Mutations of barley beta-amylase that improve substrate-binding affinity and thermostability

Simultaneous enhancement of barley β-amylase thermostability and catalytic activity by R115 and T387 residue sites mutation

OBJECTIVE

To simultaneously increase the thermostability and catalytic activity of barley β-amylase.

METHODS

The amino acid sequences of various barley β-amylases with different enzyme properties were aligned, two amino acid residues R115 and T387 were identified to be important for barley β-amylase properties. R115C and T387V were then generated using site-directed and saturation mutagenesis.

RESULTS

R115C and T387V mutants increased the enzyme catalytic activity and thermostability, respectively. After combinational mutagenesis, the T₅₀ value and t_(1/2,60^o_C) value of R115C/T387V mutant reached 59.4 °C and 48.8 min, which were 3.6 °C higher and 29.5 min longer than those of wild-type. The k_cat/K_m value of mutant R115C/T387V were 59.82/s·mM, which were 54.7% higher than that of wild-type. The increased surface hydrophobicity and newly formed strong hydrogen bonds and salt bridges might be responsible for the enzyme thermostability improvement while the two additional hydrogen bonds formed in the active center may lead to the catalytic property enhancement.

CONCLUSIONS

The mutant R115C/T387V showed high catalytic activity and thermostability indicating great potential for application in industry.

Noncanonical interactions between serpin and β-amylase in barley grain improve β-amylase activity in vitro

Serpin protease inhibitors and β-amylase starch hydrolases are very abundant seed proteins in the endosperm of grasses. β-amylase is a crucial enzyme in the beer industry providing maltose for fermenting yeast. In animals and plants, inhibitory serpins form covalent linkages that inactivate their cognate proteases. Additionally, in animals, noninhibitory functions for serpins are observed such as metabolite carriers and chaperones. The function of serpins in seeds has yet to be unveiled. In developing endosperm, serpin Z4 and β-amylase showed similar in vivo spatio-temporal accumulation properties and colocalize in the cytosol of transformed tobacco leaves. A molecular interaction between recombinant proteins of serpin Z4 and β-amylase was revealed by surface plasmon resonance and microscale thermophoresis yielding a dissociation constant of 10-7 M. Importantly, the addition of serpin Z4 significantly changes β-amylase enzymatic properties by increasing its maximal catalytic velocity. The presence of serpin Z4 stabilizes β-amylase activity during heat treatment without affecting its critical denaturing temperature. Oxidative stress, simulated by the addition of CuCl2, leads to the formation of high molecular weight polymers of β-amylase similar to those detected in vivo. The polymers were cross-linked through disulfide bonds, the formation of which was repressed when serpin Z4 was present. The results suggest an unprecedented function for a plant seed serpin as a β-amylase-specific chaperone-like partner that could optimize β-amylase activity upon germination. This report is the first to describe a noninhibitory function for a serpin in plants.

Development and characterization of an α-l-rhamnosidase mutant with improved thermostability and a higher efficiency for debittering orange juice

The glycoside hydrolase, α-l-rhamnosidase, could remove the bitter taste of naringin from citrus juices. However, most α-l-rhamnosidases are easily deactivated at high temperatures, limiting the practice in debittering citrus juices. The V529A mutant of the α-l-rhamnosidase r-Rha1 from Aspergillus niger JMU-TS528 was developed with improved thermostability using directed evolution technology and site-directed mutagenesis. The enzyme mutant had a half-live of thermal inactivation T_(1/2) of 1.92 h, 25.00 min, and 2 min at 60, 65, and 70 °C, respectively. In addition, it had improved substrate affinity and better resistance to the inhibition of glucose. The improved substrate affinity was related to its lowered binding energy. Most significantly, the naringin content was reduced to below the bitter taste threshold by treatment with 75 U/mL of the mutant during the preheating process of orange juice production. The comprehensive results indicate that thermostability improvement could promote the practical value of α-l-rhamnosidase in citrus juice processing.

