About Chris Watson

I am a Life Sciences graduate with an MSc degree in Cell and Molecular Biology from a reputed UK university. For the past two years, I have been employed by Life Technologies Corporation as a Field Application Support Officer and give support regarding the ABI Genetic Analyzer 3730xl. I also help various research groups in meeting their goals. I have been working with the prestigious International Wheat Genome Sequencing Consortium (IWGSC) and we are creating a physical map of the wheat chromosome 2A. I am the primary author of a scientific article which is to be published soon and my research posters have been presented at various conferences worldwide.

The vital role that inositides and their components play in the regulation of cell events – The synthesis and metabolism of Phosphotidylinositol(3,5)bisphosphate

1.1 Phosphotidylinositol(3,5)bisphosphate: Synthesis and

In the year 1850, Joseph Scherer discovered inositol and determined its empirical formula by its isolation from Liebig’s extract of meat. Inositides consist of phosphotidyl-inositol (PtdIns), polyphosphoinositides (PPIns) which are a phosphorylated derivative of PtdIns and inositol polyphosphate(IP). These membrane and cellular components of inositides have been found to play a vital role in the regulation of cellular events (Kangzhen Dong, 2010).

PtdIns, a member of eukaryotic membrane phospholipids, play an important role in phosphorylation of the inositol group in one or more than one place, giving rise to various PtdIns (Corvera et al., 1999). These phosphoinositides are found near the cytoplasmic face. They act as a substrate for various enzymes which convert them into secondary messengers, including PtdIns (3,5) bisphosphate Corvera et al., 1999). These enzymes include phosphoinositol kinase, phospholipase C and phospholipase D (Robinson et al., 1998). The inter-conversions of PPIns are controlled by various lipid phospholipases and kinases. Usually these enzymes will phosphor late or dephosphorylate at a particular hydroxyl group on the inositol ring (Dong., 2010).

Phosphotidyl inositol (3,5) bisphosphate (PtdIns (3,5)P2) is a newly discovered member of PPIns and plays a role in membrane trafficking (Michell et al., 2006), cytoskeletal rearrangement and responding to extracellular environmental changes (Strahl et al., 2007). It is also involved in packing proteins into multivesicular bodies after being ubiquitinated, for growth at high temperatures and for vacuole acidification (Dove et al., 2004).

In 1987, Auger et al. postulated the existence of PtdIns(3,5)P2 but its presence was not confirmed until 1997, when it was isolated and identified in a mouse’s fibroblast and in Saccharomyces cerevisiae (Whiteford et al., 1997; Dove et al., 1997). Its presence was also reported in Schizosaccharomyces pombe and in plant cells, suggesting that it exists in all eukaryotes (Dove et al., 1997).

The presence of PtdIns kinase has been observed in various eukaryotic organisms, including yeast, insects and vertebrates. These kinases have been classified into three types: type I/type III PtdIns kinase, type II PtdIns kinase and PtdIns phosphokinase. PtdIns 4 kinase, which is a type II kinase, was the first to be isolated from various mammalian sources and described in detail (Strahl et al., 2004). Later, it was realised that these PtdIns kinase catalyse a reaction on a specific inositol ring (Balla et al., 2006) and were classified according to the product they produce: PtdIns 3-kinase, PtdIns 4-kinase and PtdInsP kinase (see the review of Strahl and Thorner, 2007).

PtdIns are converted to PtdIns 3 phosphate by the action of type III PPIn

3-kinase and then to PtdIns (3,5)P2 by the action of PIPKIII (Michell et al.,2006). In Saccharomyces cerevisiae, VPS34p is responsible for the conversion of PtdIns to PtdIns 3 phosphate. Fab1 catalyses the conversion of PtdIns 3 phosphate to PtdIns(3,5)P2 (Michell et al.,2006). In 2003, Gillooly et al. found that PtdIns (3,5)P2 are synthesised in the endosomal system by the action of type III PPIn 3-kinase, suggesting that PtdIns (3,5)P2 plays a role in membrane trafficking in the endosomal and lysosomal areas of the cell.

The main function of PtdIns polyphosphate in the process of membrane trafficking is to transport the protein to a specific regions of the membrane. VPS34p is localised in the cytosol but can be transported to the endosomal membrane by the action of VPS15p (Stack et al., 1993).
When the vps15 gene mutates in such a way that it can no longer function as kinase, the result is a massive decrease in the production of PtdIns 3P and causes defects in vacuolar protein sorting (VPS). The strains that had a deleted vps15 or vps34 gene displayed common phenotypes (Herman et al., 1992). This suggests that the gene product of these genes may follow the same steps as in vacuolar protein sorting (Stack et al., 1993). Also, overproduction of VPS34p in a strain containing a mutated vps15 gene suppressed the growth and protein sorting of vacuolar protein (Herman et al., 1991).

