Linking lipids to chromatin

Phosphoinositide 5-phosphate and phosphoinositide 4-phosphate trigger distinct specific responses of Arabidopsis genes: genome-wide expression analyses

Phosphoinositide phosphates, PtdInsP, are important components of the cell lipid pool that can function as messengers in diverse cellular processes. Lack of information on downstream targets, however, has impeded our understanding of the potential of lipid-signaling to influence gene activity. Our goals here were to identify genes that altered expression in the presence of two isomeric monophosphate lipid messengers (Phosphoinositide 5-Phosphate, PtdIns(5)P, and Phosphoinositide 4-Phosphate, PtdIns(4)P) and to establish whether the two lipids influence distinct or overlapping gene-sets. Our results indicated that PtdIns(5)P and PtdIns(4)P affected genes within shared gene-families but that each messenger influenced the expression of different members within the same family. These results suggested that PtdIns(5)P and PtdIns(4)P participate in separate pathways that, ultimately, may control gene expression. The pathways may have points of convergence but may also counteract each other's effects. A significant fraction ( approximately 40%) of the PtdIns(5)P-stimulated genes belong to various families of wall-modifying genes. Wall-modifying activities are recognized as factors affecting cell extension and plant growth. Elevated PtdIns(5)P concentration influenced stem growth and the effects were different from those triggered by PtdIns(4)P. The data allow insights into plants' response to two related PtdInsP at whole-plant/genome-wide levels and demonstrate that PtdIns(5)P-and PtdIns(4)P-involving mechanisms are distinct, selective and specific.

The Arabidopsis homolog of trithorax, ATX1, binds phosphatidylinositol 5-phosphate, and the two regulate a common set of target genes

The Arabidopsis homolog of trithorax, ATX1, regulates numerous functions in Arabidopsis beyond the homeotic genes. Here, we identified genome-wide targets of ATX1 and showed that ATX1 is a receptor for a lipid messenger, phosphatidylinositol 5-phosphate, PI5P. PI5P negatively affects ATX1 activity, suggesting a regulatory pathway connecting lipid-signaling with nuclear functions. We propose a model to illustrate how plants may respond to stimuli (external or internal) that elevate cellular PI5P levels by altering expression of ATX1-controlled genes.

Nucleolar localization of phosphatidylinositol 4-kinase PI4K230 in various mammalian cells

BACKGROUND

Previous immunohistochemical investigations could not detect PI4K230, an isoform of mammalian phosphatidylinositol 4-kinases (also called type III alpha), in the nucleus and nucleolus of cells in spite of its predicted nuclear localization signals.

METHODS

Immunofluorescent detection of PI4K230 and other PI4K isoforms was performed on formaldehyde (PFA) or ethanol fixed cells and rat brain cryosections. Costaining with nucleolin and the effect of siRNA, Triton X-100, DNase, and RNase treatments were also tested to determine the localization of PI4K230.

RESULTS

PI4K230 gives a prominent signal in the nucleolus of ethanol fixed rat brain cryosections and of several cell types in addition to its presence in the nucleus and cytoplasm. The PI4K230 immunoreactivity of the nucleolus is masked in PFA fixed cells, but it can be restored by treatment of PFA fixed cells with hot wet citrate buffer or by washing the cryosections with PBS prior to PFA fixation. Nucleolar PI4K230 occurs in a Triton X-100 resistant complex. Treatment of COS-7 cells with siRNA targeting PI4K230 and permeabilized B50 cells with DNase or RNase results in the loss of PI4K230 signal from the nucleolus.

CONCLUSION

These experiments suggest the participation of PI4K230 in a DNase and RNase sensitive complex with a unique localization and function in the nucleolus.

