scholarly journals The immune Rysto receptor recognizes a broadly conserved feature of potyviral coat proteins

2021 ◽  
Author(s):  
Marta Grech-Baran ◽  
Kamil Witek ◽  
Jaroslaw Poznanski ◽  
Anna Grupa-Urbanska ◽  
Tadeusz Malinowski ◽  
...  
Keyword(s):  
Amino Acid ◽  
Rna Binding ◽  
Point Mutations ◽  
Binding Pocket ◽  
Core Region ◽  
Plum Pox Virus ◽  
Coat Proteins ◽  
Amino Acid Residues ◽  
Pvy Resistance ◽  
Wide Range

Potyviruses are the largest group of plant RNA viruses, causing significant losses in many crops. Among them, potato virus Y (PVY) is particularly important, and enhances the severity of infections by other viruses. The Rysto gene confers PVY resistance and encodes a TIR-NLR intracellular immune receptors that recognizes PVY coat protein (CP). To define a minimal CP fragment sensed by Rysto, we created a series of truncated CP variants and expressed these CP derivatives in Rysto transgenic plants. Deletions that affect the 149 amino acid CP core region lose the ability to trigger Rysto-dependent defence activation. Furthermore, point mutations in the amino acid residues Ser126, Arg157, and Asp201 of the highly conserved RNA-binding pocket of potyviral CP, reduce or abolish Rysto-dependent responses, demonstrating that appropriate folding of the CP core is required for Rysto-mediated recognition. Consistent with these data, we found Rysto recognises CPs of various viruses that share a similar core region, but not those lacking it. Finally, we demonstrated that Rysto provides immunity to plum pox virus and turnip mosaic virus, demonstrating its wide range of applications in disease-resistant crop engineering. In parallel, we showed that CP triggered Rysto activation is SAG101- but not PAD4- or SA- level dependent. Our findings shed new light on how R proteins can detect viruses by sensing highly conserved structural patterns.

scholarly journals pIPredict: a computer tool for predicting isoelectric points of peptides and proteins

2015 ◽  
Vol 61 (1) ◽  
pp. 83-91 ◽  
Author(s):  
V.S. Skvortsov ◽  
N.N. Alekseychuk ◽  
D.V. Khudyakov ◽  
I.V. Romero Reyes
Keyword(s):  
Amino Acid ◽  
Posttranslational Modifications ◽  
Support Vector ◽  
Amino Acid Residues ◽  
Computer Tool ◽  
Wide Range ◽  
Vector Machines ◽  
Isoelectric Points ◽  
Peptide Fractionation ◽  
Made In

The data on approximate values of isoelectric point (pI) of peptides obtained during their fractionation by isoelectric focusing can be successfully used for the calculation of the pKa’s scale for amino acid residues. This scale can be used for pI prediction. The data of peptide fractionation also provides information about various posttranslational modifications (PTM), so that the prediction of pI may be performed for a wide range of protein forms. In this study, pKa values were calculated using a set of 13448 peptides (including 300 peptides with PTMs significant for pI calculation). The pKa constants were calculated for N-terminal, internal and C-terminal amino acid residues separately. The comparative analysis has shown that our scale increases the accuracy of pI prediction for peptides and proteins and successfully competes with traditional scales and such methods as support vector machines and artificial neural networks. The prediction performed by this scale, can be made in our program pIPredict with GUI written in JAVA as executable jar-archive. The program is freely available for academic users at http://www.ibmc.msk.ru/LPCIT/pIPredict. The software has also the possibility of pI predicting by some other scales; it recognizes some PTM and has the ability to use a custom scale.

scholarly journals Structural basis for amino acid exchange by a human heteromeric amino acid transporter

2020 ◽  
Vol 117 (35) ◽  
pp. 21281-21287 ◽  
Author(s):  
Di Wu ◽  
Tamara N. Grund ◽  
Sonja Welsch ◽  
Deryck J. Mills ◽  
Max Michel ◽  
...  
Keyword(s):  
Amino Acid ◽  
Heavy Chain ◽  
Light Chain ◽  
Basic Amino Acid ◽  
Binding Pocket ◽  
Structural Basis ◽  
Amino Acid Transporters ◽  
Wide Range ◽  
Functional Complex ◽  
Protein Components

