Biochemical and Functional Characterization of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinases

Ives, Eric B.; Nichols, Jason M.; Wente, Susan R.; York, John D.

doi:10.1074/jbc.m007586200

Cited by 76 publications

(77 citation statements)

References 50 publications

(107 reference statements)

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“…Several observations suggest that Gle1 activates Dbp5 in a manner that requires the small metabolite inositol hexakisphosphate (InsP 6 ) 114,115 . Mutations in the InsP 6 pathway genetically interact with gle1 mutants 122 and, in vitro, InsP 6 further increases the Gle1-dependent stimulation of Figure 4 | Regulation of eIF4A during translation initiation. a | During cap-dependent initiation of translation, eukaryotic initiation factor 4A (eIF4A) binds ATP, eIF4G and RNA (top).…”

Section: Nuclear Specklesmentioning

confidence: 99%

From unwinding to clamping — the DEAD box RNA helicase family

Linder

Jankowsky

2011

Nat Rev Mol Cell Biol

956

1,069

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Nearly all aspects of RNA metabolism, from transcription and translation to mRNA decay, involve RNA helicases, which are enzymes that use ATP to bind or remodel RNA and RNA-protein complexes (ribonucleoprotein (RNP) complexes) 1 . RNA helicases are found in all three domains of life, and many viruses also encode one or more of these proteins 2,3 . Together with the structurally related DNA helicases that function in replication, recombination and repair, the RNA helicases are classified into superfamilies and families, based on sequence and structural features 3,4 . DEAD box proteins form the largest helicase family, with 37 members in humans and 26 in Saccharomyces cerevisiae 3 , and are characterized by the presence of an Asp-Glu-Ala-Asp (DEAD) motif.DEAD box helicases have central and, in many cases, essential physiological roles in cellular RNA metabolism 5 (FIG. 1). The proteins generally function as part of larger multicomponent assemblies, such as the spliceosom e or the eukaryotic translation initiation machinery 6 . Mutations and deregulation of several DEAD box proteins have been linked to disease states, including cancer 7 . Although all DEAD box proteins contain a structurally highly conserved core with conserved ATP-binding and RNA-binding sites, different proteins have been associated with diverse and seemingly unrelated functions, including the disassembly of RNPs, chaperoning during RNA folding and even stabil ization of protein complexes on RNA 5,6 . How these highly conserved proteins fulfil such an array of different functions has been a long-standing question.Research has now started to illuminate the molecular basis for this functional diversity. In this Review, we summarize how structural data, together with biochemical and biophysical studies, have revealed unexpected modes by which these proteins function. We also discuss how novel molecular and cell biological approaches have better defined the cellular roles of DEAD box helicases. We outline our current view on common structural and mechan istic themes that have emerged, and on physical models of how these 'unusual' RNA helicases work.Structures of DEAD box RNA helicases A number of structural studies have universally shown that members of the DEAD box family contain a highly conserved helicase core that harbours the binding sites for ATP and RNA 3,4,8 . The core is surrounded by variable auxiliary domains, which are thought to be critical for the diverse functions of these enzymes.Structure of the helicase core. DEAD box proteins belong to helicase superfamily 2 (SF2) 2 . Similarly to all SF2 helicases, DEAD box proteins are built around a highly conserved helicase core of two virtually identical domains that resemble the bacterial recombination protein recombinase A (RecA) 3,4,8 (FIG. 2a,b). Within this helicase core, at least 12 characteristic sequence motifs are located at conserved positions (FIG. 2a,b). Some of these motifs are conserved across the entire SF2 family, whereas others are found only in the DEAD box family 3 ....

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Section: Nuclear Specklesmentioning

confidence: 99%

From unwinding to clamping — the DEAD box RNA helicase family

Linder

Jankowsky

2011

Nat Rev Mol Cell Biol

956

1,069

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“…We identified the Arabidopsis orthologs of Ipk2 and Ipk1 through BLAST sequence homology searches. The IP 5 2-kinase amino acid sequences from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Candida albicans (13) were used as queries against the Arabidopsis genome database. Three candidate genes were identified, two of which appeared to be pseudogenes.…”

Section: Atipk1mentioning

confidence: 99%

“…Pathways (I) and (II) are inositol lipid-dependent, whereas pathway (III) does not require lipid synthesis. Pathway (I) initiates through phospholipase C and subsequent sequential phosphorylation of inositol 1,4,5-trisphosphate [I(1,4,5)P 3 ] by IP kinases (IPKs), IPK2 (7)(8)(9)(10)(11)(12) and IPK1 (13)(14)(15). Pathway (II) is also a phospholipasedependent pathway whereby I(1,4,5)P 3 is phosphorylated to inositol 1,3,4,5-tetrakisphosphate [I(1,3,4,5)P 4 ] by either Ipk2 or I(1,4,5)P 3 3-kinase, dephosphorylated to inositol 1,3,4-trisphosphate [I(1,3,4)P 3 ], and phosphorylated by a I(1,3,4)P 3 5͞6-kinase, Ipk2, and Ipk1, respectively, through the indicated intermediates (14,(16)(17)(18).…”

mentioning

confidence: 99%

Generation of phytate-free seeds in Arabidopsis through disruption of inositol polyphosphate kinases

Stevenson-Paulik

Bastidas

Chiou

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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276