Nucleocytoplasmic shuttling of phospholipase C-δ1: A link to Ca2+

Phosphoinositides (PIs) and proteins involved in the PI signaling pathway are distributed in the nucleus as well as at the plasma membrane and in the cytoplasm, although their nuclear localization mechanisms have not been clarified in detail. Generally, proteins that shuttle between the cytoplasm and nucleus contain nuclear localization signal (NLS) and nuclear export signal (NES) sequences for nuclear import and export, respectively. They bind to specific carrier proteins of the importin/exportin family and are transported to and from the nucleus. Thus there is a steady state shuttling of the cargo molecules to and from the nucleus, and the shift in equilibrium determines their nuclear or cytoplasmic localization. Our previous studies have shown that phospholipase C (PLC)-delta1, regarded as having cytoplasmic- or plasma membrane-bound localization, accumulates in the nucleus when its NES sequence is disrupted. In addition, a cluster of positively charged residues on the surface of the catalytic barrel is important for nuclear import. In quiescent cells, the shuttling equilibrium seems to be shifted to the nuclear export of PLCdelta1. In this review, recent findings regarding the molecular machineries and mechanisms of the nucleocytoplasmic shuttling of PLCdelta1 will be discussed. It is important to know when and how they are regulated. A shift in the equilibrium in a certain stage of the cell cycle or by external stimuli is possible and resulting changes in the intra-nuclear environments (or architectures) may alter proliferation and differentiation patterns. Evidences support the idea that an increase in the levels of intracellular Ca2+ shifts the equilibrium to the nuclear import of PLCdelta1. A myriad of external stimuli have also been reported to change the nuclear PI metabolism following accelerated accumulation in the nucleus of other phospholipases such as phospholipase A2 and phospholipase D in addition to PLC isoforms such as PLCbeta1 and PLCgamma1. The consequence of the nuclear accumulation of PLC is also discussed.

Nuclear inositol lipid metabolism: more than just second messenger generation?

A distinct polyphosphoinositide cycle is present in the nucleus, and growing evidence suggests its importance in DNA replication, gene transcription, and apoptosis. Even though it was initially thought that nuclear inositol lipids would function as a source for second messengers, recent findings strongly indicate that lipids present in the nucleus also fulfil other roles. The scope of this review is to highlight the most intriguing advances made in the field over the last few years, such as the possibility that nuclear phosphatidylinositol (4,5) bisphosphate is involved in maintaining chromatin in a transcriptionally active conformation, the new emerging roles for intranuclear phosphatidylinositol (3,4,5) trisphosphate and phosphoinositide 3-kinase, and the evidence which suggests a tight relationship between a decreased level of nuclear phosphoinositide specific phospholipase C-beta1 and the evolution of myelodisplastic syndrome into acute myeloid leukemia.

An emerging role for PtdIns(4,5)P2-mediated signalling in human disease

Although an established regulator of many cellular functions, the phosphoinositide phosphatidylinositol (4,5)-bisphosphate [PtdIns(4,5)P2) appears to have evaded the attention of drug-discovery companies. An increasing number of reports have identified potential links between PtdIns(4,5)P2-mediated signalling pathways and the aetiology of many human diseases. Here, we review current knowledge of the regulation and function of PtdIns(4,5)P2 and discuss how aberrant PtdIns(4,5)P2-mediated signalling might contribute to human pathologies such as cardiac failure, bipolar disorder, channelopathies and the genetic disorder Lowe syndrome.

Chromatin modification by lipids and lipoprotein components: an initiating event in atherogenesis?

PURPOSE OF REVIEW

This review examines recent evidence proposing that lipids and lipoproteins can act as nuclear factors regulating chromatin structure. These novel data broaden our understanding of the mechanisms by which lipoproteins can affect basic biological phenomena such as transcription, genome stability, and cell differentiation. Furthermore, they provide novel insights into the mechanisms of diseases associated with abnormal lipid levels, such as atherosclerosis and diabetes.

RECENT FINDINGS

Data consistent with a role for lipids and lipoprotein components as nuclear factors, as well as initiators of cytoplasmic signalling events resulting in chromatin modification, have been published in the past year. In particular, new insights into the mechanisms of interaction between chromatin and small lipid molecules such as short-chain fatty acids and cholesterol, and endogenous lipid peroxidation products have been obtained. Furthermore, it has been shown that hyperlipidaemic lipoprotein profiles are associated with aberrant DNA methylation patterns at early stages of atherosclerosis in mice and in cultured human macrophages, suggesting that a rearrangement of DNA methylation patterns is among early molecular changes associated with atherogenesis.

SUMMARY

The findings described here are prompting efforts to understand further how lipids and lipoprotein components can affect gene expression in normal and pathological cell behaviour through regulation of the chromatin structure. It is possible that novel candidate therapeutic tools will emerge from these studies.

Inositol polyphosphate multikinase is a nuclear PI3-kinase with transcriptional regulatory activity

Phosphatidylinositol 3,4,5-trisphosphate is a major intracellular messenger molecule thought to be formed almost exclusively by cytosolic, wortmannin-inhibited phosphoinositide 3-kinase family members. Inositol polyphosphate multikinase was identified as an enzyme that generates a series of water-soluble inositol phosphates. We now report the robust, physiologic, and evolutionarily conserved phosphoinositide 3-kinase activity of inositol polyphosphate multikinase, which is localized to nuclei and unaffected by wortmannin. In yeast, this inositol lipid kinase activity physiologically regulates transcription.