As previously described, PtdIns are converted to PtdIns 3 phosphate by the action of type III PPIn 3-kinase, VPS34p and then to PtdIns (3,5)P2 by the action of PIPKIII, Fab1p (Michell et al, 2006). The corrective functioning of Fab1 requires three additional proteins which are called the activator proteins of Fab1, Vac14p, Vac7p and Fig4p. The cells lacking these activator proteins show all or the same phenotypic defects as shown by cells lacking the fab1 gene (Dove et al., 2002; Duex et al., 2006).

Fig4p is a PPin phosphatase that dephosphorylates PtdIns(3,5)P2 at the 5th position on the inositol ring and degrades it into PtdIns 3P (Gary et al., 2002). In 2004, Rudge et al. created a recombinant form of Fig4p and found out that Fig4p attacks only PtdIns(3,5)P2 among the other PtdIns. Strains lacking the Fig4 gene had a substantial decrease in the production of PtdIns(3,5)P2, suggesting defective PtdIns(3,5)P2 synthesis. This puzzle was solved in recent studies showing that a large complex regulated the synthesis and degradation of PtdIns(3,5)P2. This is formed by Fab1p, vac14 and Fig4p (Dong, 2010; Botelho et al., 2008; Jin et al., 2008).

The common phenotypes that are associated with the yeast strains lack vac14 or vac7. These are the activators of Fab1p. Strains expressing Fab1p that can no longer function as a kinase, or those lacking the effectors of PtdIns(3,5)P2, have an enlarged vacuole that fills almost all of the cell. This suggests that PtdIns(3,5)P2 is required for the membrane and membrane-bound protein recycling (Michell et al., 2005). An enlarged vacuole is also observed in the vpsΔ cells. It is also observed in Schizosaccharomyces pombe when the ste12 gene has been deleted, which acts as a PIPkIII (Onishi et al., 2003; Takegawa et al., 2003). It was observed in Schizosaccharomyces pombe that the mating response to the mating factors slowed down (Michell et al., 2006). The cells were inefficient in mating, meiosis or sporulation due to the slowing down of the endocytic and exocytic membrane trafficking (Michell et al., 2006). These strains also showed inappropriate sensitivity to stresses like heat. This can be overcome by supplementing the growth medium with an abundance of osmolyte. Osmolyte is non-nutritional and corrects the defects in sporulation (Michell et al., 2006). A possible explanation for these effects is that they are due to defective cell-wall assembly that is caused by faulty membrane trafficking (Michell et al., 2006).
PPIns mediate their role on cellular activities by acting as membrane binding sites for various distinct effector proteins. PROPPIN, a family of effector proteins of PtdIns(3,5)P2, comprises tg18p/Svp1p, Atg21p/ Hsv 1p and Hsv 2p in yeast, which controls membrane trafficking between late endosome, MVB and vacuoles (Michell et al., 2006). In 2004, Dove et al. found out that Atg18p/ Svp1p has a high specificity for binding to PtdIns(3,5)P2 and plays a role in membrane trafficking from the vacuole. It was observed in Atg18pΔ cells that there was an excess of PtdIns(3,5)P2 even when it was not under stress (Michell et al., 2006). The strains containing a mutated form of Atg18p, which could not bind to PtdIns(3,5)P2, were found to have defective membrane trafficking from vacuole to endosome and vice versa (Dove et al., 2004).
In 2003, Fraint et al. found an epsin-like protein, Ent3, that plays a role as an effector protein which has a binding specificity to PtdIns(3,5)P2. The role of Ent3 has been observed in the membrane trafficking of cargo proteins between the trans-Golgi network and the vacuole (Hicke et al., 2003). Under normal conditions or a stressed state, the fusion or fragmentation of a vacuole or lysosome is one of the major functions performed by PtdIns(3,5)P2. Conformational changes in the vacuole can be studied by inducing hypo- or hyper-osmotic shock. These studies will help us to get a clear understanding of the role of PtdIns(3,5)P2 in cellular activities. The cellular levels of PtdIns(3,5)P2 increases with hyper-osmotic shock in Saccharomyces cerevisiae. This has also been observed in other organisms, including plants (Dove et al., 1997; Rugde et al., 2004). While moderate increases in the molecular levels of PtdIns(3,5)P2 was observed under modest stress and little vacuole fragmentation was observed, this could be reversed within ten minutes. However, when extensive stress was induced, a dramatic increase in the levels of PtdIns(3,5)P2 was observed with extensive fragmentation of vacuole. This took 60 minutes to reverse (Duex et al., 2006; Dove et al., 2009; Dong.,2010).

