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

  1. David R Nelson  Is a corresponding author
  2. Basel Khraiwesh
  3. Weiqi Fu
  4. Saleh Alseekh
  5. Ashish Jaiswal
  6. Amphun Chaiboonchoe
  7. Khaled M Hazzouri
  8. Matthew J O’Connor
  9. Glenn L Butterfoss
  10. Nizar Drou
  11. Jillian D Rowe
  12. Jamil Harb
  13. Alisdair R Fernie
  14. Kristin C Gunsalus
  15. Kourosh Salehi-Ashtiani  Is a corresponding author
  1. New York University Abu Dhabi, United Arab Emirates
  2. Max Planck Institute of Molecular Plant Physiology, Germany
  3. Birzeit University, Palestine
  4. New York University, United States
7 figures and 1 table

Figures

Geography and morphology of isolated Chloroidium strains.

Chloroidium strains were isolated from samples taken from the indicated locations in (a) the UAE, and (b) within Abu Dhabi city specifically. Chloroidium strains were found in estuaries, mangrove …

https://doi.org/10.7554/eLife.25783.003
Figure 2 with 2 supplements
Cell size, growth, and lipid accumulation in Chloroidium sp. UTEX 3007.

(a) Cell size distribution of Chloroidium sp. UTEX 3007 in late log phase (14 days). Cell size analysis was performed using a Cellometer Auto M10 from Nexcelcom Bioscience (Lawrence, MA, USA) on 2 × …

https://doi.org/10.7554/eLife.25783.004
Figure 2—source data 1

Cell diameter measurements.

https://doi.org/10.7554/eLife.25783.005
Figure 2—source data 2

Cell concentration time course measurements.

https://doi.org/10.7554/eLife.25783.006
Figure 2—source data 3

Flow cytometry measurements.

https://doi.org/10.7554/eLife.25783.007
Figure 2—figure supplement 1
OPS growth curve.
https://doi.org/10.7554/eLife.25783.008
Figure 2—figure supplement 2
Chlorophyll/cell count curve.
https://doi.org/10.7554/eLife.25783.009
Lipid composition of Chloroidium sp. UTEX 3007 observed with HPLC/MS and GC-FID, and comparison with other photosynthetic, oleagenic species.

(a) Chloroidium sp. UTEX 3007 fatty acid content estimated by extracting total lipid, creating methyl esters, and running the esters on a GC-FID (whiskers = range, box boundaries = 1 SD, center box …

https://doi.org/10.7554/eLife.25783.010
Figure 3—source data 1

GC-FID results for major fatty acid species in Chloroidium sp. UTEX 3007.

https://doi.org/10.7554/eLife.25783.011
Figure 3—source data 2

Fatty acid profiles of Chloroidium sp. UTEX 3007, Elaeis guineensis (Barcelos et al., 2015), and several other algal isolates (Lang et al., 2011).

https://doi.org/10.7554/eLife.25783.012
Figure 3—source data 3

HPLC-MS base peak chromatograms (BPCs) for Chloroidium sp. UTEX 3007 and Chlamydomonas reinhardtii extracts.

https://doi.org/10.7554/eLife.25783.013
Metabolic profiling of Chloroidium sp. UTEX 3007.

(a) Biolog phenotype microarrays were run using an Omnilog instrument (Biolog Inc., Hayward, USA) as previously described (Chaiboonchoe et al., 2014). In total, 380 substrate utilization assays for …

https://doi.org/10.7554/eLife.25783.014
Figure 4—source data 1

Phenotype microarray results for plates PM1, PM2, and PM3.

https://doi.org/10.7554/eLife.25783.015
Figure 4—source data 2

GC-MS results for Chloroidium sp. UTEX 3007 (Cm) and Chlamydomonas reinhardtii (Cre) intracellular polar metabolites.

https://doi.org/10.7554/eLife.25783.016
Phospholipase D (PLD; EC number: 3.1.1.4) domain-containing gene in Chloroidium sp. UTEX 3007.

Functional protein family domains in a Chloroidium sp. UTEX 3007 predicted protein with high similarity to PLD proteins from closely related organisms. PLDs are members of the phospholipase …

https://doi.org/10.7554/eLife.25783.017
Figure 5—source data 1

Locations, confidence scores, and accession numbers for PLD and C2 Pfam domains in Chloroidium sp. UTEX 3007.

https://doi.org/10.7554/eLife.25783.018
Protein family (Pfam) domains in Chloroidium sp. UTEX 3007 compared with algae from other clades.

Well-curated assemblies from genomes of algae from four other clades were downloaded from NCBI [assemblies - Micromonas pusilla, Ostreococcus taurii, and Coccomyxa subellipsoidea]. The Chlamydomonas …

https://doi.org/10.7554/eLife.25783.019
Figure 6—source data 1

Predicted Pfam designations for each species in Figure 6.

https://doi.org/10.7554/eLife.25783.020
Figure 6—source data 2

Table with QUAST results used in (b).

https://doi.org/10.7554/eLife.25783.021
Figure 6—source data 3

Interactive Venn diagram that can be viewed at interactivenn.net to obtain Pfam sets for numbers displayed in Figure 6.

https://doi.org/10.7554/eLife.25783.022
Figure 7 with 1 supplement
Chloroidium sp. UTEX 3007 genes exhibiting homology with desiccation-responsive Deinococcus genes.

(a) Gene models for the putative manganese catalases (CDS1/2/3). Functional annotation of homologs from (CDS1/2/3) is limited: 96 of the top 100 BLAST hits of CDS3 in the non-redundant database (nr …

https://doi.org/10.7554/eLife.25783.024
Figure 7—source data 1

Models of CDS1-3 in protein data bank (PDB) format.

https://doi.org/10.7554/eLife.25783.025
Figure 7—source data 2

Amino acid residue alignment of CDS1-3.

https://doi.org/10.7554/eLife.25783.026
Figure 7—figure supplement 1
Alignment of CDS3 to a Deinococcus globiensis desiccation-related protein (Yuan et al., 2012).

Metal-binding motif residues are highlighted.

https://doi.org/10.7554/eLife.25783.027

Tables

Table 1

Protein families (Pfams) with roles in (a) abiotic stress resistance and (b) saccharide metabolism unique to Chloroidium among the green algae explored. Pfam domains were predicted using HMMsearch …

https://doi.org/10.7554/eLife.25783.023

DescriptionKeyi-Evalue
(a)Iron-containing redox enzymeHaem_oxygenas_27.50E-05
Salt tolerance down-regulatorNST10.00012
Proline-richPro-rich0.00015
Peroxisome biogenesis factorPEX-2N0.003
OsmC-like proteinOsmC0.0066
NA,K-Atpase interacting proteinNKAIN0.003
MetallothioneinMetallothio_20.0074
Mercuric transport proteinMerT0.0054
(b)Beta-galactosidase jelly roll domainBetaGal_dom4_50.013
Cryptococcal mannosyltransferaseCAP59_mtransfer3.50E-15
Carbohydrate binding domain CBM49CBM490.0085
Carbohydrate binding domain (family 25)CBM_250.0023
Carbohydrate binding domainCBM_4_90.00036
Cellulose biosynthesis protein BcsNCBP_BcsN0.0018
Glycosyl hydrolase family 70Glyco_hydro_700.00054
Glycosyl hydrolase family 9 (heptosyltransferase)Glyco_transf_90.0025
Carbohydrate esterase/acetylesteraseSASA2.00E-06
Activator of aromatic catabolismXylR_N0.011

Download links