A DUF3494 ice-binding protein with a root cap domain in a streptophyte glacier ice alga

. 2023 ; 14 () : 1306511. [epub] 20240105

Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic-ecollection

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid38250448

Ice-binding proteins (IBPs) of the DUF3494 type have been found in many ice-associated unicellular photoautotrophs, including chlorophytes, haptophytes, diatoms and a cyanobacterium. Unrelated IBPs have been found in many land plants (streptophytes). Here we looked for IBPs in two streptophyte algae that grow only on glaciers, a group in which IBPs have not previously been examined. The two species, Ancylonema nordenskioeldii and Ancylonema. alaskanum, belong to the class Zygnematophyceae, whose members are the closest relatives to all land plants. We found that one of them, A. nordenskioeldii, expresses a DUF3494-type IBP that is similar to those of their chlorophyte ancestors and that has not previously been found in any streptophytes. The protein is unusual in having what appears to be a perfect array of TXT motifs that have been implicated in water or ice binding. The IBP strongly binds to ice and almost certainly has a role in mitigating the daily freeze-thaw cycles that the alga is exposed to during late summer. No IBP was found in the second species, A. alaskanum, which may rely more on glycerol production for its freeze-thaw tolerance. The IBP is also unusual in having a 280-residue domain with a β sandwich structure (which we designate as the DPH domain) that is characteristic of root cap proteins of land plants, and that may have a role in forming IBP oligomers. We also examined existing transcriptome data obtained from land plants to better understand the tissue and temperature dependence of expression of this domain.

Zobrazit více v PubMed

Basha E., O’Neill H., Vierling E. (2012). Small heat shock proteins and α-crystallins: dynamic proteins with flexible functions. Trends Biochem. Sci. 37, 106–117. doi: 10.1016/j.tibs.2011.11.005 PubMed DOI PMC

Becker B., Marin B. (2009). Streptophyte algae and the origin of embryophytes. Ann. Bot. 103, 999–1004. doi: 10.1093/aob/mcp044 PubMed DOI PMC

Bowles A. M., Bechtold U., Paps J. (2020). The origin of land plants is rooted in two bursts of genomic novelty. Curr. Biol. 30, 530–536.e532. doi: 10.1016/j.cub.2019.11.090 PubMed DOI

Bredow M., Vanderbeld B., Walker V. K. (2016). Knockdown of ice-binding proteins in Brachypodium distachyon demonstrates their role in freeze protection. PloS One 11, e0167941. doi: 10.1371/journal.pone.0167941 PubMed DOI PMC

Bredow M., Walker V. K. (2017). Ice-binding proteins in plants. Front. Plant Sci. 8, 2153. doi: 10.3389/fpls.2017.02153 PubMed DOI PMC

Cheng S., Xian W., Fu Y., Marin B., Keller J., Wu T., et al. . (2019). Genomes of subaerial Zygnematophyceae provide insights into land plant evolution. Cell 179, 1057–1067. e1014. doi: 10.1016/j.cell.2019.10.019 PubMed DOI

Graether S. P., Sykes B. D. (2004). Cold survival in freeze-intolerant insects: The structure and function of β-helical antifreeze proteins. Eur. J. Biochem. 271, 3285–3296. doi: 10.1111/j.1432-1033.2004.04256.x PubMed DOI

Haslbeck M., Vierling E. (2015). A first line of stress defense: small heat shock proteins and their function in protein homeostasis. J. Mol. Biol. 427, 1537–1548. doi: 10.1016/j.jmb.2015.02.002 PubMed DOI PMC

Janech M. G., Krell A., Mock T., Kang J. S., Raymond J. A. (2006). Ice-binding proteins from sea ice diatoms (bacillariophyceae) 1. J. phycology 42, 410–416. doi: 10.1111/j.1529-8817.2006.00208.x DOI

Jensen M. B., Perini L., Halbach L., Jakobsen H., Haraguchi L., Ribeiro S., et al. . (2023). The dark art of cultivating glacier ice algae. Bot. Lett., 1–10. doi: 10.1080/23818107.2023.2248235 DOI

John U. P., Polotnianka R. M., Sivakumaran K. A., Chew O., Mackin L., Kuiper M. J., et al. . (2009). Ice recrystallization inhibition proteins (IRIPs) and freeze tolerance in the cryophilic Antarctic hair grass Deschampsia antarctica E. Desv. Plant Cell Environ. 32, 336–348. doi: 10.1111/j.1365-3040.2009.01925.x PubMed DOI

