Identification and structural characterization of FYVE domain-containing proteins of Arabidopsis thaliana

Department of Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA.
BMC Plant Biology (Impact Factor: 3.81). 08/2010; 10(1):157. DOI: 10.1186/1471-2229-10-157
Source: PubMed


FYVE domains have emerged as membrane-targeting domains highly specific for phosphatidylinositol 3-phosphate (PtdIns(3)P). They are predominantly found in proteins involved in various trafficking pathways. Although FYVE domains may function as individual modules, dimers or in partnership with other proteins, structurally, all FYVE domains share a fold comprising two small characteristic double-stranded beta-sheets, and a C-terminal alpha-helix, which houses eight conserved Zn2+ ion-binding cysteines. To date, the structural, biochemical, and biophysical mechanisms for subcellular targeting of FYVE domains for proteins from various model organisms have been worked out but plant FYVE domains remain noticeably under-investigated.
We carried out an extensive examination of all Arabidopsis FYVE domains, including their identification, classification, molecular modeling and biophysical characterization using computational approaches. Our classification of fifteen Arabidopsis FYVE proteins at the outset reveals unique domain architectures for FYVE containing proteins, which are not paralleled in other organisms. Detailed sequence analysis and biophysical characterization of the structural models are used to predict membrane interaction mechanisms previously described for other FYVE domains and their subtle variations as well as novel mechanisms that seem to be specific to plants.
Our study contributes to the understanding of the molecular basis of FYVE-based membrane targeting in plants on a genomic scale. The results show that FYVE domain containing proteins in plants have evolved to incorporate significant differences from those in other organisms implying that they play a unique role in plant signaling pathways and/or play similar/parallel roles in signaling to other organisms but use different protein players/signaling mechanisms.

