:995–1004. https://doi.org/10.1093/molbev/msr269

    Article  CAS  PubMed  Google Scholar 

  54. Greenwold MJ, Bao W, Jarvis ED et al (2014) Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles. BMC Evol Biol 14:249. https://doi.org/10.1186/s12862-014-0249-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Li Q (2021) Structure, application, and biochemistry of microbial keratinases. Front Microbiol 12:674345. https://doi.org/10.3389/fmicb.2021.674345

    Article  PubMed  PubMed Central  Google Scholar 

  56. Qiu J, Wilkens C, Barrett K, Meyer AS (2020) Microbial enzymes catalyzing keratin degradation: classification, structure, function. Biotechnol Adv 44:107607. https://doi.org/10.1016/j.biotechadv.2020.107607

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Kothari D, Rani A, Goyal A (2017) Keratinases. In: Current developments in biotechnology and bioengineering. Elsevier, pp 447–469

    Chapter  Google Scholar 

  58. Egan S, Harder T, Burke C et al (2013) The seaweed holobiont: understanding seaweed–bacteria interactions. FEMS Microbiol Rev 37:462–476. https://doi.org/10.1111/1574-6976.12011

    Article  CAS  PubMed  Google Scholar 

  59. Goecke F, Labes A, Wiese J, Imhoff J (2010) Chemical interactions between marine macroalgae and bacteria. Mar Ecol Prog Ser 409:267–299. https://doi.org/10.3354/meps08607

    Article  CAS  Google Scholar 

  60. Miranda LN, Hutchison K, Grossman AR, Brawley SH (2013) Diversity and abundance of the bacterial community of the red Macroalga Porphyra umbilicalis: did bacterial farmers produce macroalgae? PLoS ONE 8:e58269. https://doi.org/10.1371/journal.pone.0058269

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Ficko-Blean E, Hervé C, Michel G (2015) Sweet and sour sugars from the sea: the biosynthesis and remodeling of sulfated cell wall polysaccharides from marine macroalgae. PiP 2:51–64. https://doi.org/10.1127/pip/2015/0028

    Article  Google Scholar 

  62. Graham LE (2019) Digging deeper: why we need more Proterozoic algal fossils and how to get them. J Phycol 55:1–6. https://doi.org/10.1111/jpy.12790

    Article  PubMed  Google Scholar 

  63. Clarke JT, Warnock RCM, Donoghue PCJ (2011) Establishing a time-scale for plant evolution. New Phytologist 192:266–301. https://doi.org/10.1111/j.1469-8137.2011.03794.x

    Article  PubMed  Google Scholar 

  64. Gibson TM, Shih PM, Cumming VM et al (2018) Precise age of Bangiomorpha pubescens dates the origin of eukaryotic photosynthesis. Geology 46:135–138. https://doi.org/10.1130/G39829.1

    Article  CAS  Google Scholar 

  65. Peña V, Vieira C, Braga JC et al (2020) Radiation of the coralline red algae (Corallinophycidae, Rhodophyta) crown group as inferred from a multilocus time-calibrated phylogeny. Mol Phylogenet Evol 150:106845. https://doi.org/10.1016/j.ympev.2020.106845

    Article  PubMed  Google Scholar 

  66. Saunders GW, Hommersand MH (2004) Assessing red algal supraordinal diversity and taxonomy in the context of contemporary systematic data. Am J Bot 91:1494–1507. https://doi.org/10.3732/ajb.91.10.1494

    Article  PubMed  Google Scholar 

  67. Pomin VH (2015) Sulfated glycans in sea urchin fertilization. Glycoconj J 32:9–15. https://doi.org/10.1007/s10719-015-9573-y

    Article  CAS  PubMed  Google Scholar 

  68. Santos JA, Mulloy B, Mourao PAS (1992) Structural diversity among sulfated alpha-L-galactans from ascidians (tunicates). Studies on the species Ciona intestinalis and Herdmania monus. Eur J Biochem 204:669–677. https://doi.org/10.1111/j.1432-1033.1992.tb16680.x

    Article  CAS  PubMed  Google Scholar 

  69. Aquino RS (2004) Occurrence of sulfated galactans in marine angiosperms: evolutionary implications. Glycobiology 15:11–20. https://doi.org/10.1093/glycob/cwh138