Expression and characterization of a cutinase (AnCUT2) from Aspergillus niger

Cutin hydrolase (EC 3.1.1.74), an extracellular polyesterase found in pollens, bacteria and fungi, is an efficient catalyst that exhibits hydrolytic activity on a variety of water-soluble esters, synthetic fibers, plastics and triglycerides. Thus, cutinase can be used in various applications such as ester synthesis, bio-scouring, food and detergent industries. Ancut2 is one of five genes encoding cutinases present in the Aspergillus niger ATCC 10574 genome. The cDNA of Ancut2 comprising of an open reading frame of 816 bp encoding a protein of 271 amino acid residues, was isolated and expressed in Pichia pastoris. The partially purified recombinant cutinase exhibited a molecular mass of approximately 40 kDa. The enzyme showed highest activity at 40°C with a preference for acidic pH (5.0-6.0). AnCUT2 showed hydrolytic activity towards various p-nitrophenyl esters with preference towards shorter chain esters such as p-nitrophenyl butyrate (C4). Scanning Electron Microscopy demonstrated that AnCUT2 was capable of modifying surfaces of synthetic polycaprolactone and polyethylene terephthalate plastics. The properties of this enzyme suggest that it may be applied in synthetic fiber modification and fruit processing industries.

Genetic diversity and QTL mapping of thermostability of limit dextrinase in barley

Limit dextrinase (LD) is an essential amylolytic enzyme for the complete degradation of starch, and it is closely associated with malt quality. A survey of 51 cultivated barley and 40 Tibetan wild barley genotypes showed a wide genetic diversity of LD activity and LD thermostability. Compared with cultivated barley, Tibetan wild barley showed lower LD activity and higher LD thermostability. A doubled haploid population composed of 496 DArT and 28 microsatellite markers was used for mapping Quantitative Trait Loci (QTLs). Parental line Yerong showed low LD activity and high LD thermostability, but Franklin exhibited high LD activity and low LD thermostability. Three QTLs associated with thermostable LD were identified. The major QTL is close to the LD gene on chromosome 7H. The two minor QTLs colocalized with previously reported QTLs determining malt-extract and diastatic power on chromosomes 1H and 2H, respectively. These QTLs may be useful for a better understanding of the genetic control of LD activity and LD thermostability in barley.

Discovery of novel Bmy1 alleles increasing β-amylase activity in Chinese landraces and Tibetan wild barley for improvement of malting quality via MAS

China has a large barley germplasm collection which has not been well characterized and is therefore underutilized. The Bmy1 locus encoding the β-amylase enzyme on chromosome 4H has been well characterized in the worldwide barley germplasm collections due to its importance in the malting and brewing industry. The Bmy1 locus was chosen as an indicator to understand genetic potential for improvement of malting quality in Chinese landraces and Tibetan wild barley. The genetic diversity of 91 barley accessions was assessed using allele specific Multiplex-ready molecular markers. Eight accessions were further sequenced, based on the Multiplex-ready marker diversity for Bmy1 in the germplasm. Six of the eight accessions clustered together in a unique group, and showed similarities to ‘Haruna Nijo’, wild barley accession PI296896 and ‘Ashqelon’. Sequence comparisons with the known Bmy1 alleles identified not only the existing 13 amino acid substitutions, but also a new substitution positioned at A387T from a Chinese landrace W127, which has the highest β-amylase activity. Two new alleles/haplotypes namely Bmy1-Sd1c and Bmy1-Sd5 were designated based on different amino acid combinations. We identified new amino acid combination of C115, D165, V233, S347 and V430 in the germplasm. The broad variation in both β-amylase activity and amino acid composition provides novel alleles for the improvement of malting quality for different brewing styles, which indicates the high potential value of the Chinese landraces and Tibetan wild barley.

Differential expression of two β-amylase genes (Bmy1 and Bmy2) in developing and mature barley grain

Two barley (Hordeum vulgare L.) β-amylase genes (Bmy1 and Bmy2) were studied during the late maturation phase of grain development in four genotypes. The Bmy1 and Bmy2 DNA and amino acid sequences are extremely similar. The largest sequence differences are in the introns, seventh exon, and 3' UTR. Accumulation of Bmy2 mRNA was examined in developing grain at 17, 19, and 21 days after anthesis (DAA). One genotype, PI 296897, had significantly higher Bmy2 RNA transcript accumulation than the other three genotypes at all developmental stages. All four genotypes had Bmy2 mRNA levels decrease from 17 to 19 DAA, and remain the same from 19 to 21 DAA. Levels of Bmy1 mRNA were twenty thousand to over one hundred thousand times more than Bmy2 mRNA levels in genotypes Legacy, Harrington, and Ashqelon at all developmental stages and PI 296897 at 19 and 21 DAA. PI 296897 had five thousand times more Bmy1 mRNA than Bmy2 mRNA at 17 DAA. However, Bmy2 protein was not found at 17 DAA in any genotype. The presence of Bmy2 was immunologically detected at 19 DAA and was present in greater amounts at 21 DAA. Also, Bmy2 protein was found to be stored in mature grain and localized in the soluble fraction. However, Bmy1 protein was far more prevalent than Bmy2 at all developmental stages in all genotypes. Thus, the vast majority of β-amylase activity in developing and mature grain can be attributed to endosperm-specific β-amylase.

