Comprehensive Analysis of a Yeast Lipase Family in the Yarrowia Clade

Meunchan, Muchalin; Michely, Stéphanie; Devillers, Hugo; Nicaud, Jean‐Marc; Marty, Alain; Neuvéglise, Cécile

doi:10.1371/journal.pone.0143096

Cited by 34 publications

(33 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In C. parapsilosis, C. tropicalis, and Y. lipolytica, all of which harbored the greatest number of CYP52 proteins, the extensive expansion of this family could be associated with an evolutionary process for assimilating long chain n-alkanes and fatty acids under several environmental and nutritional conditions. Similar phenomena were observed in other expanded paralogous protein families, including hexose transporters 55 , antifreeze glycoproteins 56 , histones 57 , lipases 58 , and ABC transporters involved in drug resistance 59 , among others. The phenotypic plasticity derived from differential expression of an expanded paralogous family is valuable under changing environmental conditions 60,61 .…”

Section: Discussionsupporting

confidence: 74%

Phylogeny, evolution, and potential ecological relationship of cytochrome CYP52 enzymes in Saccharomycetales yeasts

Ortiz‐Álvarez

Becerra

Méndez‐Tenorio

et al. 2020

Sci Rep

View full text Add to dashboard Cite

Cytochrome P450s from the CYP52 family participate in the assimilation of alkanes and fatty acids in fungi. In this work, the evolutionary history of a set of orthologous and paralogous CYP52 proteins from Saccharomycetales yeasts was inferred. Further, the phenotypic assimilation profiles were related with the distribution of cytochrome CYP52 members among species. The maximum likelihood phylogeny of CYP52 inferred proteins reveled a frequent ancient and modern duplication and loss events that generated orthologous and paralogous groups. Phylogeny and assimilation profiles of alkanes and fatty acids showed a family expansion in yeast isolated from hydrophobic-rich environments. Docking analysis of deduced ancient CYP52 proteins suggests that the most ancient function was the oxidation of C4-C11 alkanes, while the oxidation of >10 carbon alkanes and fatty acids is a derived character. The ancient CYP52 paralogs displayed partial specialization and promiscuous interaction with hydrophobic substrates. Additionally, functional optimization was not evident. Changes in the interaction of ancient CYP52 with different alkanes and fatty acids could be associated with modifications in spatial orientations of the amino acid residues that comprise the active site. The extended family of CYP52 proteins is likely evolving toward functional specialization, and certain redundancy for substrates is being maintained. Cytochromes P450 (CYPs) are an extended heme-thiolate enzyme superfamily that are widely distributed among different biological domains 1,2. P450s are involved in the oxidation of myriad endogenous and xenobiotic hydrophobic compounds. Hence, P450s play a critical role in the biosynthesis of structural molecules and secondary metabolites 3,4 , utilization of compounds as sole carbon and energy sources 5 , and cellular detoxification 6 , among others. The cytochrome P450s that belong to the CYP52 family are present in the orders Eurotiales, Pezizomycetes, Leotiomycetes, Dothideomycetes and Saccharomycetales of Ascomycota fungi 7. CYP52 enzymes are located in the endoplasmic reticulum (ER) membrane, and their main function is the hydroxylation of n-alkanes and fatty acids, which are successively oxidized to mono-or dicarboxylic fatty acids, respectively, by additional oxidation reactions catalyzed by alcohol and aldehyde deshydrogenases 5,8. Finally, fatty acids are degraded in the fungal peroxisome and mitochondria via the β-oxidation pathway to CO 2. This degradation produces acetyl-CoA, FADH 2 , and NADH 9-12. Candida albicans, Candida maltosa, Candida tropicalis, and Yarrowia lipolytica are model Saccharomycetales used for the study of function and transcriptional regulation of multiple orthologous and paralogous P450 encoded by CYP52 genes 7,13-18. The CYP52 genes in C. maltosa, Candida pseudoglaebosa, C. tropicalis, Kodamaea

show abstract

Section: Discussionsupporting

confidence: 74%

Phylogeny, evolution, and potential ecological relationship of cytochrome CYP52 enzymes in Saccharomycetales yeasts

Ortiz‐Álvarez

Becerra

Méndez‐Tenorio

et al. 2020

Sci Rep

View full text Add to dashboard Cite

show abstract

“…alimentaria and Y . phangngensis appear to be the most divergent and dynamic species, as exemplified by the evolution of the lipase gene family 60 . The comparison of telomeric repeat sequences between individual species enabled us to identify conserved positions within a repeat required for the binding by Tay1p homologs that seem to retain their telomeric functions.…”

