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Harold A. Scheraga - One of the best experts on this subject based on the ideXlab platform.

  • mechanism of formation of the c terminal β hairpin of the B3 Domain of the immunoglobulin binding protein g from streptococcus iv implication for the mechanism of folding of the parent protein
    Biopolymers, 2010
    Co-Authors: Agnieszka Lewandowska, Stanislaw Oldziej, Adam Liwo, Harold A. Scheraga
    Abstract:

    A 34-residue α/β peptide [IG(28–61)], derived from the C-terminal part of the B3 Domain of the immunoglobulin binding protein G from Streptoccocus, was studied using CD and NMR spectroscopy at various temperatures and by differential scanning calorimetry. It was found that the C-terminal part (a 16-residue-long fragment) of this peptide, which corresponds to the sequence of the β-hairpin in the native structure, forms structure similar to the β-hairpin only at T = 313 K, and the structure is stabilized by non-native long-range hydrophobic interactions (Val47–Val59). On the other hand, the N-terminal part of IG(28–61), which corresponds to the middle α-helix in the native structure, is unstructured at low temperature (283 K) and forms an α-helix-like structure at 305 K, and only one helical turn is observed at 313 K. At all temperatures at which NMR experiments were performed (283, 305, and 313 K), we do not observe any long-range connectivities which would have supported packing between the C-terminal (β-hairpin) and the N-terminal (α-helix) parts of the sequence. Such interactions are absent, in contrast to the folding pathway of the B Domain of protein G, proposed recently by Kmiecik and Kolinski (Biophys J 2008, 94, 726–736), based on Monte-Carlo dynamics studies. Alternative folding mechanisms are proposed and discussed. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 469–480, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

  • Mechanism of formation of the C‐terminal β‐hairpin of the B3 Domain of the immunoglobulin‐binding protein G from Streptococcus. IV. Implication for the mechanism of folding of the parent protein
    Biopolymers, 2010
    Co-Authors: Agnieszka Lewandowska, Adam Liwo, Stanisław Ołdziej, Harold A. Scheraga
    Abstract:

    A 34-residue α/β peptide [IG(28–61)], derived from the C-terminal part of the B3 Domain of the immunoglobulin binding protein G from Streptoccocus, was studied using CD and NMR spectroscopy at various temperatures and by differential scanning calorimetry. It was found that the C-terminal part (a 16-residue-long fragment) of this peptide, which corresponds to the sequence of the β-hairpin in the native structure, forms structure similar to the β-hairpin only at T = 313 K, and the structure is stabilized by non-native long-range hydrophobic interactions (Val47–Val59). On the other hand, the N-terminal part of IG(28–61), which corresponds to the middle α-helix in the native structure, is unstructured at low temperature (283 K) and forms an α-helix-like structure at 305 K, and only one helical turn is observed at 313 K. At all temperatures at which NMR experiments were performed (283, 305, and 313 K), we do not observe any long-range connectivities which would have supported packing between the C-terminal (β-hairpin) and the N-terminal (α-helix) parts of the sequence. Such interactions are absent, in contrast to the folding pathway of the B Domain of protein G, proposed recently by Kmiecik and Kolinski (Biophys J 2008, 94, 726–736), based on Monte-Carlo dynamics studies. Alternative folding mechanisms are proposed and discussed. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 469–480, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

  • mechanism of formation of the c terminal beta hairpin of the B3 Domain of the immunoglobulin binding protein g from streptococcus iii dynamics of long range hydrophobic interactions
    Proteins, 2009
    Co-Authors: Agnieszka Lewandowska, Stanislaw Oldziej, Adam Liwo, Harold A. Scheraga
    Abstract:

    A 20-residue peptide, IG(42–61), derived from the C-terminal β-hairpin of the B3 Domain of the immunoglobulin binding protein G from Streptoccocus was studied using circular dichroism, nuclear magnetic resonance (NMR) spectroscopy at various temperatures and by differential scanning calorimetry (DSC). Unlike other related peptides studied so far, this peptide displays two heat capacity peaks in DSC measurements (at a scanning rate of 1.5 deg/min at a peptide concentration of 0.07 mM), which suggests a three-state folding/unfolding process. The results from DSC and NMR measurements suggest the formation of a dynamic network of hydrophobic interactions stabilizing the structure, which resembles a β-hairpin shape over a wide range of temperatures (283–313 K). Our results show that IG (42–61) possesses a well-organized three-dimensional structure stabilized by long-range hydrophobic interactions (Tyr50 ··· Phe57 and Trp48 ··· Val59) at T = 283 K and (Trp48 ··· Val59) at 305 and 313 K. The mechanism of β-hairpin folding and unfolding, as well as the influence of peptide length on its conformational properties, are also discussed. Proteins 2010. © 2009 Wiley-Liss, Inc.