Differential RNA expression of Bmy1 during barley seed development and the association with β-amylase accumulation, activity, and total protein

The objective of this study was to determine if developing barley (Hordeum vulgare L.) seeds had differences in β-amylase 1 (Bmy1) mRNA accumulation, β-amylase (EC 3.2.1.2) activity, β-amylase protein accumulation, and total protein levels during late seed development from genotypes with different Bmy1 intron III alleles. Two North American malting barley cultivars (Hordeum vulgare ssp. vulgare) were chosen to represent the Bmy1.a and Bmy1.b alleles and, due to limited Bmy1 intron III allele variation in North American cultivars, two wild barleys (Hordeum vulgare ssp. spontaneum) were chosen to represent the Bmy1.c and Bmy1.d alleles. Wild barleys Ashqelon (Bmy1.c) and PI 296897 (Bmy1.d) had 2.5- to 3-fold higher Bmy1 mRNA levels than cultivars Legacy (Bmy1.a) and Harrington (Bmy1.b). Levels of Bmy1 mRNA were not significantly different between cultivated or between wild genotypes. In all four genotypes Bmy1 mRNA levels increased from 17 to 19 days after anthesis (DAA) and remained constant from 19 to 21 DAA. Ashqelon and PI 296897 had more β-amylase activity on a fresh weight basis than Legacy and Harrington at all developmental stages. β-Amylase protein levels increased from 17 DAA to maturity in all genotypes. Total protein in grains from wild genotypes was significantly higher than cultivated genotypes at all developmental stages. Higher levels of total protein in Ashqelon and PI 296897 could explain their higher levels of β-amylase activity, when expressed on a fresh weight basis. When β-amylase activities are expressed on a protein basis there are no statistical differences between the wild and cultivated barleys at maturity.

The development of a thermostable CiP (Coprinus cinereus peroxidase) through in silico design

Protein thermostability is a crucial issue in the practical application of enzymes, such as inorganic synthesis and enzymatic polymerization of phenol derivatives. Much attention has been focused on the enhancement and numerous successes have been achieved through protein engineering methods. Despite fruitful results based on random mutagenesis, it was still necessary to develop a novel strategy that can reduce the time and effort involved in this process. In this study, a rapid and effective strategy is described for increasing the thermal stability of a protein. Instead of random mutagenesis, a rational strategy was adopted to theoretically stabilize the thermo labile residues of a protein using computational methods. Protein residues with high flexibility can be thermo labile due to their large range of movement. Here, residue B factor values were used to identify putatively thermo labile residues and the RosettaDesign program was applied to search for stable sequences. Coprinus cinereus (CiP) heme peroxidase was selected as a model protein for its importance in commercial applications, such as the polymerization of phenolic compounds. Eleven CiP residues with the highest B factor values were chosen as target mutation sites for thermostabilization, and then redesigned using RosettaDesign to identify sequences. Eight mutants based on the redesigns, were produced as functional enzymes and two of these (S323Y and E328D) showed increased thermal stability over the wild-type in addition to conserved catalytic activity. Thus, this strategy can be used as a rapid and effective in silico design tool for obtaining thermostable proteins.

Improvement of Bacillus circulans beta-amylase activity attained using the ancestral mutation method

Thermostabilization of enzymes is one of the greatest challenges of protein engineering. The ancestral mutation method, which introduces ancestral residues into a target enzyme, has previously been developed and used to improve the thermostabilities of thermophilic enzymes. Herein, we report a study that used the ancestral mutation method to improve the thermostability of Bacillus circulans beta-amylase, a mesophilic enzyme. A bacterial, common-ancestral beta-amylase sequence was inferred using a phylogenetic tree composed of higher plant and bacterial amylase sequences. Eighteen mutants containing ancestral residues were designed, expressed in Escherichia coli and purified. Several of these mutants were more thermostable than that of the wild-type amylase. Notably, one mutant had both greater activity and greater thermostability. The relationship between the extent to which the amino acid residues within 5 A of the mutation site were evolutionarily conserved and the extent to which thermostability was improved was examined. Apparently, it is necessary to conserve the residues surrounding an ancestral residue if thermostability is to be improved by the ancestral mutation method.