    Article  CAS  PubMed  Google Scholar 

  70. Hehemann J-H, Boraston AB, Czjzek M (2014) A sweet new wave: structures and mechanisms of enzymes that digest polysaccharides from marine algae. Curr Opin Struct Biol 28:77–86. https://doi.org/10.1016/j.sbi.2014.07.009

    Article  CAS  PubMed  Google Scholar 

  71. Chauhan PS, Saxena A (2016) Bacterial carrageenases: an overview of production and biotechnological applications. 3 Biotech 6(146). https://doi.org/10.1007/s13205-016-0461-3

  72. Michel G, Nyval-Collen P, Barbeyron T et al (2006) Bioconversion of red seaweed galactans: a focus on bacterial agarases and carrageenases. Appl Microbiol Biotechnol 71:23–33. https://doi.org/10.1007/s00253-006-0377-7

    Article  CAS  PubMed  Google Scholar 

  73. Belas R (1989) Sequence analysis of the agrA gene encoding beta-agarase from Pseudomonas atlantica. J Bacteriol 171:602–605. https://doi.org/10.1128/jb.171.1.602-605.1989

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Sugano Y, Matsumoto T, Kodama H, Noma M (1993) Cloning and sequencing of agaA, a unique agarase 0107 gene from a marine bacterium, Vibrio sp. strain JT0107. Appl Environ Microbiol 59:3750–3756. https://doi.org/10.1128/aem.59.11.3750-3756.1993

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Potin P, Richard C, Rochas C, Kloareg B (1993) Purification and characterization of the alpha-agarase from Alteromonas agarlyticus (Cataldi) comb. nov., strain GJ1B. Eur J Biochem 214:599–607. https://doi.org/10.1111/j.1432-1033.1993.tb17959.x

    Article  CAS  PubMed  Google Scholar 

  76. Ohta Y, Hatada Y, Ito S, Horikoshi K (2005) High-level expression of a neoagarobiose-producing β-agarase gene from Agarivorans sp. JAMB-A11 in Bacillus subtilis and enzymic properties of the recombinant enzyme. Biotechnol Appl Biochem 41(183). https://doi.org/10.1042/BA20040083

  77. Hehemann J-H, Smyth L, Yadav A et al (2012) Analysis of Keystone Enzyme in Agar Hydrolysis Provides Insight into the Degradation (of a Polysaccharide from) Red Seaweeds. J Biol Chem 287:13985–13995. https://doi.org/10.1074/jbc.M112.345645

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Veerakumar S, Manian RP (2018) Recombinant β-agarases: insights into molecular, biochemical, and physiochemical characteristics. 3 Biotech 8(445). https://doi.org/10.1007/s13205-018-1470-1

  79. Guibet M, Colin S, Barbeyron T et al (2007) Degradation of λ-carrageenan by Pseudoalteromonas carrageenovora λ-carrageenase: a new family of glycoside hydrolases unrelated to κ- and ι-carrageenases. Biochem J 404:105. https://doi.org/10.1042/BJ20061359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Rebuffet E, Barbeyron T, Jeudy A et al (2010) Identification of catalytic residues and mechanistic analysis of family GH82 ι-carrageenases. Biochemistry 49:7590–7599. https://doi.org/10.1021/bi1003475

    Article  CAS  PubMed  Google Scholar 

  81. Ficko-Blean E, Préchoux A, Thomas F et al (2017) Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria. Nat Commun 8:1685. https://doi.org/10.1038/s41467-017-01832-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Barbeyron T, Gerard A, Potin P et al (1998) The kappa-carrageenase of the marine bacterium Cytophaga drobachiensis. Structural and phylogenetic relationships within family-16 glycoside hydrolases. Mol Biol Evol 15:528–537. https://doi.org/10.1093/oxfordjournals.molbev.a025952

    Article  CAS  PubMed  Google Scholar 

  83. Martin M, Portetelle D, Michel G, Vandenbol M (2014) Microorganisms living on macroalgae: diversity, interactions, and biotechnological applications. Appl Microbiol Biotechnol 98:2917–2935. https://doi.org/10.1007/s00253-014-5557-2

    Article  CAS  PubMed  Google Scholar 

  84. Weigl J, Yaphe W (1966) Glycosulfatase of Pseudomonas carrageenovora: desulfation of disaccharide from κ-carrageenan. Can J Microbiol 12:874–876. https://doi.org/10.1139/m66-118

