@article {159722, title = {Phosphoinositide acyl chain diversity: comparative analysis across species and mouse tissues.}, journal = {Biochim Biophys Acta Mol Cell Biol Lipids}, volume = {1870}, year = {2025}, month = {2025 Aug}, pages = {159640}, abstract = {

Cells create acyl chain compositions for their phosphoinositide (PIPn) pools that are distinct from other phospholipid classes. While some lower eukaryotes present highly heterogeneous PIPn (e.g., yeast, fly), more complex organisms typically display PIPn enriched in fewer molecular species (e.g., the C38:4 species in fish, frog and mice). A comprehensive analysis of murine tissues (using both LC-MS/MS and MSI) confirms a general enrichment for C38:4-PIPn but also highlights the existence of several cell populations with strikingly divergent acyl chain compositions, characterised by the prevalence of shorter-chain, more saturated species (e.g., C32:0 in the testes and C34:1 in the prostate). The evolutionary pressures driving the creation of these specific acyl chain compositions are still unclear; current evidence suggests there is probably a balance to be achieved in different cell types between the biophysical constraints imposed by PIPn as membrane-captive {\textquoteright}messengers{\textquoteright} (e.g., flexibility in head group presentation in different membrane environments), the demand for substantial de novo lipid synthesis (e.g., in rapid membrane expansion), the need for acyl chain remodelling (e.g., in molecular segregation of functional pools) and fatty acid availability. Moreover, it would appear inevitable that this balance will be distorted under most cell culture conditions in vitro.

}, keywords = {Animals, Male, Mice, Phosphatidylinositols, Species Specificity, Tandem Mass Spectrometry}, issn = {1879-2618}, doi = {10.1016/j.bbalip.2025.159640}, author = {Barneda, David and Janardan, Vishnu and Swales, John and Ciaccia, Maria and Goodwin, Richard and Cosulich, Sabina and Raghu, Padinjat and Clark, Jonathan and Stephens, Len and Hawkins, Phillip} } @article {885, title = {Phosphoinositide signalling in Drosophila.}, journal = {Biochim Biophys Acta}, volume = {1851}, year = {2015}, month = {2015 Jun}, pages = {770-84}, abstract = {

Phosphoinositides (PtdInsPs) are lipids that mediate a range of conserved cellular processes in eukaryotes. These include the transduction of ligand binding to cell surface receptors, vesicular transport and cytoskeletal function. The nature and functions of PtdInsPs were initially elucidated through biochemical experiments in mammalian cells. However, over the years, genetic and cell biological analysis in a range of model organisms including S. cerevisiae, D. melanogaster and C. elegans have contributed to an understanding of the involvement of PtdInsPs in these cellular events. The fruit fly Drosophila is an excellent genetic model for the analysis of cell and developmental biology as well as physiological processes, particularly analysis of the complex relationship between the cell types of a metazoan in mediating animal physiology. PtdInsP signalling pathways are underpinned by enzymes that synthesise and degrade these molecules and also by proteins that bind to these lipids in cells. In this review we provide an overview of the current understanding of PtdInsP signalling in Drosophila. We provide a comparative genomic analysis of the PtdInsP signalling toolkit between Drosophila and mammalian systems. We also review some areas of cell and developmental biology where analysis in Drosophila might provide insights into the role of this lipid-signalling pathway in metazoan biology. This article is part of a Special Issue entitled Phosphoinositides.

}, keywords = {Animals, CDP-Diacylglycerol-Inositol 3-Phosphatidyltransferase, Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, Isoenzymes, Phosphatidylinositol 4,5-Diphosphate, Phosphoinositide Phospholipase C, Phospholipid Transfer Proteins, Receptors, Cell Surface, Signal Transduction, Species Specificity, Substrate Specificity}, issn = {0006-3002}, doi = {10.1016/j.bbalip.2014.10.010}, author = {Balakrishnan, Sruthi S and Basu, Urbashi and Raghu, Padinjat} } @article {127108, title = {Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants.}, journal = {BMC Genomics}, volume = {15}, year = {2014}, month = {2014 Dec 02}, pages = {1049}, abstract = {

BACKGROUND: Micro (mi)RNAs are important regulators of plant development. Across plant lineages, Dicer-like 1 (DCL1) proteins process long ds-like structures to produce micro (mi) RNA duplexes in a stepwise manner. These miRNAs are incorporated into Argonaute (AGO) proteins and influence expression of RNAs that have sequence complementarity with miRNAs. Expression levels of AGOs are greatly regulated by plants in order to minimize unwarranted perturbations using miRNAs to target mRNAs coding for AGOs. AGOs may also have high promoter specificity-sometimes expression of AGO can be limited to just a few cells in a plant. Viral pathogens utilize various means to counter antiviral roles of AGOs including hijacking the host encoded miRNAs to target AGOs. Two host encoded miRNAs namely miR168 and miR403 that target AGOs have been described in the model plant Arabidopsis and such a mechanism is thought to be well conserved across plants because AGO sequences are well conserved.

RESULTS: We show that the interaction between AGO mRNAs and miRNAs is species-specific due to the diversity in sequences of two miRNAs that target AGOs, sequence diversity among corresponding target regions in AGO mRNAs and variable expression levels of these miRNAs among vascular plants. We used miRNA sequences from 68 plant species representing 31 plant families for this analysis. Sequences of miR168 and miR403 are not conserved among plant lineages, but surprisingly they differ drastically in their sequence diversity and expression levels even among closely related plants. Variation in miR168 expression among plants correlates well with secondary structures/length of loop sequences of their precursors.

CONCLUSIONS: Our data indicates a complex AGO targeting interaction among plant lineages due to miRNA sequence diversity and sequences of miRNA targeting regions among AGO mRNAs, thus leading to the assumption that the perturbations by viruses that use host miRNAs to target antiviral AGOs can only be species-specific. We also show that rapid evolution and likely loss of expression of miR168 isoforms in tobacco is related to the insertion of MITE-like transposons between miRNA and miRNA* sequences, a possible mechanism showing how miRNAs are lost in few plant lineages even though other close relatives have abundantly expressing miRNAs.

}, keywords = {Argonaute Proteins, Base Sequence, Binding Sites, Disease Resistance, Gene Dosage, Gene Expression Regulation, Plant, Genetic Variation, Genotype, Host-Pathogen Interactions, MicroRNAs, Molecular Sequence Data, Nucleic Acid Conformation, Plants, RNA Precursors, RNA, Messenger, RNA, Plant, Sequence Alignment, Species Specificity}, issn = {1471-2164}, doi = {10.1186/1471-2164-15-1049}, author = {Jagtap, Soham and Shivaprasad, Padubidri V} }