Lipid flippases in polarized growth

Genome-wide identification of the P4ATPase gene family and its response to biotic and abiotic stress in soybean (Glycine max L.)

BACKGROUND

Soybean is an important legume crop and has significant agricultural and economic value. P4-ATPases (aminophospholipid ATPases, ALAs), one of the classes of P-type ATPases, can transport or flip phospholipids across membranes, creating and maintaining lipid asymmetry and playing crucial roles in plant growth and development. To date, however, the ALA gene family and its expression patterns under abiotic and biotic stresses have not been studied in the soybean genome.

RESULTS

A total of 27 GmALA genes were identified in the soybean genome and these genes were unevenly distributed on 15 chromosomes and classified into five groups based on phylogenetic analysis. The GmALAs family had diverse intron-exon patterns and a highly conserved motif distribution. A total of eight domains were found in GmALAs, and all GmALAs had conserved PhoLip_ATPase_C, phosphorylation and transmembrane domains. Cis-acting elements in the promoter demonstrated that GmALAs are associated with cellular development, phytohormones, environmental stress and photoresponsiveness. Analysis of gene duplication events revealed 24 orthologous gene pairs in soybean and synteny analysis revealed that GmALAs had greater collinearity with AtALAs than with OsALAs. Evolutionary constraint analyses suggested that GmALAs have undergone strong selective pressure for purification during the evolution of soybeans. Tissue-specific expression profiles revealed that GmALAs were differentially expressed in roots, stems, seeds, flowers, nodules and leaves. The expression pattern of these genes appeared to be diverse in the different developmental tissues. Combined transcriptome and qRT-PCR data confirmed the differential expression of GmALAs under abiotic (dehydration, saline, low temperature, ozone, light, wounding and phytohormones) and biotic stresses (aphid, fungi, rhizobia and rust pathogen).

CONCLUSION

In summary, genome-wide identification and evolutionary and expression analyses of the GmALAs gene family in soybean were conducted. Our work provides an important theoretical basis for further understanding GmALAs in biological functional studies.

Heterozygous Missense Variants in the ATPase Phospholipid Transporting 9A Gene, ATP9A, Alter Dendritic Spine Maturation and Cause Dominantly Inherited Nonsyndromic Intellectual Disability

Intellectual disability is a neurodevelopmental disorder, affecting 2%-3% of the population, with a genetic cause in the majority of cases. ATP9A (Online Mendelian Inheritance in Man (OMIM)⁣∗609126, NM_006045.3) has recently been added to the list of candidate genes involved in this disorder with the identification of biallelic truncating variants in patients with a neurodevelopmental disorder. In this study, we propose a novel mode of inheritance for ATP9A-related disorders with the identification of five de novo heterozygous missense variants (p.(Thr393Arg), p.(Glu400Gln), p.(Lys461Glu), p.(Gly552Ala), and p.(His713Asp)), in patients with intellectual disability. In a patient with a similar phenotype, we also identified two truncating variants in ATP9A (p.(Arg145⁣∗), p.(Glu901⁣∗)), adding a novel family to the six already described in the literature with the recessive mode of inheritance. Functional studies were performed to assess the pathogenicity of these variants. Overexpression of four selected missense mutant forms of Atp9a in HeLa cells and in primary neuronal cultures led to a loss of mature dendritic spines. In HeLa cells, the endosomal localization of the protein encoded by three of these missense variants was preserved whereas the fourth remained blocked in the endoplasmic reticulum. To mimic the effect on neuronal morphology and spine density of nonsense variants, small hairpin RNAs (shRNAs) were used. They induced a decreased expression of ATP9A, affecting the neuronal arborization by decreasing the number of dendrites per neuron. Our results therefore demonstrate the pathogenicity of ATP9A heterozygous missense variants and confirm the role of ATP9A in neuronal maturation and in brain wiring during development. They strengthen the association of ATP9A with neurodevelopmental disorders and demonstrate that a double mode of inheritance should be considered for ATP9A-related disorders.

Arv1; a "Mover and Shaker" of Subcellular Lipids

The composition of eukaryotic membranes reflects a varied but precise amalgam of lipids. The genetic underpinning of how such diversity is achieved or maintained is surprisingly obscure, despite its clear metabolic and pathophysiological impact. The Arv1 protein is represented in all eukaryotes and was initially identified in the model eukaryote Sacccharomyces cerevisiae as a candidate transporter of lipids from the endoplasmic reticulum. Human Arv1 has been shown to directly bind cholesterol and fatty acid affinity probes. Murine in vivo studies point to a role for ARV1 in regulating obesity, glucose tolerance, insulin sensitivity and brain function. Multiple human ARV1 variants have been associated with epileptic encephalopathy, cerebellar ataxia, and severe intellectual deficits. We hypothesize that Arv1 acts as an energy independent, lipid scramblase at the endoplasmic reticulum thereby modulating membrane lipid asymmetry and thus the trafficking of sterols and the substituents of glycosyl-phosphatidylinositol and sphingolipid biosynthesis.