Download full-text


Available from: PubMed Central · License: CC BY
  • Source
    • "FYVE domains bind phosphatidylinositol 3-P, a phospholipid that is a major constituent of endosomal membranes. Hence, FYVE domain-containing proteins are implicated in intracellular trafficking (van Leeuwen et al., 2004; Wywial and Singh, 2010). In a previous work, we have shown that a null mutant of FYVE1, fyve1-1, is defective in IRON-REGULATED TRANSPORTER1 (IRT1) polarization and that FYVE1 is essential for plant growth and development (Barberon et al., 2014). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The plant vacuole is a central organelle that is involved in various biological processes throughout the plant life cycle. Elucidating the mechanism of vacuole biogenesis and maintenance is thus the basis for our understanding of these processes. Proper formation of the vacuole has been shown to depend on the intracellular membrane trafficking pathway. Although several mutants with altered vacuole morphology have been characterized in the past, the molecular basis for plant vacuole biogenesis has yet to be fully elucidated. With the aim to identify key factors that are essential for vacuole biogenesis, we performed a forward genetics screen in Arabidopsis thaliana and isolated mutants with altered vacuole morphology. The vacuolar fusion defective 1 (vfd1) mutant shows seedling lethality and defects in central vacuole formation. VFD1 encodes FYVE1, a Fab1, YOTB, Vac1 and EEA1 (FYVE)-domain containing protein that has been implicated in intracellular trafficking. FYVE1 localizes on late endosomes and interacts with SH3-domain-containing proteins. Mutants of FYVE1 are defective in ubiquitin-mediated protein degradation, protein secretion and autophagy. Altogether, our results show that FYVE1 is essential for plant growth and development and place FYVE1 as a key regulator of intracellular trafficking and vacuole biogenesis. Copyright © 2015, American Society of Plant Biologists.
    Full-text · Article · Feb 2015 · Plant physiology
  • Source
    • "While there is no direct plant homolog of Spir, numerous plant proteins harbor FYVE domains. The 15 FYVE-containing proteins of A. thaliana can be divided into five groups according to their domain architecture (Wyvial and Singh, 2010). Most of these proteins are experimentally uncharacterized, and none exhibit a significant match to any of the previously described formin interactors in BLAST searches. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Formins are evolutionarily conserved eukaryotic proteins participating in actin and microtubule organization. Land plants have three formin clades, with only two - Class I and II - present in angiosperms. Class I formins are often transmembrane proteins, residing at the plasmalemma and anchoring the cortical cytoskeleton across the membrane to the cell wall, while Class II formins possess a PTEN-related membrane-binding domain. Lower plant Class III and non-plant formins usually contain domains predicted to bind RHO GTPases that are membrane-associated. Thus, some kind of membrane anchorage appears to be a common formin feature. Direct interactions between various non-plant formins and integral or peripheral membrane proteins have indeed been reported, with varying mechanisms and biological implications. Besides of summarizing new data on Class I and Class II formin-membrane relationships, this review surveys such "non-classical" formin-membrane interactions and examines which, if any, of them may be evolutionarily conserved and operating also in plants. FYVE, SH3 and BAR domain-containing proteins emerge as possible candidates for such conserved membrane-associated formin partners.
    Full-text · Article · Nov 2013 · Frontiers in Plant Science
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Dissertação (mestrado)—Universidade de Brasília, Faculdade de Medicina, 2005. Os neutrófilos são os leucócitos mais abundantes no sangue periférico humano, representando a primeira linha de defesa contra bactérias, vírus e protozoários. Durante o processo de ativação, essas células podem liberar O2 •- e proteases para o meio extracelular, e gerar destruição tecidual. Em um trauma grave, o processo inflamatório pode tornar-se disseminado e produzir SIRS (síndrome da resposta inflamatória sistêmica). O progresso dessa situação induz o desenvolvimento de ARDS (síndrome da angústia respiratória do adulto) e MOF (falência de múltiplos órgãos). Para entender os processos patológicos e as alterações do sistema imune depois de um trauma grave, a abordagem acerca das proteínas do neutrófilo é uma ferramenta excelente. Este trabalho apresenta os resultados obtidos a partir de uma análise comparativa entre os mapas proteômicos de neutrófilos não-ativados e de neutrófilos estimulados e ativados. Com a finalidade de analisar os neutrófilos, as células nãoativadas foram coletadas de indivíduos hígidos, ao passo que as células estimuladas e ativadas foram coletadas de pacientes politraumatizados, internados no HCFMUSP, até 24 horas do evento traumático. Após a separação por gradiente de densidade, as células desses 2 grupos de neutrófilos foram lisadas e submetidas à eletroforese bidimensional em gel desnaturante de poliacrilamida, utilizando dodecilsulfato de sódio como detergente. Para cada grupo, um mapa proteômico referência foi criado, através do software Image Master, e esses dois mapas foram comparados. A comparação mostra cento e quatorze spots comuns aos 2 grupos. Além disso, 15 spots são vistos apenas no mapa trauma e 55 spots são observados somente no mapa normal. Entre os spots, 22 proteínas identificadas são mostradas dentro dos grupos mencionados. A partir de estudos em andamento, o proteoma de neutrófilos estimulados in vitro será comparado aos resultados obtidos por meio deste trabalho. São pesquisados marcadores moleculares que podem estar envolvidos em estados mórbidos vistos após politraumatismos. Pela compreensão da função dessas proteínas, novas terapias e mecanismos de profilaxia podem ser desenvolvidos. _______________________________________________________________________________ ABSTRACT Neutrophils are the most abundant leukocytes in human peripheral blood, representing the first line of defense against bacteria, viruses and protozoa. During the activating process, these cells can release O2 •- and proteases to the extracellular environment, and generate tissue damage. In severe trauma, the inflammatory process may become widespread and produce SIRS (systemic inflammatory response syndrome). The progress of this situation induces the development of ARDS (adult respiratory distress syndrome) and MOF (multiple organs failure). To understand the pathological processes and alterations of the immune system after major trauma, the neutrophil proteomic approach is an excellent tool. This work presents the results obtained from a comparative analysis between the proteomic maps of resting and activated human neutrophils. To perform the analysis of resting neutrophils, cells were collected from healthy individuals and activated neutrophils were collected from polytrauma patients at HC-FMUSP, until 24 hours from traumatic event. After separation in a density gradient, cells of these 2 groups of neutrophils were lysed and submitted to 2D-PAGE. To each group, a reference proteomic map was created using the Image Master software and these two proteomic maps were compared. The comparison shows one hundred and fourteen common spots to the two groups. Besides, fifteen spots are seen only in trauma map and fifty-five spots are noticed just in normal map. Among these, twenty-two identified proteins are shown within the mentioned groups. In ongoing studies, the proteome of neutrophils stimulated in vitro will be compared to the results obtained here. We search for molecular markers that might be involved in the morbid states seen after polytraumatisms. By understanding the function of these proteins, new therapies and prophylactic clinical care can be developed.
    Preview · Article · Mar 2011
Show more