  • mechanism of formation of the c terminal beta hairpin of the B3 Domain of the immunoglobulin binding protein g from streptococcus ii interplay of local backbone conformational dynamics and long range hydrophobic interactions in hairpin formation
    Proteins, 2009
    Co-Authors: Agnieszka Skwierawska, Stanislaw Oldziej, Wioletta Zmudzinska, Adam Liwo, Harold A. Scheraga
    Abstract:

    Two peptides, corresponding to the turn region of the C-terminal β-hairpin of the B3 Domain of the immunoglobulin binding protein G from Streptoccocus, consisting of residues 51–56 [IG(51–56)] and 50–57 [IG(50–57)], respectively, were studied by CD and NMR spectroscopy at various temperatures and by differential scanning calorimetry. Our results show that the part of the sequence corresponding to the β-turn in the native structure (DDATKT) of the B3 Domain forms bent conformations similar to those observed in the native protein. The formation of a turn is observed for both peptides in a broad range of temperatures (T = 283–323 K), which confirms the conclusion drawn from our previous studies of longer sequences from the C-terminal β-hairpin of the B3 Domain of the immunoglobulin binding protein G (16, 14 and 12 residues), that the DDATKT sequence forms a nucleation site for formation of the β-hairpin structure of peptides corresponding to the C-terminal part of all the B Domains of the immunoglobulin binding protein G. We also show and discuss the role of long-range hydrophobic interactions as well as local conformational properties of polypeptide chains in the mechanism of formation of the β-hairpin structure.

  • mechanism of formation of the c terminal beta hairpin of the B3 Domain of the immunoglobulin binding protein g from streptococcus i importance of hydrophobic interactions in stabilization of beta hairpin structure
    Proteins, 2009
    Co-Authors: Agnieszka Skwierawska, Joanna Makowska, Stanislaw Oldziej, Adam Liwo, Harold A. Scheraga
    Abstract:

    We previously studied a 16-amino acid-residue fragment of the C-terminal β-hairpin of the B3 Domain (residues 46–61), [IG(46–61)] of the immunoglobulin binding protein G from Streptoccocus, and found that hydrophobic interactions and the turn region play an important role in stabilizing the structure. Based on these results, we carried out systematic structural studies of peptides derived from the sequence of IG (46–61) by systematically shortening the peptide by one residue at a time from both the C- and the N-terminus. To determine the structure and stability of two resulting 12- and 14-amino acid-residue peptides, IG(48–59) and IG(47–60), respectively, we carried out circular dichroism, NMR, and calorimetric studies of these peptides in pure water. Our results show that IG(48–59) possesses organized three-dimensional structure stabilized by hydrophobic interactions (Tyr50–Phe57 and Trp48–Val59) at T = 283 and 305 K. At T = 313 K, the structure breaks down because of increased chain entropy, but the turn region is preserved in the same position observed for the structure of the whole protein. The breakdown of structure occurs near the melting temperature of this peptide (Tm = 310 K) measured by differential scanning calorimetry (DSC). The melting temperature of IG(47–60) determined by DSC is Tm = 330 K and its structure is similar to that of the native β-hairpin at all (lower) temperatures examined (283–313 K). Both of these truncated sequences are conserved in all known amino acid sequences of the B Domains of the immunoglobulin binding protein G from bacteria. Thus, this study contributes to an understanding of the mechanism of folding of this whole family of proteins, and provides information about the mechanism of formation and stabilization of a β-hairpin structural element. Proteins 2009. © 2008 Wiley-Liss, Inc.

Adam Liwo - One of the best experts on this subject based on the ideXlab platform.

  • Combination of SAXS and NMR Techniques as a Tool for the Determination of Peptide Structure in Solution
    The Journal of Physical Chemistry Letters, 2010
    Co-Authors: Maciej Kozak, Sylwia Rodziewicz-motowidło, Agnieszka Lewandowska, Stanisław Ołdziej, Adam Liwo
    Abstract:

    The biological activity of peptides is largely determined by their spatial structure in solution. Because of flexibility of these molecules, the NMR technique, commonly used to determine the solution structures, usually provides only the information of the local geometry of peptide chains. On the other hand, small-angle X-ray scattering (SAXS) gives interatomic distance distribution in the molecule, thereby defining the shape of a molecule. In this work we carried out a SAXS study of the 28−43 sequence fragment of the B3 Domain of immunoglobulin binding protein G from Streptococcus, IG(28−43). We fitted the conformational ensembles obtained in our previous work by using the NMR-restrained molecular dynamics simulations to the distance distribution obtained from SAXS measurements. Only two clusters of conformations with shape bent in the middle out of 11, consistent with NMR data had nonzero statistical weights. Thus, SAXS and NMR provide complementary structural information and appear to be an excellent t...