Heteromeric amino acid transporters (HATs) comprise a group of membrane proteins that belong to the solute carrier (SLC) superfamily. They are formed by two different protein components: a light chain subunit from an SLC7 family member and a heavy chain subunit from the SLC3 family. The light chain constitutes the transport subunit whereas the heavy chain mediates trafficking to the plasma membrane and maturation of the functional complex. Mutation, malfunction, and dysregulation of HATs are associated with a wide range of pathologies or represent the direct cause of inherited and acquired disorders. Here we report the cryogenic electron microscopy structure of the neutral and basic amino acid transport complex (b[0,+]AT1-rBAT) which reveals a heterotetrameric protein assembly composed of two heavy and light chain subunits, respectively. The previously uncharacterized interaction between two HAT units is mediated via dimerization of the heavy chain subunits and does not include participation of the light chain subunits. The b(0,+)AT1 transporter adopts a LeuT fold and is captured in an inward-facing conformation. We identify an amino-acid–binding pocket that is formed by transmembrane helices 1, 6, and 10 and conserved among SLC7 transporters.

scholarly journals Identification and Expression Analysis of Snf2 Family Proteins in Tomato (Solanum lycopersicum)

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Dongdong Zhang ◽  
Sujuan Gao ◽  
Ping Yang ◽  
Jie Yang ◽  
Songguang Yang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Solanum Lycopersicum ◽  
Developmental Stages ◽  
Profile Analysis ◽  
Nucleosome Position ◽  
Fruit Fly ◽  
Amino Acid Residues ◽  
Expression Profile Analysis ◽  
Wide Range ◽  
Chromatin Remodeling Complexes

As part of chromatin-remodeling complexes (CRCs), sucrose nonfermenting 2 (Snf2) family proteins alter chromatin structure and nucleosome position by utilizing the energy of ATP, which allows other regulatory proteins to access DNA. Plant genomes encode a large number of Snf2 proteins, and some of them have been shown to be the key regulators at different developmental stages in Arabidopsis. Yet, little is known about the functions of Snf2 proteins in tomato (Solanum lycopersicum). In this study, 45 Snf2s were identified by the homologous search using representative sequences from yeast (S. cerevisiae), fruit fly (D. melanogaster), and Arabidopsis (A. thaliana) against the tomato genome annotation dataset. Tomato Snf2 proteins (also named SlCHRs) could be clustered into 6 groups and distributed on 11 chromosomes. All SlCHRs contained a helicase-C domain with about 80 amino acid residues and a SNF2-N domain with more variable amino acid residues. In addition, other conserved motifs were also identified in SlCHRs by using the MEME program. Expression profile analysis indicated that tomato Snf2 family genes displayed a wide range of expressions in different tissues and some of them were regulated by the environmental stimuli such as salicylic acid, abscisic acid, salt, and cold. Taken together, these results provide insights into the functions of SlCHRs in tomato.

scholarly journals Activation of Ha-ras p21 by substitution, deletion, and insertion mutations.

1985 ◽  
Vol 5 (8) ◽  
pp. 1809-1813 ◽  
Author(s):  
R G Chipperfield ◽  
S S Jones ◽  
K M Lo ◽  
R A Weinberg
Keyword(s):  
Amino Acid ◽  
Point Mutations ◽  
Normal Function ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Amino Acid Residues ◽  
Transforming Activity ◽  
Ras P21 ◽  
Ras Oncogenes ◽  
Insertion Mutations

The transforming activity of naturally arising ras oncogenes results from point mutations that affect residue 12 or 61 of the encoded 21-kilodalton protein (p21). By use of site-directed mutagenesis, we showed that deletions and insertions of amino acid residues in the region of residue 12 are also effective in conferring oncogenic activity on p21. Common to these various alterations is the disruption that they create in this domain of the protein, which we propose results in the inactivation of a normal function of the protein.

scholarly journals Structure–function studies of human deoxyhypusine synthase: identification of amino acid residues critical for the binding of spermidine and NAD

2001 ◽  
Vol 355 (3) ◽  
pp. 841-849 ◽  
Author(s):  
Chang Hoon LEE ◽  
Patrick Y. UM ◽  
Myung Hee PARK
Keyword(s):  
Crystal Structure ◽  
Enzyme Activity ◽  
Amino Acid ◽  
Binding Sites ◽  
Binding Pocket ◽  
Complete Loss ◽  
Amino Acid Residues ◽  
Deoxyhypusine Synthase ◽  
Positive Identification ◽  
Insight Into

Deoxyhypusine synthase catalyses the first step in the biosynthesis of hypusine [Nε-(4-amino-2-hydroxybutyl)lysine]. The crystal structure of human deoxyhypusine synthase in complex with NAD revealed four NAD-binding sites per enzyme tetramer, and led to a prediction of the spermidine-binding pocket. We have replaced each of the seven amino acid residues at the predicted spermidine-binding site, and eleven residues that contact NAD, on an individual basis with alanine. Of the amino acid residues at the spermidine site, substitution of Asp-243, Trp-327, His-288, Asp-316 or Glu-323 with alanine caused an almost complete loss of spermidine binding and enzyme activity; only the mutation Tyr-305 → Ala showed partial binding and activity. His-288 → Ala was also deficient in terms of binding NAD. NAD binding was significantly reduced in all of the NAD-site mutant enzymes, except for Glu-137 → Ala, which showed a normal binding of NAD, but was totally lacking in spermidine binding. Of the NAD-site mutant enzymes, Asp-342 → Ala, Asp-313 → Ala and Asp-238 → Ala displayed the lowest binding of NAD. These enzymes and His-288Ala also showed a reduced binding of spermidine, presumably because spermidine binding is dependent on NAD. These findings permit the positive identification of amino acid residues critical for binding of spermidine and NAD, and provide a new insight into the complex molecular interactions involved in the deoxyhypusine synthase reaction.