    Article  CAS  Google Scholar 

  85. McLEAN MW, Williamson FB (1979) Glycosulphatase from Pseudomonas carrageenovora. Purification and some properties. Eur J Biochem 101:497–505. https://doi.org/10.1111/j.1432-1033.1979.tb19744.x

    Article  CAS  PubMed  Google Scholar 

  86. McLEAN MW, Williamson FB (1981) Neocarratetraose 4-O-monosulphate beta-hydrolase from Pseudomonas carrageenovora. Eur J Biochem 113:447–456. https://doi.org/10.1111/j.1432-1033.1981.tb05084.x

    Article  CAS  PubMed  Google Scholar 

  87. Lee D-G, Shin JG, Jeon MJ, Lee S-H (2013) Heterologous expression and characterization of a recombinant thermophilic arylsulfatase from Thermotoga maritima. Biotechnol Bioproc E 18:897–902. https://doi.org/10.1007/s12257-013-0094-x

    Article  CAS  Google Scholar 

  88. Préchoux A, Genicot S, Rogniaux H, Helbert W (2013) Controlling carrageenan structure using a novel formylglycine-dependent sulfatase, an endo-4s-iota-carrageenan sulfatase. Mar Biotechnol 15:265–274. https://doi.org/10.1007/s10126-012-9483-y

    Article  CAS  Google Scholar 

  89. Préchoux A, Genicot S, Rogniaux H, Helbert W (2016) Enzyme-assisted preparation of furcellaran-like κ-/β-carrageenan. Mar Biotechnol 18:133–143. https://doi.org/10.1007/s10126-015-9675-3

    Article  CAS  Google Scholar 

  90. Genicot SM, Groisillier A, Rogniaux H et al (2014) Discovery of a novel iota carrageenan sulfatase isolated from the marine bacterium Pseudoalteromonas carrageenovora. Front Chem 2. https://doi.org/10.3389/fchem.2014.00067

  91. Préchoux A, Helbert W (2014) Preparation and detailed NMR analyses of a series of oligo-α-carrageenans. Carbohydr Polym 101:864–870. https://doi.org/10.1016/j.carbpol.2013.10.007

    Article  CAS  PubMed  Google Scholar 

  92. Helbert W (2017) Marine polysaccharide sulfatases. Front Mar Sci 4. https://doi.org/10.3389/fmars.2017.00006

  93. Gobet A, Barbeyron T, Matard-Mann M et al (2018) Evolutionary evidence of algal polysaccharide degradation acquisition by pseudoalteromonas carrageenovora 9T to adapt to macroalgal niches. Front Microbiol 9:2740. https://doi.org/10.3389/fmicb.2018.02740

    Article  PubMed  PubMed Central  Google Scholar 

  94. Schultz-Johansen M, Bech PK, Hennessy RC et al (2018) A novel enzyme portfolio for red algal polysaccharide degradation in the marine bacterium paraglaciecola hydrolytica S66T encoded in a sizeable polysaccharide utilization locus. Front Microbiol 9:839. https://doi.org/10.3389/fmicb.2018.00839

    Article  PubMed  PubMed Central  Google Scholar 

  95. Ho C-L (2015) Phylogeny of algal sequences encoding carbohydrate sulfotransferases, formylglycine-dependent sulfatases, and putative sulfatase modifying factors. Front Plant Sci 6. https://doi.org/10.3389/fpls.2015.01057

  96. Lee W-K, Lim Y-Y, Leow AT-C et al (2017) Biosynthesis of agar in red seaweeds: a review. Carbohydr Polym 164:23–30. https://doi.org/10.1016/j.carbpol.2017.01.078

    Article  CAS  PubMed  Google Scholar 

  97. Brawley SH, Blouin NA, Ficko-Blean E et al (2017) Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Proc Natl Acad Sci USA 114:E6361–E6370. https://doi.org/10.1073/pnas.1703088114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Collen J, Porcel B, Carre W et al (2013) Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. Proc Natl Acad Sci 110:5247–5252. https://doi.org/10.1073/pnas.1221259110

    Article  PubMed  PubMed Central  Google Scholar 

  99. Lipinska AP, Collén J, Krueger-Hadfield SA et al (2020) To gel or not to gel: differential expression of carrageenan-related genes between the gametophyte and tetasporophyte life cycle stages of the red alga Chondrus crispus. Sci Rep 10:11498. https://doi.org/10.1038/s41598-020-67728-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Wong KF, Craigie JS (1978) Sulfohydrolase activity and carrageenan biosynthesis in Chondrus crispus (Rhodophyceae). Plant Physiol 61:663–666. https://doi.org/10.1104/pp.61.4.663