  • mechanism of formation of the c terminal β hairpin of the B3 Domain of the immunoglobulin binding protein g from streptococcus iv implication for the mechanism of folding of the parent protein
    Biopolymers, 2010
    Co-Authors: Agnieszka Lewandowska, Stanislaw Oldziej, Adam Liwo, Harold A. Scheraga
    Abstract:

    A 34-residue α/β peptide [IG(28–61)], derived from the C-terminal part of the B3 Domain of the immunoglobulin binding protein G from Streptoccocus, was studied using CD and NMR spectroscopy at various temperatures and by differential scanning calorimetry. It was found that the C-terminal part (a 16-residue-long fragment) of this peptide, which corresponds to the sequence of the β-hairpin in the native structure, forms structure similar to the β-hairpin only at T = 313 K, and the structure is stabilized by non-native long-range hydrophobic interactions (Val47–Val59). On the other hand, the N-terminal part of IG(28–61), which corresponds to the middle α-helix in the native structure, is unstructured at low temperature (283 K) and forms an α-helix-like structure at 305 K, and only one helical turn is observed at 313 K. At all temperatures at which NMR experiments were performed (283, 305, and 313 K), we do not observe any long-range connectivities which would have supported packing between the C-terminal (β-hairpin) and the N-terminal (α-helix) parts of the sequence. Such interactions are absent, in contrast to the folding pathway of the B Domain of protein G, proposed recently by Kmiecik and Kolinski (Biophys J 2008, 94, 726–736), based on Monte-Carlo dynamics studies. Alternative folding mechanisms are proposed and discussed. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 469–480, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

  • Mechanism of formation of the C‐terminal β‐hairpin of the B3 Domain of the immunoglobulin‐binding protein G from Streptococcus. IV. Implication for the mechanism of folding of the parent protein
    Biopolymers, 2010
    Co-Authors: Agnieszka Lewandowska, Adam Liwo, Stanisław Ołdziej, Harold A. Scheraga
    Abstract:

    A 34-residue α/β peptide [IG(28–61)], derived from the C-terminal part of the B3 Domain of the immunoglobulin binding protein G from Streptoccocus, was studied using CD and NMR spectroscopy at various temperatures and by differential scanning calorimetry. It was found that the C-terminal part (a 16-residue-long fragment) of this peptide, which corresponds to the sequence of the β-hairpin in the native structure, forms structure similar to the β-hairpin only at T = 313 K, and the structure is stabilized by non-native long-range hydrophobic interactions (Val47–Val59). On the other hand, the N-terminal part of IG(28–61), which corresponds to the middle α-helix in the native structure, is unstructured at low temperature (283 K) and forms an α-helix-like structure at 305 K, and only one helical turn is observed at 313 K. At all temperatures at which NMR experiments were performed (283, 305, and 313 K), we do not observe any long-range connectivities which would have supported packing between the C-terminal (β-hairpin) and the N-terminal (α-helix) parts of the sequence. Such interactions are absent, in contrast to the folding pathway of the B Domain of protein G, proposed recently by Kmiecik and Kolinski (Biophys J 2008, 94, 726–736), based on Monte-Carlo dynamics studies. Alternative folding mechanisms are proposed and discussed. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 469–480, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

  • mechanism of formation of the c terminal beta hairpin of the B3 Domain of the immunoglobulin binding protein g from streptococcus iii dynamics of long range hydrophobic interactions
    Proteins, 2009
    Co-Authors: Agnieszka Lewandowska, Stanislaw Oldziej, Adam Liwo, Harold A. Scheraga
    Abstract:

    A 20-residue peptide, IG(42–61), derived from the C-terminal β-hairpin of the B3 Domain of the immunoglobulin binding protein G from Streptoccocus was studied using circular dichroism, nuclear magnetic resonance (NMR) spectroscopy at various temperatures and by differential scanning calorimetry (DSC). Unlike other related peptides studied so far, this peptide displays two heat capacity peaks in DSC measurements (at a scanning rate of 1.5 deg/min at a peptide concentration of 0.07 mM), which suggests a three-state folding/unfolding process. The results from DSC and NMR measurements suggest the formation of a dynamic network of hydrophobic interactions stabilizing the structure, which resembles a β-hairpin shape over a wide range of temperatures (283–313 K). Our results show that IG (42–61) possesses a well-organized three-dimensional structure stabilized by long-range hydrophobic interactions (Tyr50 ··· Phe57 and Trp48 ··· Val59) at T = 283 K and (Trp48 ··· Val59) at 305 and 313 K. The mechanism of β-hairpin folding and unfolding, as well as the influence of peptide length on its conformational properties, are also discussed. Proteins 2010. © 2009 Wiley-Liss, Inc.