Geographic distributions of Idh-1 alleles in a cricket are linked to differential enzyme kinetic performance across thermal environments

Background

Geographic clines within species are often interpreted as evidence of adaptation to varying environmental conditions. However, clines can also result from genetic drift, and these competing hypotheses must therefore be tested empirically. The striped ground cricket, Allonemobius socius, is widely-distributed in the eastern United States, and clines have been documented in both life-history traits and genetic alleles. One clinally-distributed locus, isocitrate dehydrogenase (Idh-1), has been shown previously to exhibit significant correlations between allele frequencies and environmental conditions (temperature and rainfall). Further, an empirical study revealed a significant genotype-by-environmental interaction (GxE) between Idh-1 genotype and temperature which affected fitness. Here, we use enzyme kinetics to further explore GxE between Idh-1 genotype and temperature, and test the predictions of kinetic activity expected under drift or selection.

Results

We found significant GxE between temperature and three enzyme kinetic parameters, providing further evidence that the natural distributions of Idh-1 allele frequencies in A. socius are maintained by natural selection. Differences in enzyme kinetic activity across temperatures also mirror many of the geographic patterns observed in allele frequencies.

Conclusion

This study further supports the hypothesis that the natural distribution of Idh-1 alleles in A. socius is driven by natural selection on differential enzymatic performance. This example is one of several which clearly document a functional basis for both the maintenance of common alleles and observed clines in allele frequencies, and provides further evidence for the non-neutrality of some allozyme alleles.

Plant domestication, a unique opportunity to identify the genetic basis of adaptation

Despite the fundamental role of plant domestication in human history and the critical importance of a relatively small number of crop plants to modern societies, we still know little about adaptation under domestication. Here we focus on efforts to identify the genes responsible for adaptation to domestication. We start from a historical perspective, arguing that Darwin's conceptualization of domestication and unconscious selection provides valuable insight into the evolutionary history of crops and also provides a framework to evaluate modern methods used to decipher the genetic mechanisms underlying phenotypic change. We then review these methods, framing the discussion in terms of the phenotype-genotype hierarchy. Top-down approaches, such as quantitative trait locus and linkage disequilibrium mapping, start with a phenotype of interest and use genetic analysis to identify candidate genes. Bottom-up approaches, alternatively, use population genetic analyses to identify potentially adaptive genes and then rely on standard bioinformatics and reverse genetic tools to connect selected genes to a phenotype. We discuss the successes, advantages, and challenges of each, but we conclude that bottom-up approaches to understanding domestication as an adaptive process hold greater promise both for the study of adaptation and as a means to identify genes that contribute to agronomically important traits.

Genetic variation of Bmy1 alleles in barley (Hordeum vulgare L.) investigated by CAPS analysis

The enzyme beta-amylase is one of the most important hydrolytic enzymes in the grain of malting barley and is encoded by the gene Bmy1. To learn more about its structure and function, a total of 657 barley accessions including 541 Hordeum vulgare ssp. vulgare (HV), and 116 H. vulgare ssp. spontaneum (HS) were selected for the cleaved amplified polymorphic sequence (CAPS) analysis. These materials, covering all the 16 kinds of beta-amylase phenotypes screened from more than 8,500 accessions of the world barley germplasm, were classified into 13 CAPS types in the present study. A combined assay of phenotypes and CAPS types revealed extensive genetic variation at the Bmy1 locus, and in total 23 Bmy1 allele types were identified. The newly identified alleles (A-I-11, A-II-6, A-II-7, A-II-10, B-I-3, B-I-12 and B-I-13) provided us with a novel resource for barley breeding and Bmy1 study. In HV barley, six out of seven major allele types (C-II-1, B-II-2, B-Ia-3, A-II-5, A-II-6, and A-II-7) were shared with HS barley; the B-I-8 allele, which was predominant in north European cultivated barley, was found to be unique. Remarkably, very low Bmy1 genetic variation was detected in Tibetan barleys, which puts the validity of the hypothesis that Tibet is one of the original centers of cultivated barley into question.