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Genicot-Joncour S, Poinas A, Richard O et al (2009) The Cyclization of the 3,6-anhydro-galactose ring of ι-carrageenan is catalyzed by two d-galactose-2,6-sulfurylases in the red alga Chondrus crispus. Plant Physiol 151:1609–1616. https://doi.org/10.1104/pp.109.144329

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Del Cortona A, Jackson CJ, Bucchini F et al (2020) Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds. Proc Natl Acad Sci USA 117:2551–2559. https://doi.org/10.1073/pnas.1910060117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Leliaert F, Smith DR, Moreau H et al (2012) Phylogeny and molecular evolution of the green algae. Crit Rev Plant Sci 31:1–46. https://doi.org/10.1080/07352689.2011.615705

    Article  Google Scholar 

  104. Cocquyt E, Verbruggen H, Leliaert F, De Clerck O (2010) Evolution and cytological diversification of the green seaweeds (Ulvophyceae). Mol Biol Evol 27:2052–2061. https://doi.org/10.1093/molbev/msq091

    Article  CAS  PubMed  Google Scholar 

  105. Fučíková K, Leliaert F, Cooper ED et al (2014) New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data. Front Ecol Evol 2. https://doi.org/10.3389/fevo.2014.00063

  106. Leliaert F, Lopez-Bautista JM (2015) The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin. BMC Genom 16:204. https://doi.org/10.1186/s12864-015-1418-3

    Article  CAS  Google Scholar 

  107. Turmel M, Otis C, Lemieux C (2017) Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae. Sci Rep 7:994. https://doi.org/10.1038/s41598-017-01144-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Berney C, Pawlowski J (2006) A molecular time-scale for eukaryote evolution recalibrated with the continuous microfossil record. Proc R Soc B 273:1867–1872. https://doi.org/10.1098/rspb.2006.3537

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Moczydłowska M (2016) Algal affinities of Ediacaran and Cambrian organic-walled microfossils with internal reproductive bodies: Tanarium and other morphotypes. Palynology 40:83–121. https://doi.org/10.1080/01916122.2015.1006341

    Article  Google Scholar 

  110. Loron C, Moczydłowska M (2018) Tonian (Neoproterozoic) eukaryotic and prokaryotic organic-walled microfossils from the upper Visingsö Group, Sweden. Palynology 42:220–254. https://doi.org/10.1080/01916122.2017.1335656

    Article  Google Scholar 

  111. Butterfield NJ, Knoll AH, Swett K (1994) Paleobiology of the neoproterozoic svanbergfjellet formation, spitsbergen. Lethaia 27:76–76. https://doi.org/10.1111/j.1502-3931.1994.tb01558.x

    Article  Google Scholar 

  112. Tang Q, Pang K, Yuan X, Xiao S (2020) A one-billion-year-old multicellular chlorophyte. Nat Ecol Evol 4:543–549. https://doi.org/10.1038/s41559-020-1122-9

    Article  PubMed  PubMed Central  Google Scholar 

  113. Butterfield NJ, Knoll AH, Swett K (1988) Exceptional preservation of fossils in an Upper Proterozoic shale. Nature 334:424–427. https://doi.org/10.1038/334424a0

    Article  CAS  PubMed  Google Scholar 

  114. Arouri KR, Greenwood PF, Walter MR (2000) Biological affinities of Neoproterozoic acritarchs from Australia: microscopic and chemical characterisation. Org Geochem 31:75–89. https://doi.org/10.1016/S0146-6380(99)00145-X

    Article  CAS  Google Scholar 

  115. Colbath GK, Grenfell HR (1995) Review of biological affinities of Paleozoic acid-resistant, organic-walled eukaryotic algal microfossils (including “acritarchs”). Rev Palaeobot Palynol 86:287–314. https://doi.org/10.1016/0034-6667(94)00148-D

    Article  Google Scholar 

  116. Hanschen ER, Starkenburg SR (2020) The state of algal genome quality and diversity. Algal Res 50:101968. https://doi.org/10.1016/j.algal.2020.101968

    Article  Google Scholar 

  117. De Clerck O, Kao S-M, Bogaert KA et al (2018) Insights into the evolution of multicellularity from the Sea lettuce genome. Curr Biol 28:2921–2933.e5. https://doi.org/10.1016/j.cub.2018.08.015