There are three fab1 mutants which help to develop a corresponding relationship between vacuole fragmentation and synthesis of PtdIns(3,5)P2:a fab1 mutant that can no longer function as a kinase (D2134R), had an enlarged vacuole (Gary et al., 1998; Odorizzi et al., 1998); FAB1-5 that produces an extraordinarily large amount of PtdIns(3,5)P2 and had a fragmented or shrunken vacuole; and a fab1 mutant which showed little fragmentation of the vacuole (Gary et al., 1998; Odorizzi et al., 1998) as it maintains only 10% of PtdIns(3,5)P2 levels (Dong.,2010).

1.2 Arrestin: Adaptors for Ubiquitin membrane trafficking

Changes in the cell membrane are brought about by the eukaryotic cells for the correct sensing of- and response to environmental cues. Yeast plasma membranes are remodelled either by degrading or recycling the plasma-membrane transporters by the process of endocytosis. Endocytosis is a mechanism by which the cells change their plasma membrane proteins which help in cell growth and differentiation. Ubiquitination is required for endocytosis which leads to vacuole degradation. In almost of the cases reported to date, Rsp5, a ubiquitin ligase is deployed near the plasma membrane (Hicki et al., 2003).
There are 3 WW domains present on Rsp5 that recognise the PY motif with a specific sequence: PPXY or LPXY (Nikko et al., 2009). Various adaptors have been discovered that take part in ubiquitination of protein including Bsd2 (Hettma et al., 2004), Tre1/2 (Stimpson et al., 2006) and soluble proteins Bul1 and Bul2 (Helliwell., 2001; Soetens et al., 2001). Recent work has found that members of yeast arrestin-like proteins take part in the endocytosis of the metal transporter Smt1 and various amino acid transporters including Can1, Mup1 and Lyp1 under stressed condition or in presence of respective amino acids (Lin et al., 2008; Nikko et al.,2008).


1989. Phosphatidylinositol 3-kinase and its novel product, phosphatidylinositol 3-phosphate, are present in Saccharomyces cerevisiae. Journal of Biological Chemistry, 264 (34), 20181-20184.

BALLA, T., 2006. Phosphoinositide-derived messengers in endocrine signaling. The Journal of Endocrinology, 188 (2), 135-153.

BONANGELINO, C.J., NAU, J.J., DUEX, J.E., BRINKMAN, M., WURMSER, A.E., GARY, J.D., EMR, S.D. and WEISMAN, L.S., 2002. Osmotic stress–induced increase of phosphatidylinositol 3,5-bisphosphate requires Vac14p, an activator of the lipid kinase Fab1p. The Journal of Cell Biology, 156 (6), 1015-1028.

BOTELHO, R.J., EFE, J.A., TEIS, D. and EMR, S.D., 2008. Assembly of a Fab1 phosphoinositide kinase signaling complex requires the Fig4 phosphoinositide phosphatase. Molecular Biology of the Cell, 19 (10), 4273-4286.

CORVERA, S., 2001. Phosphatidylinositol 3-kinase and the control of endosome dynamics: new players defined by structural motifs. Traffic (Copenhagen, Denmark), 2 (12), 859-866.

DOVE, S.K., COOKE, F.T., DOUGLAS, M.R., SAYERS, L.G., PARKER, P.J. and MICHELL, R.H., 1997. Osmotic stress activates phosphatidylinositol-3,5-bisphosphate synthesis. Nature, 390 (6656), 187-192.

DOVE, S.K., DONG, K., KOBAYASHI, T., WILLIAMS, F.K. and MICHELL, R.H., 2009. Phosphatidylinositol 3,5-bisphosphate and Fab1p/PIKfyve underPPIn endo-lysosome function. The Biochemical Journal, 419 (1), 1-13.

DOVE, S.K., and JOHNSON, Z.E., 2007. Our FABulous VACation: a decade of phosphatidylinositol 3,5-bisphosphate. Biochemical Society Symposium, (74) (74), 129-139.

DOVE, S.K., MCEWEN, R.K., MAYES, A., HUGHES, D.C., BEGGS, J.D. and MICHELL, R.H., 2002. Vac14 controls PtdIns(3,5)P(2) synthesis and Fab1-dependent protein trafficking to the multivesicular body. Current Biology : CB, 12 (11), 885-893.