Jumper J., Evans R., Pritzel A., Green T., Figurnov M., Ronneberger O., et al. . (2021). Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589. doi: 10.1038/s41586-021-03819-2 PubMed DOI PMC

Kendrick N., Powers G., Johansen J., Hoelter M., Koll A., Carlson S., et al. . (2020). Preparation of a phosphotyrosine-protein standard for use in semiquantitative western blotting with enhanced chemiluminescence. PloS One 15, e0234645. doi: 10.1371/journal.pone.0234645 PubMed DOI PMC

Krieger E., Vriend G. (2014). YASARA View—molecular graphics for all devices—from smartphones to workstations. Bioinformatics 30, 2981–2982. doi: 10.1093/bioinformatics/btu426 PubMed DOI PMC

Kuiper M. J., Davies P. L., Walker V. K. (2001). A theoretical model of a plant antifreeze protein from Lolium perenne . Biophys. J. 81, 3560–3565. doi: 10.1016/S0006-3495(01)75986-3 PubMed DOI PMC

Kumpf R. P., Nowack M. K. (2015). The root cap: a short story of life and death. J. Exp. Bot. 66, 5651–5662. doi: 10.1093/jxb/erv295 PubMed DOI

Levy Karin E., Mirdita M., Söding J. (2020). MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. Microbiome 8, 1–15. doi: 10.1186/s40168-020-00808-x PubMed DOI PMC

Matsuyama T., Satoh H., Yamada Y., Hashimoto T. (1999). A maize glycine-rich protein is synthesized in the lateral root cap and accumulates in the mucilage. Plant Physiol. 120, 665–674. doi: 10.1104/pp.120.3.665 PubMed DOI PMC

Middleton A. J., Marshall C. B., Faucher F., Bar-Dolev M., Braslavsky I., Campbell R. L., et al. . (2012). Antifreeze protein from freeze-tolerant grass has a beta-roll fold with an irregularly structured ice-binding site. J. Mol. Biol. 416, 713–724. doi: 10.1016/j.jmb.2012.01.032 PubMed DOI

Mirdita M., Schütze K., Moriwaki Y., Heo L., Ovchinnikov S., Steinegger M. (2022). ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682. doi: 10.1038/s41592-022-01488-1 PubMed DOI PMC

Nedelcu A. M., Borza T., Lee R. W. (2006). A land plant–specific multigene family in the unicellular Mesostigma argues for its close relationship to Streptophyta. Mol. Biol. Evol. 23, 1011–1015. doi: 10.1093/molbev/msj108 PubMed DOI

Pettersen E. F., Goddard T. D., Huang C. C., Meng E. C., Couch G. S., Croll T. I., et al. . (2021). UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82. doi: 10.1002/pro.3943 PubMed DOI PMC

Procházková L., Řezanka T., Nedbalová L., Remias D. (2021). Unicellular versus Filamentous: The Glacial Alga Ancylonema alaskana comb. et stat. nov. and Its Ecophysiological Relatedness to Ancylonema nordenskioeldii (Zygnematophyceae, Streptophyta). Microorganisms 9, 1103. doi: 10.3390/microorganisms9051103 PubMed DOI PMC

Rabanus-Wallace M. T., Hackauf B., Mascher M., Lux T., Wicker T., Gundlach H., et al. . (2021). Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential. Nat. Genet. 53, 564–573. doi: 10.1038/s41588-021-00807-0 PubMed DOI PMC

Raymond J. A., Fritsen C. H. (2000). Ice-active substances associated with Antarctic freshwater and terrestrial photosynthetic organisms. Antarctic Sci. 12, 418–424. doi: 10.1017/S0954102000000493 PubMed DOI

Raymond J. A., Fritsen C. H. (2001). Semipurification and ice recrystallization inhibition activity of ice-active substances associated with Antarctic photosynthetic organisms. Cryobiology 43, 63–70. doi: 10.1006/cryo.2001.2341 PubMed DOI

Raymond J. A., Fritsen C., Shen K. (2007). An ice-binding protein from an Antarctic sea ice bacterium. FEMS Microbiol. Ecol. 61, 214–221. doi: 10.1111/j.1574-6941.2007.00345.x PubMed DOI

Raymond J. A., Janech M. G., Fritsen C. H. (2009). Novel ice-binding proteins from a psychrophilic antarctic alga (Chlamydomonadaceae, Chlorophyceae). J. Phycology 45, 130–136. doi: 10.1111/j.1529-8817.2008.00623.x PubMed DOI

Raymond J. A., Janech M. G., Mangiagalli M. (2021). Ice-binding proteins associated with an Antarctic cyanobacterium, Nostoc sp. HG1. Appl. Environ. Microbiol. 87, e02499–e02420. doi: 10.1128/AEM.02499-20 PubMed DOI PMC

Raymond J. A., Kim H. J. (2012). Possible role of horizontal gene transfer in the colonization of sea ice by algae. PloS One 7, 1–9. doi: 10.1371/journal.pone.0035968 PubMed DOI PMC

Raymond J. A., Remias D. (2019). Ice-binding proteins in a Chrysophycean snow alga: acquisition of an essential gene by horizontal gene transfer. Front. Microbiol. 10. doi: 10.3389/fmicb.2019.02697 PubMed DOI PMC

Remias D., Procházková L. (2023). The first cultivation of the glacier ice alga Ancylonema alaskanum (Zygnematophyceae, Streptophyta): differences in morphology and photophysiology of field vs laboratory strain cells. J. Glaciology 69, 1080–1084. doi: 10.1017/jog.2023.22 DOI

Remias D., Procházková L., Nedbalová L., Benning L. G., Lutz S. (2023). Novel insights in cryptic diversity of snow and glacier ice algae communities combining 18S rRNA gene and ITS2 amplicon sequencing. FEMS Microbiol. Ecol. 99, fiad134. doi: 10.1093/femsec/fiad134 PubMed DOI PMC

Remias D., Schwaiger S., Aigner S., Leya T., Stuppner H., Lütz C. (2012). Characterization of an UV-and VIS-absorbing, purpurogallin-derived secondary pigment new to algae and highly abundant in Mesotaenium berggrenii (Zygnematophyceae, Chlorophyta), an extremophyte living on glaciers. FEMS Microbiol. Ecol. 79, 638–648. doi: 10.1111/j.1574-6941.2011.01245.x PubMed DOI

Rensing S. A. (2018). Great moments in evolution: the conquest of land by plants. Curr. Opin. Plant Biol. 42, 49–54. doi: 10.1016/j.pbi.2018.02.006 PubMed DOI

Roser D. J., Melick D., Ling H., Seppelt R. (1992). Polyol and sugar content of terrestrial plants from continental Antarctica. Antarctic Sci. 4, 413–420. doi: 10.1017/S0954102092000610 DOI

Sekimoto H., Komiya A., Tsuyuki N., Kawai J., Kanda N., Ootsuki R., et al. . (2023). A divergent RWP-RK transcription factor determines mating type in heterothallic Closterium . New Phytol. 237, 1636–1651. doi: 10.1111/nph.18662 PubMed DOI

Sformo T. L., Raymond J. A. (2020). An ice-binding protein from an Arctic population of American dunegrass, Leymus mollis. F1000Research 9, 648. (London: Taylor and Francis; ). doi: 10.12688/f1000research.24328.2 PubMed DOI PMC

Vance T. D. R., Bayer-Giraldi M., Davies P. L., Mangiagalli M. (2019). Ice-binding proteins and the ‘domain of unknown function’ 3494 family. FEBS J. 286, 855–873. doi: 10.1111/febs.14764 PubMed DOI

Vance T. D., Graham L. A., Davies P. L. (2018). An ice-binding and tandem beta-sandwich domain-containing protein in Shewanella frigidimarina is a potential new type of ice adhesin. FEBS J. 285, 1511–1527. doi: 10.1111/febs.14424 PubMed DOI

Wastian H. (2010). Snow algae: analysis of soluble carbohydrates and ecophysiological aspects. Masters thesis, Innsbruck University, Innsbruck, Austria.

Waters E. R., Vierling E. (2020). Plant small heat shock proteins–evolutionary and functional diversity. New Phytol. 227, 24–37. doi: 10.1111/nph.16536 PubMed DOI

Wisniewski M., Willick I. R., Duman J. G., Livingston D., Newton S. S. (2020). “Plant antifreeze proteins,” in Antifreeze Proteins Volume 1: Environment, Systematics and Evolution (Springer Nature, London: ), 189–226.

Wood D. E., Salzberg S. L. (2014). Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, 1–12. doi: 10.1186/gb-2014-15-3-r46 PubMed DOI PMC

Zhang C., Fei S. Z., Arora R., Hannapel D. J. (2010). Ice recrystallization inhibition proteins of perennial ryegrass enhance freezing tolerance. Planta 232, 155–164. doi: 10.1007/s00425-010-1163-4 PubMed DOI

Najít záznam

Citační ukazatele

Nahrávání dat ...

    Možnosti archivace