Section: Introductionmentioning

confidence: 99%

Identification of telomerase RNAs in species of the Yarrowia clade provides insights into the co-evolution of telomerase, telomeric repeats and telomere-binding proteins

Červenák

Juríková

Devillers

et al. 2019

Sci Rep

Self Cite

View full text Add to dashboard Cite

Telomeric repeats in fungi of the subphylum Saccharomycotina exhibit great inter- and intra-species variability in length and sequence. Such variations challenged telomeric DNA-binding proteins that co-evolved to maintain their functions at telomeres. Here, we compare the extent of co-variations in telomeric repeats, encoded in the telomerase RNAs (TERs), and the repeat-binding proteins from 13 species belonging to the Yarrowia clade. We identified putative TER loci, analyzed their sequence and secondary structure conservation, and predicted functional elements. Moreover, in vivo complementation assays with mutant TERs showed the functional importance of four novel TER substructures. The TER-derived telomeric repeat unit of all species, except for one, is 10 bp long and can be represented as 5′-TTNNNNAGGG-3′, with repeat sequence variations occuring primarily outside the vertebrate telomeric motif 5′-TTAGGG-3′. All species possess a homologue of the Yarrowia lipolytica Tay1 protein, YlTay1p. In vitro, YlTay1p displays comparable DNA-binding affinity to all repeat variants, suggesting a conserved role among these species. Taken together, these results add significant insights into the co-evolution of TERs, telomeric repeats and telomere-binding proteins in yeasts.

show abstract

“…Blast analysis of the EYK1 promoter did not evidenced any conserved motif within Yarrowia lipolytica genome (data not shown). Therefore, we compared the promoter region of the EYK1 gene to those present in other species of the Yarrowia clade (namely, Yarrowia phangngensis , Yarrowia yakushimensis , Yarrowia alimentaria and Yarrowia galli that have been recently sequenced and annotated in our laboratory [ 47 ] and Neuveglise N., Devillers H. et collaborator (unpublished). Alignment of the EYK1 promoter sequences (Fig.…”

Section: Resultsmentioning

confidence: 99%

New inducible promoter for gene expression and synthetic biology in Yarrowia lipolytica

et al. 2017

Self Cite

View full text Add to dashboard Cite

BackgroundThe oleaginous yeast Yarrowia lipolytica is increasingly used as alternative cell factory for the production of recombinant proteins. At present, several promoters with different strengths have been developed based either on the constitutive pTEF promoter or on oleic acid inducible promoters such as pPOX2 and pLIP2. Although these promoters are highly efficient, there is still a lack of versatile inducible promoters for gene expression in Y. lipolytica. ResultsWe have isolated and characterized the promoter of the EYK1 gene coding for an erythrulose kinase. pEYK1 induction was found to be impaired in media supplemented with glucose and glycerol, while the presence of erythritol and erythrulose strongly increased the promoter induction level. Promoter characterization and mutagenesis allowed the identification of the upstream activating sequence UAS1EYK1. New hybrid promoters containing tandem repeats of either UAS1XPR2 or UAS1EYK1 were developed showing higher expression levels than the native pEYK1 promoter. Furthermore, promoter strength was improved in a strain carrying a deletion in the EYK1 gene, allowing thus the utilization of erythritol and erythrulose as free inducer.ConclusionsNovel tunable and regulated promoters with applications in the field of heterologous protein production, metabolic engineering, and synthetic biology have been developed, thus filling the gap of the absence of versatile inducible promoter in the yeast Y. lipolytica.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-017-0755-0) contains supplementary material, which is available to authorized users.

show abstract

Comprehensive Analysis of a Yeast Lipase Family in the Yarrowia Clade

Cited by 34 publications

References 56 publications

Phylogeny, evolution, and potential ecological relationship of cytochrome CYP52 enzymes in Saccharomycetales yeasts

Phylogeny, evolution, and potential ecological relationship of cytochrome CYP52 enzymes in Saccharomycetales yeasts

Identification of telomerase RNAs in species of the Yarrowia clade provides insights into the co-evolution of telomerase, telomeric repeats and telomere-binding proteins

New inducible promoter for gene expression and synthetic biology in Yarrowia lipolytica

Contact Info

Product

Resources

About