DOVE, S.K., PIPER, R.C., MCEWEN, R.K., YU, J.W., KING, M.C., HUGHES, D.C., THURING, J., HOLMES, A.B., COOKE, F.T., MICHELL, R.H., PARKER, P.J. and LEMMON, M.A., 2004a. Svp1p defines a family of phosphatidylinositol 3,5-bisphosphate effectors. The EMBO Journal,
23 (9), 1922-1933.
DOVE, S.K., PIPER, R.C., MCEWEN, R.K., YU, J.W., KING, M.C., HUGHES, D.C., THURING, J., HOLMES, A.B., COOKE, F.T., MICHELL, R.H., PARKER, P.J. and LEMMON, M.A., 2004b. Svp1p defines a family of phosphatidylinositol 3,5-bisphosphate effectors. The EMBO Journal,
23 (9), 1922-1933.
DUEX, J.E., NAU, J.J., KAUFFMAN, E.J. and WEISMAN, L.S., 2006.
Phosphoinositide 5-phosphatase Fig 4p is required for both acute rise and subsequent fall in stress-induced phosphatidylinositol 3,5- bisphosphate levels. Eukaryotic Cell, 5 (4), 723-731.

Ubiquitin and endocytic internalization in yeast and animal cells.
Biochimica Et Biophysica Acta (BBA) – Molecular Cell Research,
1695 (1-3), 89-111.

GARY, J.D., SATO, T.K., STEFAN, C.J., BONANGELINO, C.J., WEISMAN, L.S. and EMR, S.D., 2002. Regulation of Fab1 phosphatidylinositol
3-phosphate 5-kinase pathway by Vac7 protein and Fig4, a polyphosphoinositide phosphatase family member. Molecular
Biology of the Cell, 13 (4), 1238-1251.

GARY, J.D., WURMSER, A.E., BONANGELINO, C.J., WEISMAN, L.S. and EMR, S.D., 1998. Fab1p is essential for PtdIns(3)P 5-kinase activity and the maintenance of vacuolar size and membrane homeostasis. The Journal of Cell Biology, 143 (1), 65-79.

Phosphatidylinositol 3-phosphate is found in microdomains of early endosomes. Histochemistry and Cell Biology, 120 (6), 445-453.

HELLIWELL, S.B., LOSKO, S. and KAISER, C.A., 2001. Components of a ubiquitin ligase complex specify polyubiquitination and intracellular trafficking of the general amino acid permease. The Journal of Cell Biology, 153 (4), 649-662.

HERMAN, P.K., and EMR, S.D., 1990. Characterization of VPS34, a gene required for vacuolar protein sorting and vacuole segregation in Saccharomyces cerevisiae. Molecular and Cellular Biology, 10 (12),

HETTEMA, E.H., VALDEZ-TAUBAS, J. and PELHAM, H.R., 2004. Bsd2 binds the ubiquitin ligase Rsp5 and mediates the ubiquitination of transmembrane proteins. The EMBO Journal, 23 (6), 1279-1288.

HICKE, L., 2003. PtdIns(3,5)P2 finds a partner. Developmental Cell, 5 (3),

JIN, N., CHOW, C.Y., LIU, L., ZOLOV, S.N., BRONSON, R., DAVISSON, M., PETERSEN, J.L., ZHANG, Y., PARK, S., DUEX, J.E., GOLDOWITZ, D., MEISLER, M.H. and WEISMAN, L.S., 2008. VAC14 nucleates a protein complex essential for the acute interconversion of PI3P and PI(3,5)P(2) in yeast and mouse. The EMBO Journal, 27 (24), 3221-

KANGZHEN DONG, 2010. Polyphosphoinositide-derived signals in the regulation of vacuole membrane fusion and fission. PhD., University of Birmingham.

KRAUß, M., and HAUCKE, V., 2007. Phosphoinositides: Regulators of membrane traffic and protein function. FEBS Letters, 581 (11),

LAI, K., BOLOGNESE, C.P., SWIFT, S. and MCGRAW, P., 1995. Regulation of inositol transport in Saccharomyces cerevisiae involves inositol- induced changes in permease stability and endocytic degradation in the vacuole. The Journal of Biological Chemistry, 270 (6), 2525-

LIN, C.H., MACGURN, J.A., CHU, T., STEFAN, C.J. and EMR, S.D., 2008.
Arrestin-Related Ubiquitin-Ligase Adaptors Regulate Endocytosis and Protein Turnover at the Cell Surface. Cell, 135 (4), 714-725.