Novel haplotype description and structural background of the eventual functional significance of the barley beta-amylase gene intron III rearrangements

To extend the knowledge on the haplotype variability of the Bmy1 gene, region of the intron III was sequenced in a set of 20 Latvian accessions and Danish variety Maja, the data were compared to the previously reported allelic variants of the structural gene. Taking into account the polymorphisms of 59 loci and the microsatellite (MS) motif, 11 Latvian varieties turned out to have haplotype similar to cultivar Adorra, 1 - to Haruna Nijo, and 8 - to the newly described Abava Bmy1 intron III haplotype. High level of polymorphisms of (TG)(m) as well as (G)(n) component of MS was revealed for all the haplotypes studied. We conclude that the MS motif rather than the MS size length polymorphism correlates with mutations in the coding region of the beta-amylase gene. Five graphical haplotype-specific intron III structures were constructed on the basis of the co-localization of the transcription factor binding sites (TFBSs), remnants of the transposable elements, and intron III polymorphic loci. Inter- and intrahaplotype variability was analyzed on the eventual functional significance of the Bmy1 intron III rearrangements. Novel data on the intron III nucleotide sequences of the Bmy1 gene were deposited in the GenBank (http://www.ncbi.nlm.nih.gov/) under accession numbers DQ316895-DQ316905.

Distribution and inheritance of β-amylase alleles in north European barley varieties

Allelic diversity and inheritance of polymorphic sites of the intron III-exon IV region of the seed specific beta-amylase gene Bmy1 were studied in a set of 55 barley accessions composed mainly of old Latvian and Scandinavian commercial varieties and three Hordeum spontaneum lines from Israel. A CAPS-marker was used for genotyping the C698 --> T polymorphism encoding alleles of beta-amylase with different thermostability. The genotype C698 which is diagnostic for a more thermostable isoform of the beta-amylase was detected in 13 of the investigated accessions. In most cases the origin of the C698 genotype could be traced back to the old Danish variety Binder in the pedigree. However, this genotype was lost in later varieties originating from Binder. A 6+1 bp deletion event in intron III of the beta-amylase gene was in all cases linked to the presence of the C698 mutation, while the repeat number of a microsatellite in intron III had no correlation to the presence of the C698 mutation. Sequence analysis revealed a number of haplotypes within exon IV that did not result in amino acid changes due to the degenerated genetic code.

Production and partial characterization of a beta-amylase by Xanthophyllomyces dendrorhous

AIMS

The characterization of a beta-amylase produced by Xanthophyllomyces dendrorhous.

METHODS AND RESULTS

Growth in different culture media showed that X. dendrorhous produces an amylase whose synthesis is repressed by the carbon source and induced by starch and maltose. Enzymatic assays using substrates with different degrees of polymerization together with viscosity experiments revealed that the enzyme was beta-amylase. According to the biochemical characterization, the enzyme has a molecular weight of 240 kDa and a Km of 1.35 mg ml-1. The optimum pH and temperature were 5.5 and 50 degrees C, respectively. Using different inhibitors of the enzymatic activity it was shown that cysteine, tryptophan and serine are essential amino acids for catalysis.

CONCLUSIONS

Xanthophyllomyces dendrorhous CECT1690 synthesizes and secretes beta-amylase that could be a by-product, in addition to carotenoid pigments, in the fermentation downstream.

SIGNIFICANCE AND IMPACT OF THE STUDY

The beta-amylase produced by X. dendrorhous may have certain industrial applications.

Proteome analysis of grain filling and seed maturation in barley

In monocotyledonous plants, the process of seed development involves the deposition of reserves in the starchy endosperm and development of the embryo and aleurone layer. The final stages of seed development are accompanied by an increase in desiccation tolerance and drying out of the mature seed. We have used two-dimensional gel electrophoresis for a time-resolved study of the changes in proteins that occur during seed development in barley (Hordeum vulgare). About 1,000 low-salt extractable protein spots could be resolved on the two-dimensional gels. Protein spots were divided into six categories according to the timing of appearance or disappearance during the 5-week period of comparison. Nineteen different proteins or protein fragments in 36 selected spots were identified by matrix-assisted laser-desorption ionization time of flight mass spectrometry (MS) or nano-electrospray tandem MS/MS. Some proteins were present throughout development (for example, cytosolic malate dehydrogenase), whereas others were associated with the early grain filling (ascorbate peroxidase) or desiccation (Cor14b) stages. Most noticeably, the development process is characterized by an accumulation of low-M(r) alpha-amylase/trypsin inhibitors, serine protease inhibitors, and enzymes involved in protection against oxidative stress. We present examples of proteins not previously experimentally observed, differential extractability of thiol-bound proteins, and possible allele-specific spot variation. Our results both confirm and expand on knowledge gained from previous analyses of individual proteins involved in grain filling and maturation.