1
|
Goonetilleke SN, Croxford AE, March TJ, Wirthensohn MG, Hrmova M, Mather DE. Variation among S-locus haplotypes and among stylar RNases in almond. Sci Rep 2020; 10:583. [PMID: 31953457 PMCID: PMC6969032 DOI: 10.1038/s41598-020-57498-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 12/31/2019] [Indexed: 11/23/2022] Open
Abstract
In many plant species, self-incompatibility systems limit self-pollination and mating among relatives. This helps maintain genetic diversity in natural populations but imposes constraints in agriculture and plant breeding. In almond [Prunus dulcis (Mill.) D.A. Webb], the specificity of self-incompatibility is mainly determined by stylar ribonuclease (S-RNase) and S-haplotype-specific F-box (SFB) proteins, both encoded within a complex locus, S. Prior to this research, a nearly complete sequence was available for one S-locus haplotype. Here, we report complete sequences for four haplotypes and partial sequences for 11 haplotypes. Haplotypes vary in sequences of genes (particularly S-RNase and SFB), distances between genes and numbers and positions of long terminal repeat transposons. Haplotype variation outside of the S-RNase and SFB genes may help maintain functionally important associations between S-RNase and SFB alleles. Fluorescence-based assays were developed to distinguish among some S-RNase alleles. With three-dimensional modelling of five S-RNase proteins, conserved active sites were identified and variation was observed in electrostatic potential and in the numbers, characteristics and positions of secondary structural elements, loop anchoring points and glycosylation sites. A hypervariable region on the protein surface and differences in the number, location and types of glycosylation sites may contribute to determining S-RNase specificity.
Collapse
Affiliation(s)
- Shashi N Goonetilleke
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Adam E Croxford
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Timothy J March
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Michelle G Wirthensohn
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Maria Hrmova
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia.,School of Life Sciences, Huaiyin Normal University, Huai'an, 223300, China
| | - Diane E Mather
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia.
| |
Collapse
|
2
|
Xu Y, Strickland EC, Fitzgerald MC. Thermodynamic Analysis of Protein Folding and Stability Using a Tryptophan Modification Protocol. Anal Chem 2014; 86:7041-8. [DOI: 10.1021/ac501278j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yingrong Xu
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Erin C. Strickland
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Michael C. Fitzgerald
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| |
Collapse
|
3
|
Deshpande RA, Khan MI, Shankar V. Equilibrium unfolding of RNase Rs from Rhizopus stolonifer: pH dependence of chemical and thermal denaturation. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1648:184-94. [PMID: 12758161 DOI: 10.1016/s1570-9639(03)00133-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The conformational stability of RNase Rs was determined with chemical and thermal denaturants over the pH range of 1-10. Equilibrium unfolding with urea showed that values of D(1/2) (5.7 M) and DeltaG(H(2)O) (12.8 kcal/mol) were highest at pH 5.0, its pI and the maximum conformational stability of RNase Rs was observed near pH 5.0. Denaturation with guanidine hydrochloride (GdnHCl), at pH 5.0, gave similar values of DeltaG(H(2)O) although GdnHCl was 2-fold more potent denaturant with D(1/2) value of 3.1 M. The curves of fraction unfolded (f(U)) obtained with fluorescence and CD measurements overlapped at pH 5.0. Denaturation of RNase Rs with urea in the pH range studied was reversible but the enzyme denatured irreversibly >pH 11.0. Thermal denaturation of RNase Rs was reversible in the pH range of 2.0-3.0 and 6.0-9.0. Thermal denaturation in the pH range 4.0-5.5 resulted in aggregation and precipitation of the protein above 55 degrees C. The aggregate was amorphous or disordered precipitate as observed in TE micrographs. Blue shift in emission lambda(max) and enhancement of fluorescence intensity of ANS at 70 degrees C indicated the presence of solvent exposed hydrophobic surfaces as a result of heat treatment. Aggregation could be prevented partially with alpha-cyclodextrin (0.15 M) and completely with urea at concentrations >3 M. Aggregation was probably due to intermolecular hydrophobic interaction favored by minimum charge-charge repulsion at the pI of the enzyme. Both urea and temperature-induced denaturation studies showed that RNase Rs unfolds through a two-state F right arrow over left arrow U mechanism. The pH dependence of stability described by DeltaG(H(2)O) (urea) and DeltaG (25 degrees C) suggested that electrostatic interactions among the charged groups make a significant contribution to the conformational stability of RNase Rs. Since RNase Rs is a disulfide-containing protein, the major element for structural stability are the covalent disulfide bonds.
Collapse
|
4
|
Irie M. Structure-function relationships of acid ribonucleases: lysosomal, vacuolar, and periplasmic enzymes. Pharmacol Ther 1999; 81:77-89. [PMID: 10190580 DOI: 10.1016/s0163-7258(98)00035-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
It is surprising that only relatively recently has attention been directed to the characterization of the properties of acid ribonucleases (RNases), leading to some understanding of their biochemistry and their functional roles. The present review summarizes current progress in this field under the following general topics: (1) the wide distribution of acid RNases in organisms from viruses to animals; (2) recent findings concerning their primary and three-dimensional structure; (3) the structure-function relationship of acid RNases, with a fungal RNase from Rhizopus niveus as a model enzyme; (4) the unique localization of acid RNases in the periplasm of bacteria, vacuoles in plants, and lysosomes of animals and protozoa; and (5) the diversity of physiological roles, depending on the organism, such as self-incompatibility factors and defense proteins in some plants, the surface protein of an animal virus related to pathogenicity, and possible relationship to human cancer.
Collapse
Affiliation(s)
- M Irie
- Department of Microbiology, Hoshi College of Pharmacy, Tokyo, Japan
| |
Collapse
|