Format

Send to

Choose Destination
Sci Rep. 2019 Jul 19;9(1):10482. doi: 10.1038/s41598-019-46869-3.

Gains and losses of metabolic function inferred from a phylotranscriptomic analysis of algae.

Author information

1
Yale-NUS College Singapore, 138527, Singapore, Singapore.
2
Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore.
3
Department of Biochemistry, Yong Loo Lin School of Medicine National University of Singapore, Singapore, 117596, Singapore.
4
Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, Canada.
5
Department of Medicine, University of Alberta, Edmonton, T6G 2E1, Canada.
6
BGI-Shenzhen, Shenzhen, 518083, China.
7
Botanical Institute, Cologne Biocenter, University of Cologne, 50674, Cologne, Germany.
8
Yale-NUS College Singapore, 138527, Singapore, Singapore. neil.clarke@yale-nus.edu.sg.
9
Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore. neil.clarke@yale-nus.edu.sg.
10
Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore. neil.clarke@yale-nus.edu.sg.

Abstract

Hidden Markov models representing 167 protein sequence families were used to infer the presence or absence of homologs within the transcriptomes of 183 algal species/strains. Statistical analyses of the distribution of HMM hits across major clades of algae, or at branch points on the phylogenetic tree of 98 chlorophytes, confirmed and extended known cases of metabolic loss and gain, most notably the loss of the mevalonate pathway for terpenoid synthesis in green algae but not, as we show here, in the streptophyte algae. Evidence for novel events was found as well, most remarkably in the recurrent and coordinated gain or loss of enzymes for the glyoxylate shunt. We find, as well, a curious pattern of retention (or re-gain) of HMG-CoA synthase in chlorophytes that have otherwise lost the mevalonate pathway, suggesting a novel, co-opted function for this enzyme in select lineages. Finally, we find striking, phylogenetically linked distributions of coding sequences for three pathways that synthesize the major membrane lipid phosphatidylcholine, and a complementary phylogenetic distribution pattern for the non-phospholipid DGTS (diacyl-glyceryl-trimethylhomoserine). Mass spectrometric analysis of lipids from 25 species was used to validate the inference of DGTS synthesis from sequence data.

Supplemental Content

Full text links

Icon for Nature Publishing Group Icon for PubMed Central
Loading ...
Support Center