    Article  CAS  PubMed  Google Scholar 

  118. Arimoto A, Nishitsuji K, Higa Y et al (2019) A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants. DNA Res 26:183–192. https://doi.org/10.1093/dnares/dsz002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Reisky L, Préchoux A, Zühlke M-K et al (2019) A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Nat Chem Biol 15:803–812. https://doi.org/10.1038/s41589-019-0311-9

    Article  CAS  PubMed  Google Scholar 

  120. Lahaye M, Brunel M, Bonnin E (1997) Fine chemical structure analysis of oligosaccharides produced by an ulvan-lyase degradation of the water-soluble cell-wall polysaccharides from Ulva sp. (Ulvales, Chlorophyta). Carbohydrate Research 304:325–333. https://doi.org/10.1016/S0008-6215(97)00270-X

    Article  CAS  PubMed  Google Scholar 

  121. Nyvall Collén P, Sassi J-F, Rogniaux H et al (2011) Ulvan lyases isolated from the flavobacteria persicivirga ulvanivorans are the first members of a new polysaccharide lyase family. J Biol Chem 286:42063–42071. https://doi.org/10.1074/jbc.M111.271825

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Kopel M, Helbert W, Belnik Y et al (2016) New family of ulvan lyases identified in three isolates from the Alteromonadales order. J Biol Chem 291:5871–5878. https://doi.org/10.1074/jbc.M115.673947

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Ulaganathan T, Boniecki MT, Foran E et al (2017) New ulvan-degrading polysaccharide lyase family: structure and catalytic mechanism suggests convergent evolution of active site architecture. ACS Chem Biol 12:1269–1280. https://doi.org/10.1021/acschembio.7b00126

    Article  CAS  PubMed  Google Scholar 

  124. Ulaganathan T, Helbert W, Kopel M et al (2018) Structure–function analyses of a PL24 family ulvan lyase reveal key features and suggest its catalytic mechanism. J Biol Chem 293:4026–4036. https://doi.org/10.1074/jbc.RA117.001642

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Konasani VR, Jin C, Karlsson NG, Albers E (2018) A novel ulvan lyase family with broad-spectrum activity from the ulvan utilisation loci of Formosa agariphila KMM 3901. Sci Rep 8:14713. https://doi.org/10.1038/s41598-018-32922-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Tsubaki S, Nishimura H, Imai T et al (2020) Probing rapid carbon fixation in fast-growing seaweed Ulva meridionalis using stable isotope 13C-labelling. Sci Rep 10:20399. https://doi.org/10.1038/s41598-020-77237-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Collén PN, Jeudy A, Sassi J-F et al (2014) A Novel Unsaturated β-glucuronyl hydrolase involved in ulvan degradation unveils the versatility of stereochemistry requirements in family GH105. J Biol Chem 289:6199–6211. https://doi.org/10.1074/jbc.M113.537480

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Silberfeld T, Leigh JW, Verbruggen H et al (2010) A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): investigating the evolutionary nature of the “brown algal crown radiation.”. Mol Phylogenet Evol 56:659–674. https://doi.org/10.1016/j.ympev.2010.04.020

    Article  CAS  PubMed  Google Scholar 

  129. Starko S, Soto Gomez M, Darby H et al (2019) A comprehensive kelp phylogeny sheds light on the evolution of an ecosystem. Mol Phylogenet Evol 136:138–150. https://doi.org/10.1016/j.ympev.2019.04.012

    Article  PubMed  Google Scholar 

  130. Brown JW, Sorhannus U (2010) A molecular genetic timescale for the diversification of autotrophic stramenopiles (ochrophyta): substantive underestimation of putative fossil ages. PLoS ONE 5:e12759. https://doi.org/10.1371/journal.pone.0012759

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Bringloe TT, Starko S, Wade RM et al (2020) Phylogeny and evolution of the brown algae. Crit Rev Plant Sci 39:281–321. https://doi.org/10.1080/07352689.2020.1787679

    Article  CAS  Google Scholar 

  132. Cánovas FG, Mota CF, Serrão EA, Pearson GA (2011) Driving south: a multi-gene phylogeny of the brown algal family Fucaceae reveals relationships and recent drivers of a marine radiation. BMC Evol Biol 11:371. https://doi.org/10.1186/1471-2148-11-371