Nuclear speckles and nucleoli targeting by PIP2-PDZ domain interactions

PDZ (Postsynaptic density protein, Disc large, Zona occludens) domains are protein-protein interaction modules that predominate in submembranous scaffolding proteins. Recently, we showed that the PDZ domains of syntenin-1 also interact with phosphatidylinositol 4,5-bisphosphate (PIP2) and that this interaction controls the recruitment of the protein to the plasma membrane. Here we evaluate the general importance of PIP2-PDZ domain interactions. We report that most PDZ proteins bind weakly to PIP2, but that syntenin-2, the closest homolog of syntenin-1, binds with high affinity to PIP2 via its PDZ domains. Surprisingly, these domains target syntenin-2 to nuclear PIP2 pools, in nuclear speckles and nucleoli. Targeting to these sites is abolished by treatments known to affect these PIP2 pools. Mutational and domain-swapping experiments indicate that high-affinity binding to PIP2 requires both PDZ domains of syntenin-2, but that its first PDZ domain contains the nuclear PIP2 targeting determinants. Depletion of syntenin-2 disrupts the nuclear speckles-PIP2 pattern and affects cell survival and cell division. These findings show that PIP2-PDZ domain interactions can directly contribute to subnuclear assembly processes.

Modification of protein sub-nuclear localization by synthetic phosphoinositides: Evidence for nuclear phosphoinositide signaling mechanisms

PtdInsPs are critical signaling molecules that regulate diverse cellular functions. One method to study PtdInsP biology involves using synthetic PtdInsP analogs to activate endogenous PtdInsP-mediated events in living cells. Such methodology has been successfully employed to explore the role of several PtdInsP-biological outcomes in the cytoplasm. However, this strategy has not previously been used to examine the function of PtdInsPs in the nucleus of live cells, primarily because there has not been a well-defined PtdInsP-binding protein to provide functional nuclear readouts. Here we have shown that synthetic PtdIns(5)P analogs access and function in the nucleus. We have found that these molecules modify the sub-nuclear localization of PHD finger-containing proteins in live cells and in real time. This work demonstrates that synthetic PtdInsPs and PtdInsP derivatives may be powerful tools for probing nuclear PtdInsP functions. Finally, our work supports a model that endogenous PtdInsPs regulate sub-nuclear localization and function of endogenous nuclear PtdInsP-binding proteins.

Emerging roles of phosphatidylinositol monophosphates in cellular signaling and trafficking

The phosphoinositide metabolism that is highly controlled by a set of kinases, phosphatases and phospholipases leads to the production of several second messengers playing critical roles in intracellular signal transduction mechanisms. Recent discoveries have unraveled unexpected roles for the three phosphatidylinositol monophosphates, PtdIns(3)P, PtdIns(4)P and PtdIns(5)P, that appear now as important lipid messengers able to specifically interact with proteins. The formation of functionally distinct and independently regulated pools of phosphatidylinositol monophosphates probably contributes to the specificity of the interactions with their targets. The relative enrichment of organelles in a particular species of phosphoinositides (i.e. PtdIns(3)P in endosomes, PtdIns(4)P in Golgi and PtdIns(4,5)P2 in plasma membrane) suggests the notion of lipid-defined organelle identity. PtdIns(3)P is now clearly involved in vesicular trafficking by interaction with a set of FYVE domain-containing proteins both in yeast and in mammals. PtdIns(4)P, which until now was only considered as a precursor for PtdIns(4,5)P2, appears as a regulator on its own, by recruiting a set of proteins to the trans-Golgi network. PtdIns(5)P, the most recently discovered inositol lipid, is also emerging as a potentially important signaling molecule.

The fellowships of the INGs

The inhibitor of growth (ING) family of proteins is an evolutionarily conserved family, with members present from yeast to humans. The mammalian ING proteins are candidate tumor suppressor proteins and accordingly can cooperate with p53 to arrest proliferation and induce apoptosis. ING proteins are also reported to function in the promotion of cellular senescence, the regulation of DNA damage responses and the inhibition of angiogenesis. At the molecular level, ING proteins are thought to function as chromatin regulatory molecules, acting as co-factors for distinct histone and factor acetyl-transferase (H/FAT) and deacetylase (HDAC) enzyme complexes. Further, ING proteins interact with a number of additional proteins involved in the regulation of critical nuclear processes, such as gene expression and DNA replication, and also function as nuclear phosphoinositide (PtdInsP) receptors. Despite the increasing number of known molecular interacting partners for ING proteins, the specific biochemical action of mammalian ING proteins and its relationship to tumor suppression remain elusive. In this Prospect, we summarize the present understanding of the binding partners and physiologic roles of ING proteins and propose a general molecular paradigm for how ING proteins might function to prevent cancer.