  • mechanism of formation of the c terminal beta hairpin of the B3 Domain of the immunoglobulin binding protein g from streptococcus ii interplay of local backbone conformational dynamics and long range hydrophobic interactions in hairpin formation
    Proteins, 2009
    Co-Authors: Agnieszka Skwierawska, Stanislaw Oldziej, Wioletta Zmudzinska, Adam Liwo, Harold A. Scheraga
    Abstract:

    Two peptides, corresponding to the turn region of the C-terminal β-hairpin of the B3 Domain of the immunoglobulin binding protein G from Streptoccocus, consisting of residues 51–56 [IG(51–56)] and 50–57 [IG(50–57)], respectively, were studied by CD and NMR spectroscopy at various temperatures and by differential scanning calorimetry. Our results show that the part of the sequence corresponding to the β-turn in the native structure (DDATKT) of the B3 Domain forms bent conformations similar to those observed in the native protein. The formation of a turn is observed for both peptides in a broad range of temperatures (T = 283–323 K), which confirms the conclusion drawn from our previous studies of longer sequences from the C-terminal β-hairpin of the B3 Domain of the immunoglobulin binding protein G (16, 14 and 12 residues), that the DDATKT sequence forms a nucleation site for formation of the β-hairpin structure of peptides corresponding to the C-terminal part of all the B Domains of the immunoglobulin binding protein G. We also show and discuss the role of long-range hydrophobic interactions as well as local conformational properties of polypeptide chains in the mechanism of formation of the β-hairpin structure.

Donald R. Mccarty - One of the best experts on this subject based on the ideXlab platform.

  • Distinct functions of COAR and B3 Domains of maize VP1 in induction of ectopic gene expression and plant developmental phenotypes in Arabidopsis.
    Plant molecular biology, 2014
    Co-Authors: Masaharu Suzuki, Donald R. Mccarty
    Abstract:

    Arabidopsis ABI3 and maize VP1 are orthologous transcription factors that regulate seed maturation. ABI3 and VP1 have a C-terminal B3 DNA binding Domain and a conserved N-terminal co-activator/co-repressor (COAR) Domain consisting of A1, B1, B2 sub-Domains. The COAR Domain mediates abscisic acid signaling via a physical interaction with ABI5-related bZIP proteins. In order to delineate the COAR and B3 Domain dependent functions of VP1, we created site directed mutations in the B3 Domain that disrupted DNA binding activity and characterized gene regulation by the mutant proteins in transgenic abi3 mutant Arabidopsis plants. In seeds, COAR Domain function of VP1 mutants that lacked B3 DNA binding activity was sufficient for complementation of the desiccation intolerant seed phenotype of abi3. Similarly in seedlings, the B3 Domain was dispensable for most VP1 induced gene expression and ectopic developmental phenotypes, except for a small subset of the genes that showed B3 dependent regulation. Unexpectedly, over-expression of the DNA-binding deficient VP1-K519R mutant protein caused quantitative changes in floral organ size including elongation of pistils and shortened stamen filaments that resulted in a self-incompatible longistyly flower morphology, a key component of heterostyly type self-incompatibility.

  • Distinct Roles of LAFL Network Genes in Promoting the Embryonic Seedling Fate in the Absence of VAL Repression
    Plant physiology, 2013
    Co-Authors: Haiyan Jia, Donald R. Mccarty, Masaharu Suzuki
    Abstract:

    The transition between seed and seedling phases of development is coordinated by an interaction between the closely related ABSCISIC ACID-INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEAFY COTYLEDON2 (LEC2; AFL) and VIVIPAROUS1/ABI3-LIKE (VAL) clades of the B3 transcription factor family that respectively activate and repress the seed maturation program. In the val1 val2 double mutant, derepression of the LEC1, LEC1-LIKE (L1L), and AFL (LAFL) network is associated with misexpression of embryonic characteristics resulting in arrested seedling development. We show that while the frequency of the embryonic fate in val1 val2 seedlings depends on the developmental timing of seed rescue, VAL proteins repress LAFL genes during germination, but not during seed development. Quantitative analysis of LAFL mutants that suppress the val1 val2 seedling phenotype revealed distinct roles of LAFL genes in promoting activation of the LAFL network. LEC2 and FUS3 are both essential for coordinate activation of the network, whereas effects of LEC1, L1L, and ABI3 are additive. Suppression of the val1 val2 seedling phenotype by the B3 Domain-deficient abi3-12 mutation indicates that ABI3 activation of the LAFL network requires the B3 DNA-binding Domain. In the VAL-deficient background, coordinate regulation of the LAFL network is observed over a wide range of genetic and developmental conditions. Our findings highlight distinct functional roles and interactions of LAFL network genes that are uncovered in the absence of VAL repressors.

  • Regulation of the seed to seedling developmental phase transition by the LAFL and VAL transcription factor networks
    Wiley interdisciplinary reviews. Developmental biology, 2013
    Co-Authors: Haiyan Jia, Masaharu Suzuki, Donald R. Mccarty
    Abstract:

    In the seed, a fundamental transition between embryo and vegetative phases of plant development is coordinated by the interaction between the AFL and VAL sub-clades of the plant specific B3 Domain transcription factor family. The AFL B3 factors together with LEC1-type HAP3 transcription factors promote embryo maturation; whereas the VAL B3 factors repress the LEC1/AFL (LAFL) network during seed germination. Recent advances reveal that genes in key developmental programs and hormone signaling pathways are downstream targets of the LAFL network highlighting the central role of the LAFL network in integration of intrinsic developmental and hormonal signals during plant development. The VAL B3 proteins are proposed to mediate repression by recruiting a histone deacetylase complex (HDAC) to LAFL genes that contain the Sph/RY cis-element recognized by AFL and VAL B3-DNA-binding Domains. In addition to VAL B3 factors, epigenetic mechanisms are implicated in maintaining repression of LAFL network during vegetative development. WIREs Dev Biol 2014, 3:135–145. doi: 10.1002/wdev.126

  • Functional symmetry of the B3 network controlling seed development.
    Current opinion in plant biology, 2008
    Co-Authors: Masaharu Suzuki, Donald R. Mccarty
    Abstract:

    Two subfamilies of plant-specific B3 Domain transcription factors regulate the fundamental transition between seed and vegetative phases of development. The AFL B3 genes activate the embryo maturation program, while the closely related VAL B3 genes shutdown the AFL network before germination. VP8/AMP1 signaling most probably acts upstream of the AFL network. Key downstream AFL targets elaborate seed-specific abscisic acid (ABA), gibberellin (GA), and auxin signaling. ABA feeds back into network via ABI3 interaction with ABI5. GA promotes repression of the AFL network by the VAL repressors and the PICKLE (PKL) chromatin-remodeling factor before germination. Strikingly, the functional symmetry of the AFL and VAL B3 genes is mirrored in patterns of chromatin modification.

  • Abscisic acid and stress signals induce Viviparous1 expression in seed and vegetative tissues of maize.
    Plant Physiology, 2007
    Co-Authors: Liliana M Costa, Donald R. Mccarty, Corinne Biderre-petit, Bouchab Kbhaya, Pascual Perez, Jose F Gutierrez-marcos, Philip W Becraft
    Abstract:

    Viviparous1 (Vp1) encodes a B3 Domain-containing transcription factor that is a key regulator of seed maturation in maize (Zea mays). However, the mechanisms of Vp1 regulation are not well understood. To examine physiological factors that may regulate Vp1 expression, transcript levels were monitored in maturing embryos placed in culture under different conditions. Expression of Vp1 decreased after culture in hormone-free medium, but was induced by salinity or osmotic stress. Application of exogenous abscisic acid (ABA) also induced transcript levels within 1 h in a dose-dependent manner. The Vp1 promoter fused to beta-glucuronidase or green fluorescent protein reproduced the endogenous Vp1 expression patterns in transgenic maize plants and also revealed previously unknown expression Domains of Vp1. The Vp1 promoter is active in the embryo and aleurone cells of developing seeds and, upon drought stress, was also found in phloem cells of vegetative tissues, including cobs, leaves, and stems. Sequence analysis of the Vp1 promoter identified a potential ABA-responsive complex, consisting of an ACGT-containing ABA response element (ABRE) and a coupling element 1-like motif. Electrophoretic mobility shift assay confirmed that the ABRE and putative coupling element 1 components specifically bound proteins in embryo nuclear protein extracts. Treatment of embryos in hormone-free Murashige and Skoog medium blocked the ABRE-protein interaction, whereas exogenous ABA or mannitol treatment restored this interaction. Our data support a model for a VP1-dependent positive feedback mechanism regulating Vp1 expression during seed maturation.