359

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Phytate (inositol hexakisphosphate, IP6) is a regulator of intracellular signaling, a highly abundant animal antinutrient, and a phosphate store in plant seeds. Here, we report a requirement for inositol polyphosphate kinases, AtIPK1 and AtIPK2␤, for the later steps of phytate synthesis in Arabidopsis thaliana. Coincident disruption of these kinases nearly ablates seed phytate without accumulation of phytate precursors, increases seed-free phosphate by 10-fold, and has normal seed yield. Additionally, we find a requirement for inositol tetrakisphosphate (IP 4)͞inositol pentakisphosphate (IP 5) 2-kinase activity in phosphate sensing and root hair elongation. Our results define a commercially viable strategy for the genetic engineering of phytate-free grain and provide insights into the role of inositol polyphosphate kinases in phosphate signaling biology.genetically engineered crops ͉ low phytate ͉ signal transduction ͉ phosphate sensing

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“…Purification of a protein corresponding to this kinase activity from immature soybean seeds revealed that the enzyme had a molecular mass of 52,000 D as determined by SDS-PAGE and a pH optimum at 6.8 (Phillippy et al, 1994). More recently, progress on characterization of this kinase at the molecular level has followed the discovery of the Ins(1,3,4,5,6)P 5 2-kinase gene (IPK1) in budding yeast (York et al, 1999;Ives et al, 2000). Orthologs of IPK1 were subsequently isolated from Schizosaccharomyces pombe (Ives et al, 2000), human (Verbsky et al, 2002), Drosophila (Seeds et al, 2004), and Arabidopsis (Stevenson-Paulik et al, 2005;Sweetman et al, 2006).…”

mentioning

confidence: 99%

“…More recently, progress on characterization of this kinase at the molecular level has followed the discovery of the Ins(1,3,4,5,6)P 5 2-kinase gene (IPK1) in budding yeast (York et al, 1999;Ives et al, 2000). Orthologs of IPK1 were subsequently isolated from Schizosaccharomyces pombe (Ives et al, 2000), human (Verbsky et al, 2002), Drosophila (Seeds et al, 2004), and Arabidopsis (Stevenson-Paulik et al, 2005;Sweetman et al, 2006). T-DNA insertional disruption of the Arabidopsis AtIPK1 gene was shown to result in accumulation of Ins (1,3,4,5,6)P 5 in seeds, and Arabidopsis lines containing insertional disruptions in both AtIPK1 and AtIPK2b gave rise to phytate-free seeds (Stevenson-Paulik et al, 2005).…”

mentioning

confidence: 99%

Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase from Maize: Molecular and Biochemical Characterization

Sun¹,

Thompson²,

Lin³

et al. 2007

Plant Physiol.

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Discovery R&D, Dow AgroSciences, Indianapolis, Indiana 46268 Inositol 1,3,4,5,6-pentakisphosphate 2-kinase, an enzyme encoded by the gene IPK1, catalyzes the terminal step in the phytic acid biosynthetic pathway. We report here the isolation and characterization of IPK1 cDNA and genomic clones from maize (Zea mays). DNA Southern-blot analysis revealed that ZmIPK1 in the maize genome constitutes a small gene family with two members. Two nearly identical ZmIPK1 paralogs, designated as ZmIPK1A and ZmIPK1B, were identified. The transcripts of ZmIPK1A were detected in various maize tissues, including leaves, silks, immature ears, seeds at 12 d after pollination, midstage endosperm, and maturing embryos. However, the transcripts of ZmIPK1B were exclusively detected in roots. A variety of alternative splicing products of ZmIPK1A were discovered in maize leaves and seeds. These products are derived from alternative acceptor sites, alternative donor sites, and retained introns in the transcripts. Consequently, up to 50% of the ZmIPK1A transcripts in maize seeds and leaves have an interrupted open reading frame. In contrast, only one type of splicing product of ZmIPK1B was detected in roots. When expressed in Escherichia coli and subsequently purified, the ZmIPK1 enzyme catalyzes the conversion of myo-inositol 1,3,4,5,6-pentakisphosphate to phytic acid. In addition, it is also capable of catalyzing the phosphorylation of myo-inositol 1,4,6-trisphosphate, myo-inositol 1,4,5,6-tetrakisphosphate, and myo-inositol 3,4,5,6-tetrakisphosphate. Nuclear magnetic resonance spectroscopy analysis indicates that the phosphorylation product of myoinositol 1,4,6-trisphosphate is inositol 1,2,4,6-tetrakisphosphate. Kinetic studies showed that the K m for ZmIPK1 using myo-inositol 1,3,4,5,6-pentakisphosphate as a substrate is 119 mM with a V max at 625 nmol/min/mg. These data describing the tissue-specific accumulation and alternative splicing of the transcripts from two nearly identical ZmIPK1 paralogs suggest that maize has a highly sophisticated regulatory mechanism controlling phytic acid biosynthesis.

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Biochemical and Functional Characterization of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinases

Cited by 76 publications

References 50 publications

From unwinding to clamping — the DEAD box RNA helicase family

From unwinding to clamping — the DEAD box RNA helicase family

Generation of phytate-free seeds in Arabidopsis through disruption of inositol polyphosphate kinases

Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase from Maize: Molecular and Biochemical Characterization

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