Plant phospholipase D mining unravels new conserved residues important for catalytic activity

Arhab, Yani; Abousalham, Abdelkarim; Noiriel, Alexandre

doi:10.1016/j.bbalip.2019.01.008

Cited by 15 publications

(13 citation statements)

References 73 publications

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“…One common feature found in the plant PLDα isoform, along with other PLDs from microbes and eukaryotes, was the duplicated catalytic HKD motif, found as well in TDP1α and TDP1β. Among the different organisms investigated in this study, the authors reported some initial anomalies present in algal sequences (e.g., the presence of an unorthodox HKS motif), which were however dismissed upon further analyses, concluding that some of the deposited sequences are unreliable [69]. The origin of plant PLDα still needs to be clarified as well, since green algae do not seem to possess this sequence, with few exceptions (C. subellipsoidea, Phaeodactylum tricornutum) hypothesized to be the result of a horizontal transfer from microbes [70].…”

Section: Discussionmentioning

confidence: 83%

“…Finally, Amborella, despite being the sister lineage to all extant flowering plants, shows no evidence of lineage-specific duplications or transposons insertions [63]. A recent publication investigating the PLD family of proteins, to which TDP1 belongs, has revealed the importance of multiple conserved motifs that may have different regulatory and catalytic functions [69]. One common feature found in the plant PLDα isoform, along with other PLDs from microbes and eukaryotes, was the duplicated catalytic HKD motif, found as well in TDP1α and TDP1β.…”

Section: Discussionmentioning

confidence: 99%

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Plant TDP1 (Tyrosyl-DNA Phosphodiesterase 1): A Phylogenetic Perspective and Gene Expression Data Mining

Mutti

Raveane

Pagano

et al. 2020

Genes

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The TDP1 (tyrosyl-DNA phosphodiesterase 1) enzyme removes the non-specific covalent intermediates between topoisomerase I and DNA, thus playing a crucial role in preventing DNA damage. While mammals possess only one TDP1 gene, in plants two genes (TDP1α and TDP1β) are present constituting a small gene subfamily. These display a different domain structure and appear to perform non-overlapping functions in the maintenance of genome integrity. Namely, the HIRAN domain identified in TDP1β is involved in the interaction with DNA during the recognition of stalled replication forks. The availability of transcriptomic databases in a growing variety of experimental systems provides new opportunities to fill the current gaps of knowledge concerning the evolutionary origin and the specialized roles of TDP1 genes in plants. Whereas a phylogenetic approach has been used to track the evolution of plant TDP1 protein, transcriptomic data from a selection of representative lycophyte, eudicots, and monocots have been implemented to explore the transcriptomic dynamics in different tissues and a variety of biotic and abiotic stress conditions. While the phylogenetic analysis indicates that TDP1α is of non-plant origin and TDP1β is plant-specific originating in ancient vascular plants, the gene expression data mining comparative analysis pinpoints for tissue- and stress-specific responses.

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Section: Discussionmentioning

confidence: 83%

Section: Discussionmentioning

confidence: 99%

Plant TDP1 (Tyrosyl-DNA Phosphodiesterase 1): A Phylogenetic Perspective and Gene Expression Data Mining

Mutti

Raveane

Pagano

et al. 2020

Genes

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“…Our inspection of predicted protein sequences revealed the presence of both of the HKD motifs in all the protein variants (see Supplementary Fig. S7) which is supported by the fact that most eukaryotic PLDs require two functional HKD sites to remain catalytically active 87 . Also, the three amino acid residues involved in PIP 2 activation were found conserved in all the variants 88 .…”

Section: Phylogenetic Relationships Of Ospldα1 Gene Among Diverese Wimentioning

confidence: 52%

Novel allelic variation in the Phospholipase D alpha1 gene (OsPLDα1) of wild Oryza species implies to its low expression in rice bran