    Article  PubMed  PubMed Central  Google Scholar 

  133. Rehm BHA, Valla S (1997) Bacterial alginates: biosynthesis and applications. Appl Microbiol Biotechnol 48:281–288. https://doi.org/10.1007/s002530051051

    Article  CAS  PubMed  Google Scholar 

  134. Cohen E, Merzendorfer H (2019) Extracellular sugar-based biopolymers matrices, 1st edn. Springer, Cham

    Book  Google Scholar 

  135. Moradali MF, BHA R (2018) Alginates and their biomedical applications, 1st edn Springer: Imprint: Springer, Singapore

    Google Scholar 

  136. Kawai H (2003) A new filamentous marine chromophyte belonging to a new class, Schizocladiophyceae. Protist 154:211–228. https://doi.org/10.1078/143446103322166518

    Article  CAS  PubMed  Google Scholar 

  137. Shao Z, Zhang P, Lu C et al (2019) Transcriptome sequencing of Saccharina japonica sporophytes during whole developmental periods reveals regulatory networks underlying alginate and mannitol biosynthesis. BMC Genom 20:975. https://doi.org/10.1186/s12864-019-6366-x

    Article  CAS  Google Scholar 

  138. Michel G, Tonon T, Scornet D et al (2010) The cell wall polysaccharide metabolism of the brown alga Ectocarpus siliculosus. Insights into the evolution of extracellular matrix polysaccharides in Eukaryotes. New Phytologist 188:82–97. https://doi.org/10.1111/j.1469-8137.2010.03374.x

    Article  CAS  PubMed  Google Scholar 

  139. Chi S, Liu T, Wang X et al (2018) Functional genomics analysis reveals the biosynthesis pathways of important cellular components (alginate and fucoidan) of Saccharina. Curr Genet 64:259–273. https://doi.org/10.1007/s00294-017-0733-4

    Article  CAS  PubMed  Google Scholar 

  140. Nyvall P, Corre E, Boisset C et al (2003) Characterization of mannuronan C-5-epimerase genes from the brown alga Laminaria digitata. Plant Physiol 133:726–735. https://doi.org/10.1104/pp.103.025981

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  141. Zueva AO, Silchenko AS, Rasin AB et al (2020) Expression and biochemical characterization of two recombinant fucoidanases from the marine bacterium Wenyingzhuangia fucanilytica CZ1127T. Int J Biol Macromol 164:3025–3037. https://doi.org/10.1016/j.ijbiomac.2020.08.131

    Article  CAS  PubMed  Google Scholar 

  142. Silchenko AS, Rasin AB, Kusaykin MI et al (2018) Modification of native fucoidan from Fucus evanescens by recombinant fucoidanase from marine bacteria Formosa algae. Carbohydr Polym 193:189–195. https://doi.org/10.1016/j.carbpol.2018.03.094

    Article  CAS  PubMed  Google Scholar 

  143. Vickers C, Liu F, Abe K et al (2018) Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to α-l-fucosidases from GH29. J Biol Chem 293:18296–18308. https://doi.org/10.1074/jbc.RA118.005134

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Sichert A, Corzett CH, Schechter MS et al (2020) Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol 5:1026–1039. https://doi.org/10.1038/s41564-020-0720-2

    Article  CAS  PubMed  Google Scholar 

  145. Silchenko A, Kusaykin M, Kurilenko V et al (2013) Hydrolysis of fucoidan by fucoidanase isolated from the marine bacterium, Formosa algae. Mar Drugs 11:2413–2430. https://doi.org/10.3390/md11072413

    Article  PubMed  PubMed Central  Google Scholar 

  146. Rodríguez-Jasso RM, Mussatto SI, Pastrana L et al (2010) Fucoidan-degrading fungal strains: screening, morphometric evaluation, and influence of medium composition. Appl Biochem Biotechnol 162:2177–2188. https://doi.org/10.1007/s12010-010-8992-2

    Article  CAS  PubMed  Google Scholar 

  147. Silchenko AS, Kusaykin MI, Zakharenko AM et al (2014) Endo-1,4-fucoidanase from Vietnamese marine mollusk Lambis sp. which producing sulphated fucooligosaccharides. J Mol Catal B Enzym 102:154–160. https://doi.org/10.1016/j.molcatb.2014.02.007

    Article  CAS  Google Scholar 

  148. Daniel R, Berteau O, Jozefonvicz J, Goasdoue N (1999) Degradation of algal (Ascophyllum nodosum) fucoidan by an enzymatic activity contained in digestive glands of the marine mollusc Pecten maximus. Carbohydr Res 322:291–297. https://doi.org/10.1016/S0008-6215(99)00223-2