Randy D Allen - One of the best experts on this subject based on the ideXlab platform.

  • HSI2/VAL1 and HSL1/VAL2 function redundantly to repress DOG1 expression in Arabidopsis seeds and seedlings.
    The New phytologist, 2020
    Co-Authors: Naichong Chen, Vijaykumar Veerappan, Haggag Abdelmageed, Hui Wang, Million Tadege, Randy D Allen
    Abstract:

    DELAY OF GERMINATION1 (DOG1) is a primary regulator of seed dormancy. Accumulation of DOG1 in seeds leads to deep dormancy and delayed germination in Arabidopsis. B3 Domain-containing transcriptional repressors HSI2/VAL1 and HSL1/VAL2 silence seed dormancy and enable the subsequent germination and seedling growth. However, the roles of HSI2 and HSL1 in regulation of DOG1 expression and seed dormancy remain elusive. Seed dormancy was analysed by measurement of maximum germination percentage of freshly harvested Arabidopsis seeds. In vivo protein-protein interaction analysis, ChIP-qPCR and EMSA were performed and suggested that HSI2 and HSL1 can form dimers to directly regulate DOG1. HSI2 and HSL1 dimers interact with RY elements at DOG1 promoter. Both B3 and PHD-like Domains are required for enrichment of HSI2 and HSL1 at the DOG1 promoter. HSI2 and HSL1 recruit components of polycomb-group proteins, including CURLY LEAF (CLF) and LIKE HETERCHROMATIN PROTEIN 1 (LHP1), for consequent deposition of H3K27me3 marks, leading to repression of DOG1 expression. Our findings suggest that HSI2- and HSL1-dependent histone methylation plays critical roles in regulation of seed dormancy during seed germination and early seedling growth.

  • hsi2 val1 silences agl15 to regulate the developmental transition from seed maturation to vegetative growth in arabidopsis
    The Plant Cell, 2018
    Co-Authors: Naichong Chen, Vijaykumar Veerappan, Haggag Abdelmageed, Miyoung Kang, Randy D Allen
    Abstract:

    Gene expression during seed development in Arabidopsis thaliana is controlled by transcription factors including LEAFY COTYLEDON1 (LEC1) and LEC2, ABA INSENSITIVE3 (ABI3), FUSCA3 (FUS3), known as LAFL proteins, and AGAMOUS-LIKE15 (AGL15). The transition from seed maturation to germination and seedling growth requires the transcriptional silencing of these seed maturation-specific factors leading to downregulation of structural genes including those that encode seed storage proteins, oleosins, and dehydrins. During seed germination and vegetative growth, B3-Domain protein HSI2/VAL1 is required for the transcriptional silencing of LAFL genes. Here, we report chromatin immunoprecipitation analysis indicating that HSI2/VAL1 binds to the upstream sequences of the AGL15 gene but not at LEC1, ABI3, FUS3, or LEC2 loci. Functional analysis indicates that the HSI2/VAL1 B3 Domain interacts with two RY elements upstream of the AGL15 coding region and at least one of them is required for HSI2/VAL1-dependent AGL15 repression. Expression analysis of the major seed maturation regulatory genes LEC1, ABI3, FUS3, and LEC2 in different genetic backgrounds demonstrates that HSI2/VAL1 is epistatic to AGL15 and represses the seed maturation regulatory program through downregulation of AGL15 by deposition of H3K27me3 at this locus. This hypothesis is further supported by results that show that HSI2/VAL1 physically interacts with the Polycomb Repressive Complex 2 component protein MSI1, which is also enriched at the AGL15 locus.

  • HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis.
    The Plant cell, 2018
    Co-Authors: Naichong Chen, Vijaykumar Veerappan, Haggag Abdelmageed, Miyoung Kang, Randy D Allen
    Abstract:

    Gene expression during seed development in Arabidopsis thaliana is controlled by transcription factors including LEAFY COTYLEDON1 (LEC1) and LEC2, ABA INSENSITIVE3 (ABI3), FUSCA3 (FUS3), known as LAFL proteins, and AGAMOUS-LIKE15 (AGL15). The transition from seed maturation to germination and seedling growth requires the transcriptional silencing of these seed maturation-specific factors leading to downregulation of structural genes including those that encode seed storage proteins, oleosins, and dehydrins. During seed germination and vegetative growth, B3-Domain protein HSI2/VAL1 is required for the transcriptional silencing of LAFL genes. Here, we report chromatin immunoprecipitation analysis indicating that HSI2/VAL1 binds to the upstream sequences of the AGL15 gene but not at LEC1, ABI3, FUS3, or LEC2 loci. Functional analysis indicates that the HSI2/VAL1 B3 Domain interacts with two RY elements upstream of the AGL15 coding region and at least one of them is required for HSI2/VAL1-dependent AGL15 repression. Expression analysis of the major seed maturation regulatory genes LEC1, ABI3, FUS3, and LEC2 in different genetic backgrounds demonstrates that HSI2/VAL1 is epistatic to AGL15 and represses the seed maturation regulatory program through downregulation of AGL15 by deposition of H3K27me3 at this locus. This hypothesis is further supported by results that show that HSI2/VAL1 physically interacts with the Polycomb Repressive Complex 2 component protein MSI1, which is also enriched at the AGL15 locus.

  • A novel HSI2 mutation in Arabidopsis affects the PHD-like Domain and leads to derepression of seed-specific gene expression
    Planta, 2012
    Co-Authors: Vijaykumar Veerappan, Miyoung Kang, Jing Wang, Yuhong Tang, Ravishankar Palanivelu, Randy D Allen
    Abstract:

    Two related B3 Domain transcriptional repressors, HSI2 (HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE GENE2)/VAL1 (VP1/ABI3-LIKE1) and HSL1 (HSI2-LIKE1)/VAL2, function redundantly to repress key transcriptional regulators of seed maturation genes in Arabidopsis thaliana seedlings. Using a forward genetic screen designed to isolate trans -acting mutants that affected expression of a transgene containing the glutathione S -transferase F8 promoter::luciferase ( GSTF8::LUC ) reporter, we identified a novel HSI2 mutant allele, hsi2 - 4 , that exhibits constitutively elevated luciferase expression while expression of the endogenous GSTF8 transcript remains unchanged. The hsi2 - 4 lesion was found to be a missense mutation that results in the substitution of a conserved cysteine within the plant homeoDomain-like (PHD) motif of HSI2. Microarray analysis of hsi2 - 4 and hsi2 - 4 hsl1 mutants indicated that the HSI2 PHD-like Domain functions non-redundantly to repress a subset of seed maturation genes, including those that encode AGL15 (AGAMOUS-LIKE15), FUSCA3 (FUS3), cruciferins, cupin family proteins, late-embryogenesis abundant protein, oleosins, 2S albumins and other seed-specific proteins in Arabidopsis seedlings. Many genes that are responsive to this mutation in the HSI2 PHD-like Domain are enriched in histone H3 trimethylation on lysine 27 residues (H3K27me3), a repressive epigenetic mark. Chromatin immunoprecipitation analysis showed that sequences of the GSTF8:: LUC transgene are enriched in H3K27me3 in a HSI2 PHD Domain-dependent manner. These results indicate that the transcriptional repression activity of the HSI2 PHD Domain could be mediated, at least in part, by its participation in the deposition of H3K27me3 on the chromatin of specific target genes.

Agnieszka Lewandowska - One of the best experts on this subject based on the ideXlab platform.

  • Combination of SAXS and NMR Techniques as a Tool for the Determination of Peptide Structure in Solution
    The Journal of Physical Chemistry Letters, 2010
    Co-Authors: Maciej Kozak, Sylwia Rodziewicz-motowidło, Agnieszka Lewandowska, Stanisław Ołdziej, Adam Liwo
    Abstract:

    The biological activity of peptides is largely determined by their spatial structure in solution. Because of flexibility of these molecules, the NMR technique, commonly used to determine the solution structures, usually provides only the information of the local geometry of peptide chains. On the other hand, small-angle X-ray scattering (SAXS) gives interatomic distance distribution in the molecule, thereby defining the shape of a molecule. In this work we carried out a SAXS study of the 28−43 sequence fragment of the B3 Domain of immunoglobulin binding protein G from Streptococcus, IG(28−43). We fitted the conformational ensembles obtained in our previous work by using the NMR-restrained molecular dynamics simulations to the distance distribution obtained from SAXS measurements. Only two clusters of conformations with shape bent in the middle out of 11, consistent with NMR data had nonzero statistical weights. Thus, SAXS and NMR provide complementary structural information and appear to be an excellent t...