LORENZ, M.C., MUIR, R.S., LIM, E., MCELVER, J., WEBER, S.C. and HEITMAN, J., 1995. Gene disruption with PCR products in Saccharomyces cerevisiae. Gene, 158 (1), 113-117.

MICHELL, R.H., HEATH, V.L., LEMMON, M.A. and DOVE, S.K., 2006a.
Phosphatidylinositol 3,5-bisphosphate: metabolism and cellular functions. Trends in Biochemical Sciences, 31 (1), 52-63.

MICHELL, R.H., HEATH, V.L., LEMMON, M.A. and DOVE, S.K., 2006b.
Phosphatidylinositol 3,5-bisphosphate: metabolism and cellular functions. Trends in Biochemical Sciences, 31 (1), 52-63.

MICHELL, R.H., HEATH, V.L., LEMMON, M.A. and DOVE, S.K., 2006c.
Phosphatidylinositol 3,5-bisphosphate: metabolism and cellular functions. Trends in Biochemical Sciences, 31 (1), 52-63.

NIKAWA, J., and KAWABATA, M., 1998. PCR- and ligation-mediated synthesis of marker cassettes with long flanking homology regions for gene disruption in Saccharomyces cerevisiae. Nucleic Acids Research, 26 (3), 860-861.

NIKKO, E., and PELHAM, H.R., 2009. Arrestin-mediated endocytosis of yeast plasma membrane transporters. Traffic (Copenhagen, Denmark), 10 (12), 1856-1867.

ODORIZZI, G., BABST, M. and EMR, S.D., 1998. Fab1p PtdIns(3)P 5- Kinase Function Essential for Protein Sorting in the Multivesicular Body. Cell, 95 (6), 847-858.

2003. Isolation of suppressor mutants of phosphatidylinositol 3- phosphate 5-kinase deficient cells in Schizosaccharomyces pombe. Bioscience, Biotechnology, and Biochemistry, 67 (8), 1772-1779.

POLO, S., and DI FIORE, P.P., 2008a. Finding the right partner: science or
ART? Cell, 135 (4), 590-592.

POLO, S., and DI FIORE, P.P., 2008b. Finding the Right Partner: Science or ART? Cell, 135 (4), 590-592.

RUDGE, S.A., ANDERSON, D.M. and EMR, S.D., 2004. Vacuole size control: regulation of PtdIns(3,5)P2 levels by the vacuole- associated Vac14-Fig4 complex, a PtdIns(3,5)P2-specific phosphatase. Molecular Biology of the Cell, 15 (1), 24-36.

SOETENS, O., DE CRAENE, J. and ANDRÉ, B., 2001. Ubiquitin Is Required for Sorting to the Vacuole of the Yeast General Amino Acid Permease, Gap1. Journal of Biological Chemistry, 276 (47), 43949-

STACK, J.H., and EMR, S.D., 1994. Vps34p required for yeast vacuolar protein sorting is a multiple specificity kinase that exhibits both protein kinase and phosphatidylinositol-specific PI 3-kinase activities. Journal of Biological Chemistry, 269 (50), 31552-31562.

STACK, J.H., HERMAN, P.K., SCHU, P.V. and EMR, S.D., 1993. A membrane-associated complex containing the Vps15 protein kinase and the Vps34 PI 3-kinase is essential for protein sorting to the yeast lysosome-like vacuole. The EMBO Journal, 12 (5), 2195-2204.

STIMPSON, H.E., LEWIS, M.J. and PELHAM, H.R., 2006. Transferrin receptor-like proteins control the degradation of a yeast metal transporter. The EMBO Journal, 25 (4), 662-672.

STRAHL, T., and THORNER, J., 2007. Synthesis and function of membrane phosphoinositides in budding yeast, Saccharomyces cerevisiae. Biochimica Et Biophysica Acta (BBA) – Molecular and Cell Biology of Lipids, 1771 (3), 353-404.

TAKEGAWA, K., IWAKI, T., FUJITA, Y., MORITA, T., HOSOMI, A. and TANAKA, N., 2003. Vesicle-mediated protein transport pathways to the vacuole in Schizosaccharomyces pombe. Cell Structure and Function, 28 (5), 399-417.

WEST, M.A., BRIGHT, N.A. and ROBINSON, M.S., 1997. The Role of ADP- ribosylation Factor and Phospholipase D in Adaptor Recruitment. The Journal of Cell Biology, 138 (6), 1239-1254.

Phosphatidylinositol 3,5-bisphosphate defines a novel PI 3-kinase pathway in resting mouse fibroblasts. The Biochemical Journal, 323 ( Pt 3) (Pt 3), 597-601.


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