    Article  CAS  Google Scholar 

  149. Tenhaken R, Voglas E, Cock JM et al (2011) Characterization of GDP-mannose dehydrogenase from the brown alga ectocarpus siliculosus providing the precursor for the alginate polymer. J Biol Chem 286:16707–16715. https://doi.org/10.1074/jbc.M111.230979

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2

    Article  CAS  PubMed  Google Scholar 

  151. Sayers EW, Cavanaugh M, Clark K et al (2019) GenBank. Nucleic Acids Res 47:D94–D99. https://doi.org/10.1093/nar/gky989

    Article  CAS  PubMed  Google Scholar 

  152. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268–274. https://doi.org/10.1093/molbev/msu300

    Article  CAS  PubMed  Google Scholar 

  153. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780. https://doi.org/10.1093/molbev/mst010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Thomas F, Barbeyron T, Tonon T et al (2012) Characterization of the first alginolytic operons in a marine bacterium: from their emergence in marine Flavobacteriia to their independent transfers to marine Proteobacteria and human gut Bacteroides: emergence and transfer of alginolytic operons. Environ Microbiol 14:2379–2394. https://doi.org/10.1111/j.1462-2920.2012.02751.x

    Article  CAS  PubMed  Google Scholar 

  155. Inoue A, Ojima T (2019) Functional identification of alginate lyase from the brown alga Saccharina japonica. Sci Rep 9:4937. https://doi.org/10.1038/s41598-019-41351-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Eme L, Sharpe SC, Brown MW, Roger AJ (2014) On the age of eukaryotes: evaluating evidence from fossils and molecular clocks. Cold Spring Harb Perspect Biol 6:a016139–a016139. https://doi.org/10.1101/cshperspect.a016139

    Article  PubMed  PubMed Central  Google Scholar 

  157. Sánchez-Baracaldo P, Raven JA, Pisani D, Knoll AH (2017) Early photosynthetic eukaryotes inhabited low-salinity habitats. Proc Natl Acad Sci USA 114:E7737–E7745. https://doi.org/10.1073/pnas.1620089114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Morris JL, Puttick MN, Clark JW et al (2018) The timescale of early land plant evolution. Proc Natl Acad Sci USA 115:E2274–E2283. https://doi.org/10.1073/pnas.1719588115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Dohrmann M, Wörheide G (2017) Dating early animal evolution using phylogenomic data. Sci Rep 7:3599. https://doi.org/10.1038/s41598-017-03791-w

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Rubinstein CV, Gerrienne P, de la Puente GS et al (2010) Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana). New Phytologist 188:365–369. https://doi.org/10.1111/j.1469-8137.2010.03433.x

    Article  CAS  PubMed  Google Scholar 

  161. Yue J, Hu X, Sun H et al (2012) Widespread impact of horizontal gene transfer on plant colonization of land. Nat Commun 3:1152. https://doi.org/10.1038/ncomms2148

    Article  CAS  PubMed  Google Scholar 

  162. McNamara JT, Morgan JLW, Zimmer J (2015) A molecular description of cellulose biosynthesis. Annu Rev Biochem 84:895–921. https://doi.org/10.1146/annurev-biochem-060614-033930

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Berlemont R, Martiny AC (2013) Phylogenetic distribution of potential cellulases in bacteria. Appl Environ Microbiol 79:1545–1554. https://doi.org/10.1128/AEM.03305-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  164. Sadhu S (2013) Cellulase production by bacteria: a review. BMRJ 3:235–258. https://doi.org/10.9734/BMRJ/2013/2367

    Article  Google Scholar 

  165. (1991) The evolution of cellulose digestion in insects. Phil Trans R Soc Lond B 333:281–288. https://doi.org/10.1098/rstb.1991.0078

  166. Drula E, Garron M-L, Dogan S et al (2022) The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res 50:D571–D577. https://doi.org/10.1093/nar/gkab1045

    Article  CAS  PubMed  Google Scholar 

  167. Kundu S, Sharma R (2018) Origin, evolution, and divergence of plant class C GH9 endoglucanases. BMC Evol Biol 18:79. https://doi.org/10.1186/s12862-018-1185-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Davison A, Blaxter M (2005) Ancient origin of glycosyl hydrolase family 9 cellulase genes. Mol Biol Evol 22:1273–1284. https://doi.org/10.1093/molbev/msi107