Flipping the script: Advances in understanding how and why P4-ATPases flip lipid across membranes

Type IV P-type ATPases (P4-ATPases) are a family of transmembrane enzymes that translocate lipid substrates from the outer to the inner leaflet of biological membranes and thus create an asymmetrical distribution of lipids within membranes. On the cellular level, this asymmetry is essential for maintaining the integrity and functionality of biological membranes, creating platforms for signaling events and facilitating vesicular trafficking. On the organismal level, this asymmetry has been shown to be important in maintaining blood homeostasis, liver metabolism, neural development, and the immune response. Indeed, dysregulation of P4-ATPases has been linked to several diseases; including anemia, cholestasis, neurological disease, and several cancers. This review will discuss the evolutionary transition of P4-ATPases from cation pumps to lipid flippases, the new lipid substrates that have been discovered, the significant advances that have been achieved in recent years regarding the structural mechanisms underlying the recognition and flipping of specific lipids across biological membranes, and the consequences of P4-ATPase dysfunction on cellular and physiological functions. Additionally, we emphasize the requirement for additional research to comprehensively understand the involvement of flippases in cellular physiology and disease and to explore their potential as targets for therapeutics in treating a variety of illnesses. The discussion in this review will primarily focus on the budding yeast, C. elegans, and mammalian P4-ATPases.

Plant P4-ATPase lipid flippases: How are they regulated?

P4 ATPases are active membrane transporters that translocate lipids towards the cytosolic side of the biological membranes in eukaryotic cells. Due to their essential cellular functions, P4 ATPase activity is expected to be tightly controlled, but fundamental aspects of the regulation of plant P4 ATPases remain unstudied. In this mini-review, our knowledge of the regulatory mechanisms of yeast and mammalian P4 ATPases will be summarized, and sequence comparison and structural modelling will be used as a basis to discuss the putative regulation of the corresponding plant lipid transporters.

Two distinct lipid transporters together regulate invasive filamentous growth in the human fungal pathogen Candida albicans

Flippases transport lipids across the membrane bilayer to generate and maintain asymmetry. The human fungal pathogen Candida albicans has 5 flippases, including Drs2, which is critical for filamentous growth and phosphatidylserine (PS) distribution. Furthermore, a drs2 deletion mutant is hypersensitive to the antifungal drug fluconazole and copper ions. We show here that such a flippase mutant also has an altered distribution of phosphatidylinositol 4-phosphate [PI(4)P] and ergosterol. Analyses of additional lipid transporters, i.e. the flippases Dnf1-3, and all the oxysterol binding protein (Osh) family lipid transfer proteins, i.e. Osh2-4 and Osh7, indicate that they are not critical for filamentous growth. However, deletion of Osh4 alone, which exchanges PI(4)P for sterol, in a drs2 mutant can bypass the requirement for this flippase in invasive filamentous growth. In addition, deletion of the lipid phosphatase Sac1, which dephosphorylates PI(4)P, in a drs2 mutant results in a synthetic growth defect, suggesting that Drs2 and Sac1 function in parallel pathways. Together, our results indicate that a balance between the activities of two putative lipid transporters regulates invasive filamentous growth, via PI(4)P. In contrast, deletion of OSH4 in drs2 does not restore growth on fluconazole, nor on papuamide A, a toxin that binds PS in the outer leaflet of the plasma membrane, suggesting that Drs2 has additional role(s) in plasma membrane organization, independent of Osh4. As we show that C. albicans Drs2 localizes to different structures, including the Spitzenkörper, we investigated if a specific localization of Drs2 is critical for different functions, using a synthetic physical interaction approach to restrict/stabilize Drs2 at the Spitzenkörper. Our results suggest that the localization of Drs2 at the plasma membrane is critical for C. albicans growth on fluconazole and papuamide A, but not for invasive filamentous growth.

The phospholipid flippase ALA3 regulates pollen tube growth and guidance in Arabidopsis

Pollen tube guidance regulates the growth direction and ovule targeting of pollen tubes in pistils, which is crucial for the completion of sexual reproduction in flowering plants. The Arabidopsis (Arabidopsis thaliana) pollen-specific receptor kinase (PRK) family members PRK3 and PRK6 are specifically tip-localized and essential for pollen tube growth and guidance. However, the mechanisms controlling the polar localization of PRKs at the pollen tube tip are unclear. The Arabidopsis P4-ATPase ALA3 helps establish the polar localization of apical phosphatidylserine (PS) in pollen tubes. Here, we discovered that loss of ALA3 function caused pollen tube defects in growth and ovule targeting and significantly affected the polar localization pattern of PRK3 and PRK6. Both PRK3 and PRK6 contain two polybasic clusters in the intracellular juxtamembrane domain, and they bound to PS in vitro. PRK3 and PRK6 with polybasic cluster mutations showed reduced or abolished binding to PS and altered polar localization patterns, and they failed to effectively complement the pollen tube-related phenotypes of prk mutants. These results suggest that ALA3 influences the precise localization of PRK3, PRK6, and other PRKs by regulating the distribution of PS, which plays a key role in regulating pollen tube growth and guidance.