scholarly journals A Superfamily 3 DNA Helicase Encoded by Plasmid pSSVi from the Hyperthermophilic Archaeon Sulfolobus solfataricus Unwinds DNA as a Higher-Order Oligomer and Interacts with Host Primase

2010 ◽  
Vol 192 (7) ◽  
pp. 1853-1864 ◽  
Author(s):  
Xin Guo ◽  
Li Huang
Keyword(s):  
Amino Acid ◽  
Adenine Nucleotide ◽  
Sulfolobus Solfataricus ◽  
Dna Helicase ◽  
Higher Order ◽  
Hyperthermophilic Archaea ◽  
Amino Acid Residues ◽  
Protein Dimerization ◽  
Wide Range ◽  
Large Oligomer

ABSTRACT Replication proteins encoded by nonconjugative plasmids from the hyperthermophilic archaea of the order Sulfolobales show great diversity in amino acid sequence. We have biochemically characterized ORF735, a replication protein from pSSVi, an integrative nonconjugative plasmid from Sulfolobus solfataricus P2. We show that ORF735 is a DNA helicase of superfamily 3. It unwound double-stranded DNA (dsDNA) in a 3′-to-5′ direction in the presence of ATP over a wide range of temperatures, from 37°C to 75°C, and possessed DNA-stimulated ATPase activity. ORF735 existed in solution as a salt-stable dimer and was capable of assembling into a salt-sensitive oligomer that was significantly larger than a hexamer in the presence of a divalent cation (Mg2+) and an adenine nucleotide (ATP, dATP, or ADP) or its analog (ATPγS or AMPPNP). Both N-terminal and C-terminal portions of ORF735 (87 and 160 amino acid residues, respectively, in size) were required for protein dimerization but dispensable for the formation of the higher-order oligomer. The protein unwound DNA only as a large oligomer. Yeast two-hybrid and coimmunoprecipitation assays revealed that ORF735 interacted with the noncatalytic subunit of host primase. These findings provide clues to the functional role of ORF735 in pSSVi DNA replication.

scholarly journals Mefloquine and New Related Compounds Target the F0 Complex of the F0F1 H+-ATPase of Streptococcus pneumoniae

2002 ◽  
Vol 46 (6) ◽  
pp. 1680-1687 ◽  
Author(s):  
Antonio Javier Martín-Galiano ◽  
Begoña Gorgojo ◽  
Calvin M. Kunin ◽  
Adela G. de la Campa
Keyword(s):  
Streptococcus Pneumoniae ◽  
Amino Acid ◽  
Proton Translocation ◽  
Point Mutations ◽  
Amino Acid Residues ◽  
Transmembrane Helices ◽  
Inhibition Of Growth ◽  
Pneumococcal Strain ◽  
Resistant Strains ◽  
Related Compounds

ABSTRACT The activities of mefloquine (MFL) and related compounds against previously characterized Streptococcus pneumoniae strains carrying defined amino acid substitutions in the c subunit of the F0F1 H+-ATPase were studied. In addition, a series of MFL-resistant (Mflr) strains were isolated and characterized. A good correlation was observed between inhibition of growth and inhibition of the membrane-associated F0F1 H+-ATPase activity. MFL was about 10-fold more active than optochin and about 200-fold more active than quinine in inhibiting both the growth and the ATPase activities of laboratory pneumococcal strain R6. Mutant strains were inhibited by the different compounds to different degrees, depending on their specific mutations in the c subunit. The resistant strains studied had point mutations that changed amino acid residues in either the c subunit or the a subunit of the F0 complex. Changes in the c subunit were located in one of the two transmembrane α helices: residues M13, G14, G20, M23, and N24 of helix 1 and residues M44, G47, V48, A49, and V57 of helix 2. Changes in the a subunit were also found in either of the transmembrane α helices, helix 5 or 6: residue L186 of helix 5 and residues W206, F209, and S214 of helix 6. These results suggest that the transmembrane helices of the c and a subunits interact and that the mutated residues are important for the structure of the F0 complex and proton translocation.

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