    Article  CAS  PubMed  Google Scholar 

  169. Lo N, Watanabe H, Sugimura M (2003) Evidence for the presence of a cellulase gene in the last common ancestor of bilaterian animals. Proc R Soc Lond B 270. https://doi.org/10.1098/rsbl.2003.0016

  170. Artzi L, Bayer EA, Moraïs S (2017) Cellulosomes: bacterial nanomachines for dismantling plant polysaccharides. Nat Rev Microbiol 15:83–95. https://doi.org/10.1038/nrmicro.2016.164

    Article  CAS  PubMed  Google Scholar 

  171. Rothman DH, Fournier GP, French KL et al (2014) Methanogenic burst in the end-Permian carbon cycle. Proc Natl Acad Sci 111:5462–5467. https://doi.org/10.1073/pnas.1318106111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  172. Weng J, Chapple C (2010) The origin and evolution of lignin biosynthesis. New Phytologist 187:273–285. https://doi.org/10.1111/j.1469-8137.2010.03327.x

    Article  CAS  PubMed  Google Scholar 

  173. Renault H, Alber A, Horst NA et al (2017) A phenol-enriched cuticle is ancestral to lignin evolution in land plants. Nat Commun 8:14713. https://doi.org/10.1038/ncomms14713

    Article  PubMed  PubMed Central  Google Scholar 

  174. Cagide C, Castro-Sowinski S (2020) Technological and biochemical features of lignin-degrading enzymes: a brief review. Environ Sustain 3:371–389. https://doi.org/10.1007/s42398-020-00140-y

    Article  CAS  Google Scholar 

  175. Pollegioni L, Tonin F, Rosini E (2015) Lignin-degrading enzymes. FEBS J 282:1190–1213. https://doi.org/10.1111/febs.13224

    Article  CAS  PubMed  Google Scholar 

  176. Fan S, Liu A, Zou X et al (2021) Evolution of pectin synthesis relevant galacturonosyltransferase gene family and its expression during cotton fiber development. J Cotton Res 4:22. https://doi.org/10.1186/s42397-021-00099-z

    Article  CAS  Google Scholar 

  177. Kuivanen J, Biz A, Richard P (2019) Microbial hexuronate catabolism in biotechnology. AMB Express 9:16. https://doi.org/10.1186/s13568-019-0737-1

    Article  PubMed  PubMed Central  Google Scholar 

  178. Zheng L, Xu Y, Li Q, Zhu B (2021) Pectinolytic lyases: a comprehensive review of sources, category, property, structure, and catalytic mechanism of pectate lyases and pectin lyases. Bioresour Bioprocess 8:79. https://doi.org/10.1186/s40643-021-00432-z

    Article  Google Scholar 

  179. Uluisik S, Seymour GB (2020) Pectate lyases: their role in plants and importance in fruit ripening. Food Chem 309:125559. https://doi.org/10.1016/j.foodchem.2019.125559

    Article  CAS  PubMed  Google Scholar 

  180. Wang D, Yeats TH, Uluisik S et al (2018) Fruit softening: revisiting the role of pectin. Trends Plant Sci 23:302–310. https://doi.org/10.1016/j.tplants.2018.01.006

    Article  CAS  PubMed  Google Scholar 

  181. Hugouvieux-Cotte-Pattat N, Condemine G, Shevchik VE (2014) Bacterial pectate lyases, structural and functional diversity: bacterial pectate lyases. Environ Microbiol Rep 6:427–440. https://doi.org/10.1111/1758-2229.12166

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA

    Gregory P. Fournier, Chris W. Parsons, Elise M. Cutts & Erik Tamre

Authors
  1. Gregory P. Fournier
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chris W. Parsons
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Elise M. Cutts
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Erik Tamre
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gregory P. Fournier .

Editor information

Editors and Affiliations

  1. School of Life Sciences, Earth and Environmental Sciences Programme, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China

    Haiwei Luo

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Fournier, G.P., Parsons, C.W., Cutts, E.M., Tamre, E. (2022). Standard Candles for Dating Microbial Lineages. In: Luo, H. (eds) Environmental Microbial Evolution. Methods in Molecular Biology, vol 2569. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2691-7_3

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2691-7_3

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2690-0

  • Online ISBN: 978-1-0716-2691-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation