The Genome and Phenome of the Green Alga UTEX 3007 Reveal Adaptive Traits for Desert Acclimatization

Overview

Journal Elife

Specialty Biology

Date 2017 Jun 18

PMID 28623667

Citations 5

Authors

David R Nelson

Basel Khraiwesh

Weiqi Fu

Saleh Alseekh

Ashish Jaiswal

Amphun Chaiboonchoe

Khaled M Hazzouri

Matthew J OConnor

Glenn L Butterfoss

Nizar Drou

Jillian D Rowe

Jamil Harb

Alisdair R Fernie

Kristin C Gunsalus

Kourosh Salehi-Ashtiani

Affiliations

Soon will be listed here.

Abstract

To investigate the phenomic and genomic traits that allow green algae to survive in deserts, we characterized a ubiquitous species, , which we isolated from multiple locations in the United Arab Emirates (UAE). Metabolomic analyses of indicated that the alga accumulates a broad range of carbon sources, including several desiccation tolerance-promoting sugars and unusually large stores of palmitate. Growth assays revealed capacities to grow in salinities from zero to 60 g/L and to grow heterotrophically on >40 distinct carbon sources. Assembly and annotation of genomic reads yielded a 52.5 Mbp genome with 8153 functionally annotated genes. Comparison with other sequenced green algae revealed unique protein families involved in osmotic stress tolerance and saccharide metabolism that support phenomic studies. Our results reveal the robust and flexible biology utilized by a green alga to successfully inhabit a desert coastline.

Citing Articles

Cyanobacteria and Algae in Clouds and Rain in the Area of puy de Dôme, Central France.

Dillon K, Correa F, Judon C, Sancelme M, Fennell D, Delort A Appl Environ Microbiol. 2020; 87(1).

PMID: 33097513 PMC: 7755241. DOI: 10.1128/AEM.01850-20.

Bioengineering of Microalgae: Recent Advances, Perspectives, and Regulatory Challenges for Industrial Application.

Kumar G, Shekh A, Jakhu S, Sharma Y, Kapoor R, Sharma T Front Bioeng Biotechnol. 2020; 8:914.

PMID: 33014997 PMC: 7494788. DOI: 10.3389/fbioe.2020.00914.

Emerging Technologies to Enable Sustainable Controlled Environment Agriculture in the Extreme Environments of Middle East-North Africa Coastal Regions.

Lefers R, Tester M, Lauersen K Front Plant Sci. 2020; 11:801.

PMID: 32714341 PMC: 7343771. DOI: 10.3389/fpls.2020.00801.

Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae.

Nelson D, Chaiboonchoe A, Fu W, Hazzouri K, Huang Z, Jaiswal A iScience. 2019; 11:450-465.

PMID: 30684492 PMC: 6348204. DOI: 10.1016/j.isci.2018.12.035.

The genome and phenome of the green alga UTEX 3007 reveal adaptive traits for desert acclimatization.

Nelson D, Khraiwesh B, Fu W, Alseekh S, Jaiswal A, Chaiboonchoe A Elife. 2017; 6.

PMID: 28623667 PMC: 5509433. DOI: 10.7554/eLife.25783.

References

Vaas L, Sikorski J, Michael V, Goker M, Klenk H . Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS One. 2012; 7(4):e34846. PMC: 3334903. DOI: 10.1371/journal.pone.0034846. View

Leaver-Fay A, Tyka M, Lewis S, Lange O, Thompson J, Jacak R . ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 2010; 487:545-74. PMC: 4083816. DOI: 10.1016/B978-0-12-381270-4.00019-6. View

Merchant S, Prochnik S, Vallon O, Harris E, Karpowicz S, Witman G . The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science. 2007; 318(5848):245-50. PMC: 2875087. DOI: 10.1126/science.1143609. View

Furuyoshi S, Shi Y, Rando R . Acyl group transfer from the sn-1 position of phospholipids in the biosynthesis of n-dodecyl palmitate. Biochemistry. 1993; 32(20):5425-30. DOI: 10.1021/bi00071a018. View

Lunn J, Delorge I, Figueroa C, Van Dijck P, Stitt M . Trehalose metabolism in plants. Plant J. 2014; 79(4):544-67. DOI: 10.1111/tpj.12509. View

Dahlqvist A, Stahl U, Lenman M, Banas A, Lee M, Sandager L . Phospholipid:diacylglycerol acyltransferase: an enzyme that catalyzes the acyl-CoA-independent formation of triacylglycerol in yeast and plants. Proc Natl Acad Sci U S A. 2000; 97(12):6487-92. PMC: 18631. DOI: 10.1073/pnas.120067297. View

Umen J, Olson B . Genomics of Volvocine Algae. Adv Bot Res. 2015; 64:185-243. PMC: 4396658. DOI: 10.1016/B978-0-12-391499-6.00006-2. View

Newbold T, Hudson L, Hill S, Contu S, Lysenko I, Senior R . Global effects of land use on local terrestrial biodiversity. Nature. 2015; 520(7545):45-50. DOI: 10.1038/nature14324. View

Alam I, Hubbard S, Oliver S, Rattray M . A kingdom-specific protein domain HMM library for improved annotation of fungal genomes. BMC Genomics. 2007; 8:97. PMC: 1854895. DOI: 10.1186/1471-2164-8-97. View

10.

Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher C . The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 2013; 42(Database issue):D459-71. PMC: 3964957. DOI: 10.1093/nar/gkt1103. View

11.

Blanc G, Agarkova I, Grimwood J, Kuo A, Brueggeman A, Dunigan D . The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. Genome Biol. 2012; 13(5):R39. PMC: 3446292. DOI: 10.1186/gb-2012-13-5-r39. View

12.

Kunst L, Browse J, Somerville C . Enhanced thermal tolerance in a mutant of Arabidopsis deficient in palmitic Acid unsaturation. Plant Physiol. 1989; 91(1):401-8. PMC: 1062006. DOI: 10.1104/pp.91.1.401. View

13.

Cvikrova M, Gemperlova L, Dobra J, Martincova O, Prasil I, Gubis J . Effect of heat stress on polyamine metabolism in proline-over-producing tobacco plants. Plant Sci. 2011; 182:49-58. DOI: 10.1016/j.plantsci.2011.01.016. View

14.

Peppino Margutti M, Reyna M, Meringer M, Racagni G, Villasuso A . Lipid signalling mediated by PLD/PA modulates proline and HO levels in barley seedlings exposed to short- and long-term chilling stress. Plant Physiol Biochem. 2017; 113:149-160. DOI: 10.1016/j.plaphy.2017.02.008. View

15.

Bihani S, Chakravarty D, Ballal A . Purification, crystallization and preliminary crystallographic analysis of KatB, a manganese catalase from Anabaena PCC 7120. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013; 69(Pt 11):1299-302. PMC: 3818058. DOI: 10.1107/S1744309113028017. View

16.

Andrews S . The Ferritin-like superfamily: Evolution of the biological iron storeman from a rubrerythrin-like ancestor. Biochim Biophys Acta. 2010; 1800(8):691-705. DOI: 10.1016/j.bbagen.2010.05.010. View

17.

Abrams J, Hohn S, Rixen T, Baum A, Merico A . The impact of Indonesian peatland degradation on downstream marine ecosystems and the global carbon cycle. Glob Chang Biol. 2015; 22(1):325-37. DOI: 10.1111/gcb.13108. View

18.

Barber G . The synthesis of L-glucose by plant enzyme systems. Arch Biochem Biophys. 1971; 147(2):619-23. DOI: 10.1016/0003-9861(71)90420-6. View

19.

Yue S, Brodie J, Zipkin E, Bernard H . Oil palm plantations fail to support mammal diversity. Ecol Appl. 2016; 25(8):2285-92. DOI: 10.1890/14-1928.1. View

20.

Sinha S, Lynn A . HMM-ModE: implementation, benchmarking and validation with HMMER3. BMC Res Notes. 2014; 7:483. PMC: 4236727. DOI: 10.1186/1756-0500-7-483. View