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Classification and substrate head-group specificity of membrane fatty acid desaturases

View Article: PubMed Central - PubMed

ABSTRACT

Membrane fatty acid desaturases are a diverse superfamily of enzymes that catalyze the introduction of double bonds into fatty acids. They are essential in a range of metabolic processes, such as the production of omega-3 fatty acids. However, our structure–function understanding of this superfamily is still developing and their range of activities and substrate specificities are broad, and often overlapping, which has made their systematic characterization challenging. A central issue with characterizing these proteins has been the lack of a structural model, which has been overcome with the recent publication of the crystal structures of two mammalian fatty acid desaturases. In this work, we have used sequence similarity networks to investigate the similarity among over 5000 related membrane fatty acid desaturase sequences, leading to a detailed classification of the superfamily, families and subfamilies with regard to their function and substrate head-group specificity. This work will facilitate rapid prediction of the function and specificity of new and existing sequences, as well as forming a basis for future efforts to manipulate the substrate specificity of these proteins for biotechnology applications.

No MeSH data available.


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The representative network of the MEs cluster in Fig. 2 show more detailed subgroupings. The plant FAD2, FAD3, FAD6, FAD7 and FAD8 desaturases are denoted. A and B are the same networks generated from the MEs cluster in Fig. 2 at a higher stringency, LogE < − 56. The prokaryotic Δ5 PLs formed a separate cluster. The nodes are coloured by organism kingdom information (A) and their substrate specificities reported in the literature (B).
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f0030: The representative network of the MEs cluster in Fig. 2 show more detailed subgroupings. The plant FAD2, FAD3, FAD6, FAD7 and FAD8 desaturases are denoted. A and B are the same networks generated from the MEs cluster in Fig. 2 at a higher stringency, LogE < − 56. The prokaryotic Δ5 PLs formed a separate cluster. The nodes are coloured by organism kingdom information (A) and their substrate specificities reported in the literature (B).

Mentions: The methyl-end desaturase subfamily can be separated into two groups at the LogE filter of − 30: a prokaryotic Δ5 phospholipid FAD group (Δ5 PLs) and the canonical MEs including Δ12-specific [45], Δ15-specific [46] and bifunctional (Δ12 and Δ15) FADs [47] (Fig. 6). The Δ5 PL desaturase from Bacillus subtilis (UniProt ID: O34653) has been experimentally proven to have a six-transmembrane (TM) helix topology [27], [28]. Functionally, the Δ5 PL cluster is similar to the first desaturases, although it shares higher sequence similarity with the ME family. Given the high amino acid sequence identity between these clusters (higher than 21%), the 6-TM-helix topology is likely to be the common topology of the MEs cluster and makes this subfamily structurally distinct from the FDs. Even though the bacterial B. subtilis Δ5 desaturase is suggested to be specific for phospholipid, this study did not specify the class of phospholipid that is the primary substrate [27], [28]. Several enzymes from the ME cluster have been shown to catalyze the desaturation of phosphatidylcholine including the plant FAD2 FAD3, FAD6, FAD7 and FAD8 desaturases (Fig. 6) [48], [49], [50], [51]. Thus, it is likely that both clusters utilize phospholipid substrates. It is notable that the Δ5 phospholipid FAD group consists almost entirely of prokaryotic and cyanobacterial sequences (with a handful of sequences from plants and protists), whereas the canonical ME cluster consists of sequences from fungi, animals, plants, cyanobacteria and other prokaryotes.


Classification and substrate head-group specificity of membrane fatty acid desaturases
The representative network of the MEs cluster in Fig. 2 show more detailed subgroupings. The plant FAD2, FAD3, FAD6, FAD7 and FAD8 desaturases are denoted. A and B are the same networks generated from the MEs cluster in Fig. 2 at a higher stringency, LogE < − 56. The prokaryotic Δ5 PLs formed a separate cluster. The nodes are coloured by organism kingdom information (A) and their substrate specificities reported in the literature (B).
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5037126&req=5

f0030: The representative network of the MEs cluster in Fig. 2 show more detailed subgroupings. The plant FAD2, FAD3, FAD6, FAD7 and FAD8 desaturases are denoted. A and B are the same networks generated from the MEs cluster in Fig. 2 at a higher stringency, LogE < − 56. The prokaryotic Δ5 PLs formed a separate cluster. The nodes are coloured by organism kingdom information (A) and their substrate specificities reported in the literature (B).
Mentions: The methyl-end desaturase subfamily can be separated into two groups at the LogE filter of − 30: a prokaryotic Δ5 phospholipid FAD group (Δ5 PLs) and the canonical MEs including Δ12-specific [45], Δ15-specific [46] and bifunctional (Δ12 and Δ15) FADs [47] (Fig. 6). The Δ5 PL desaturase from Bacillus subtilis (UniProt ID: O34653) has been experimentally proven to have a six-transmembrane (TM) helix topology [27], [28]. Functionally, the Δ5 PL cluster is similar to the first desaturases, although it shares higher sequence similarity with the ME family. Given the high amino acid sequence identity between these clusters (higher than 21%), the 6-TM-helix topology is likely to be the common topology of the MEs cluster and makes this subfamily structurally distinct from the FDs. Even though the bacterial B. subtilis Δ5 desaturase is suggested to be specific for phospholipid, this study did not specify the class of phospholipid that is the primary substrate [27], [28]. Several enzymes from the ME cluster have been shown to catalyze the desaturation of phosphatidylcholine including the plant FAD2 FAD3, FAD6, FAD7 and FAD8 desaturases (Fig. 6) [48], [49], [50], [51]. Thus, it is likely that both clusters utilize phospholipid substrates. It is notable that the Δ5 phospholipid FAD group consists almost entirely of prokaryotic and cyanobacterial sequences (with a handful of sequences from plants and protists), whereas the canonical ME cluster consists of sequences from fungi, animals, plants, cyanobacteria and other prokaryotes.

View Article: PubMed Central - PubMed

ABSTRACT

Membrane fatty acid desaturases are a diverse superfamily of enzymes that catalyze the introduction of double bonds into fatty acids. They are essential in a range of metabolic processes, such as the production of omega-3 fatty acids. However, our structure&ndash;function understanding of this superfamily is still developing and their range of activities and substrate specificities are broad, and often overlapping, which has made their systematic characterization challenging. A central issue with characterizing these proteins has been the lack of a structural model, which has been overcome with the recent publication of the crystal structures of two mammalian fatty acid desaturases. In this work, we have used sequence similarity networks to investigate the similarity among over 5000 related membrane fatty acid desaturase sequences, leading to a detailed classification of the superfamily, families and subfamilies with regard to their function and substrate head-group specificity. This work will facilitate rapid prediction of the function and specificity of new and existing sequences, as well as forming a basis for future efforts to manipulate the substrate specificity of these proteins for biotechnology applications.

No MeSH data available.


Related in: MedlinePlus