Kaur

Neelam

Kaur

et al. 2020

Sci Rep

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Rice bran, a by-product after milling, is a rich source of phytonutrients like oryzanols, tocopherols, tocotrienols, phytosterols, and dietary fibers. Moreover, exceptional properties of the rice bran oil make it unparalleled to other vegetable oils. However, a lipolytic enzyme Phospholipase D alpha1 (OsPLDα1) causes rancidity and 'stale flavor' in the oil, and thus limits the rice bran usage for human consumption. To improve the rice bran quality, sequence based allele mining at OsPLDα1 locus (3.6 Kb) was performed across 48 accessions representing 11 wild Oryza species, 8 accessions of African cultivated rice, and 7 Oryza sativa cultivars. From comparative sequence analysis, 216 SNPs and 30 InDels were detected at the OsPLDα1 locus. Phylogenetic analysis revealed 20 OsPLDα1 cDNA variants which further translated into 12 protein variants. The O. officinalis protein variant, when compared to Nipponbare, showed maximum variability comprising 22 amino acid substitutions and absence of two peptides and two β-sheets. Further, expression profiling indicated significant differences in transcript abundance within as well as between the OsPLDα1 variants. Also, a new OsPLDα1 transcript variant having third exon missing in it, Os01t0172400-06, has been revealed. An O. officinalis accession (IRGC101152) had lowest gene expression which suggests the presence of novel allele, named as OsPLDα1-1a (GenBank accession no. MF966931). The identified novel allele could be further deployed in the breeding programs to overcome rice bran rancidity in elite cultivars.

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“…Compared with chemicalmediated methods, enzyme-mediated methods can offer considerable advantages, such as high selectivity and mild conditions, leading to the generation of products that cannot easily be obtained by chemical methods [5,17]. Lipases and phospholipase are two main kinds of enzymes used to catalyze the production of SPLs, and they are widely found in animals (specific cells that synthesize lipases, or other host animals present in the gastrointestinal tract in animals to digest fats and lipids), plants (seeds or grains, fruits, leaves, and some other organisms) and microorganisms (fungi, yeast, and bacteria) [18][19][20][21].…”

Section: Introductionmentioning

confidence: 99%

Progress & Prospect of Enzyme-Mediated Structured Phospholipids Preparation

Dai

Liu

2022

Catalysts

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In recent years, structured phospholipids (SPLs), which are modified phospholipids (PLs), have attracted more attention due to their great potential for application in the field of pharmacy, food, cosmetics, and health. SPLs not only possess enhanced chemical, physical and nutritional properties, but also present superior bioavailability in comparison with other lipid forms, such as triacylglycerols, which make SPLs become more competitive carriers to increase the absorption of the specific fatty acids in the body. Compared with chemical-mediated SPLs, the process of enzyme-mediated SPLs has the advantages of high product variety, high substrate selectivity, and mild operation conditions. Both lipases and phospholipases can be used in the enzymatic production of SPLs, and the main reaction type contains esterification, acidolysis, and transesterification. During the preparation, reaction medium, acyl migration, water content/activity, substrates and enzymes, and some other parameters have significant effects on the production and purity of the desired PLs products. In this paper, the progress in enzymatic modification of PLs over the last 20 years is reviewed. Reaction types and characteristic parameters are summarized in detail and the parameters affecting acyl migration are first discussed to give the inspiration to optimize the enzyme-mediated SPLs preparation. To expand the application of enzyme-mediated SPLs in the future, the prospect of further study on SPLs is also proposed at the end of the paper.

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Plant phospholipase D mining unravels new conserved residues important for catalytic activity

Cited by 15 publications

References 73 publications

Plant TDP1 (Tyrosyl-DNA Phosphodiesterase 1): A Phylogenetic Perspective and Gene Expression Data Mining

Plant TDP1 (Tyrosyl-DNA Phosphodiesterase 1): A Phylogenetic Perspective and Gene Expression Data Mining

Novel allelic variation in the Phospholipase D alpha1 gene (OsPLDα1) of wild Oryza species implies to its low expression in rice bran

Progress & Prospect of Enzyme-Mediated Structured Phospholipids Preparation

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