  • mechanism of formation of the c terminal β hairpin of the B3 Domain of the immunoglobulin binding protein g from streptococcus iv implication for the mechanism of folding of the parent protein
    Biopolymers, 2010
    Co-Authors: Agnieszka Lewandowska, Stanislaw Oldziej, Adam Liwo, Harold A. Scheraga
    Abstract:

    A 34-residue α/β peptide [IG(28–61)], derived from the C-terminal part of the B3 Domain of the immunoglobulin binding protein G from Streptoccocus, was studied using CD and NMR spectroscopy at various temperatures and by differential scanning calorimetry. It was found that the C-terminal part (a 16-residue-long fragment) of this peptide, which corresponds to the sequence of the β-hairpin in the native structure, forms structure similar to the β-hairpin only at T = 313 K, and the structure is stabilized by non-native long-range hydrophobic interactions (Val47–Val59). On the other hand, the N-terminal part of IG(28–61), which corresponds to the middle α-helix in the native structure, is unstructured at low temperature (283 K) and forms an α-helix-like structure at 305 K, and only one helical turn is observed at 313 K. At all temperatures at which NMR experiments were performed (283, 305, and 313 K), we do not observe any long-range connectivities which would have supported packing between the C-terminal (β-hairpin) and the N-terminal (α-helix) parts of the sequence. Such interactions are absent, in contrast to the folding pathway of the B Domain of protein G, proposed recently by Kmiecik and Kolinski (Biophys J 2008, 94, 726–736), based on Monte-Carlo dynamics studies. Alternative folding mechanisms are proposed and discussed. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 469–480, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

  • Mechanism of formation of the C‐terminal β‐hairpin of the B3 Domain of the immunoglobulin‐binding protein G from Streptococcus. IV. Implication for the mechanism of folding of the parent protein
    Biopolymers, 2010
    Co-Authors: Agnieszka Lewandowska, Adam Liwo, Stanisław Ołdziej, Harold A. Scheraga
    Abstract:

    A 34-residue α/β peptide [IG(28–61)], derived from the C-terminal part of the B3 Domain of the immunoglobulin binding protein G from Streptoccocus, was studied using CD and NMR spectroscopy at various temperatures and by differential scanning calorimetry. It was found that the C-terminal part (a 16-residue-long fragment) of this peptide, which corresponds to the sequence of the β-hairpin in the native structure, forms structure similar to the β-hairpin only at T = 313 K, and the structure is stabilized by non-native long-range hydrophobic interactions (Val47–Val59). On the other hand, the N-terminal part of IG(28–61), which corresponds to the middle α-helix in the native structure, is unstructured at low temperature (283 K) and forms an α-helix-like structure at 305 K, and only one helical turn is observed at 313 K. At all temperatures at which NMR experiments were performed (283, 305, and 313 K), we do not observe any long-range connectivities which would have supported packing between the C-terminal (β-hairpin) and the N-terminal (α-helix) parts of the sequence. Such interactions are absent, in contrast to the folding pathway of the B Domain of protein G, proposed recently by Kmiecik and Kolinski (Biophys J 2008, 94, 726–736), based on Monte-Carlo dynamics studies. Alternative folding mechanisms are proposed and discussed. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 469–480, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

  • mechanism of formation of the c terminal beta hairpin of the B3 Domain of the immunoglobulin binding protein g from streptococcus iii dynamics of long range hydrophobic interactions
    Proteins, 2009
    Co-Authors: Agnieszka Lewandowska, Stanislaw Oldziej, Adam Liwo, Harold A. Scheraga
    Abstract:

    A 20-residue peptide, IG(42–61), derived from the C-terminal β-hairpin of the B3 Domain of the immunoglobulin binding protein G from Streptoccocus was studied using circular dichroism, nuclear magnetic resonance (NMR) spectroscopy at various temperatures and by differential scanning calorimetry (DSC). Unlike other related peptides studied so far, this peptide displays two heat capacity peaks in DSC measurements (at a scanning rate of 1.5 deg/min at a peptide concentration of 0.07 mM), which suggests a three-state folding/unfolding process. The results from DSC and NMR measurements suggest the formation of a dynamic network of hydrophobic interactions stabilizing the structure, which resembles a β-hairpin shape over a wide range of temperatures (283–313 K). Our results show that IG (42–61) possesses a well-organized three-dimensional structure stabilized by long-range hydrophobic interactions (Tyr50 ··· Phe57 and Trp48 ··· Val59) at T = 283 K and (Trp48 ··· Val59) at 305 and 313 K. The mechanism of β-hairpin folding and unfolding, as well as the influence of peptide length on its conformational properties, are also discussed. Proteins 2010. © 2009 Wiley-Liss, Inc.