scholarly journals Phytic Acid and Transporters: What Can We Learn from low phytic acid Mutants?

Plants ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 69 ◽  
Author(s):  
Eleonora Cominelli ◽  
Roberto Pilu ◽  
Francesca Sparvoli
Keyword(s):  
Phytic Acid ◽  
Seed Quality ◽  
Sulfur Metabolism ◽  
In Silico Analysis ◽  
Point Of View ◽  
Low Phytic Acid ◽  
Cellular Processes ◽  
Report Data ◽  
Silico Analysis

Phytic acid has two main roles in plant tissues: Storage of phosphorus and regulation of different cellular processes. From a nutritional point of view, it is considered an antinutritional compound because, being a cation chelator, its presence reduces mineral bioavailability from the diet. In recent decades, the development of low phytic acid (lpa) mutants has been an important goal for nutritional seed quality improvement, mainly in cereals and legumes. Different lpa mutations affect phytic acid biosynthetic genes. However, other lpa mutations isolated so far, affect genes coding for three classes of transporters: A specific group of ABCC type vacuolar transporters, putative sulfate transporters, and phosphate transporters. In the present review, we summarize advances in the characterization of these transporters in cereals and legumes. Particularly, we describe genes, proteins, and mutants for these different transporters, and we report data of in silico analysis aimed at identifying the putative orthologs in some other cereal and legume species. Finally, we comment on the advantage of using such types of mutants for crop biofortification and on their possible utility to unravel links between phosphorus and sulfur metabolism (phosphate and sulfate homeostasis crosstalk).

In-Vitro and In-Silico Characterization of Xylose Reductase from Emericella nidulans

2019 ◽  
Vol 13 (2) ◽  
pp. 159-170 ◽  
Author(s):  
Vishal Ahuja ◽  
Aashima Sharma ◽  
Ranju Kumari Rathour ◽  
Vaishali Sharma ◽  
Nidhi Rana ◽  
...  
Keyword(s):  
Production Process ◽  
In Silico ◽  
Xylose Reductase ◽  
In Silico Analysis ◽  
Emericella Nidulans ◽  
Higher Temperature ◽  
In Silico Characterization ◽  
Silico Analysis

Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.

In silico analysis of selenoprotein N (Gallus gallus): absence of EF-hand motif and the role of CUGS-helix domain in antioxidant protection

Metallomics ◽  
2021 ◽  
Vol 13 (3) ◽  
Author(s):  
Shi-Yong Zhu ◽  
Li-Li Liu ◽  
Yue-Qiang Huang ◽  
Xiao-Wei Li ◽  
Milton Talukder ◽  
...  
Keyword(s):  
In Silico ◽  
Common Ancestor ◽  
In Silico Analysis ◽  
Antioxidant Protection ◽  
Jnk Pathway ◽  
Downstream Target ◽  
Ef Hand ◽  
Silico Analysis

Abstract Selenoprotein N (SEPN1) is critical to the normal muscular physiology. Mutation of SEPN1 can raise congenital muscular disorder in human. It is also central to maturation and structure of skeletal muscle in chicken. However, human SEPN1 contained an EF-hand motif, which was not found in chicken. And the biochemical and molecular characterization of chicken SEPN1 remains unclear. Hence, protein domains, transcription factors, and interactions of Ca2+ in SEPN1 were analyzed in silico to provide the divergence and homology between chicken and human in this work. The results showed that vertebrates’ SEPN1 evolved from a common ancestor. Human and chicken's SEPN1 shared a conserved CUGS-helix domain with function in antioxidant protection. SEPN1 might be a downstream target of JNK pathway, and it could respond to multiple stresses. Human's SEPN1 might not combine with Ca2+ with a single EF-hand motif in calcium homeostasis, and chicken SEPN1 did not have the EF-hand motif in the prediction, indicating the EF-hand motif malfunctioned in chicken SEPN1.

scholarly journals Metabolomic Characterization of a Low Phytic Acid and High Anti-oxidative Cultivar of Turmeric

2015 ◽  
Vol 10 (2) ◽  
pp. 1934578X1501000
Author(s):  
Ken Tanaka ◽  
Masanori Arita ◽  
Donghan Li ◽  
Naoaki Ono ◽  
Yasuhiro Tezuka ◽  
...  
Keyword(s):  
Phytic Acid ◽  
Metal Ion ◽  
Curcuma Longa ◽  
Food Additives ◽  
Chemical Properties ◽  
Lower Amount ◽  
Low Phytic Acid ◽  
History Of ◽  
History Of Use

Turmeric, the rhizome of Curcuma longa, has a long history of use as a spice and also as a traditional medicine in many Asian countries. To reveal unique morphological features of a newly registered Curcuma cultivar, C longa cv. Okinawa Ougon (Ougon), non-targeted LC-MS and GC-MS analyses were conducted. The analysis revealed its distinctive chemical properties: lower amount of phytic acid and inorganic metals such as Fe, Mn, and Al, as well as higher concentrations of reduced derivatives of curcuminoids, such as dihydrobisdemethoxycurcumin, tetrahydrobisdemethoxycurcumin, dihydrodemethoxycurcumin, and tetrahydrodemethoxycurcumin. In addition, germacrane-type sesquiterpenes were almost absent although α-humulene and β-caryophyllene, generated by the same biosynthetic route, were present. Presumably the alternation of the metal ion content, serving as a cofactor of sesquiterpene synthase, modulates the resulting variation of the sesquiterpenes. In summary, the cultivar Ougon is considered a promising candidate for functional food additives.

scholarly journals Low phytic acid Crops: Observations Based on Four Decades of Research

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 140 ◽  
Author(s):  
Victor Raboy
Keyword(s):  
Phytic Acid ◽  
Agricultural Production ◽  
Seed Quality ◽  
Animal Health ◽  
Field Performance ◽  
Mineral Density ◽  
Low Phytic Acid ◽  
Populations At Risk ◽  
Potential Benefits

The low phytic acid (lpa), or “low-phytate” seed trait can provide numerous potential benefits to the nutritional quality of foods and feeds and to the sustainability of agricultural production. Major benefits include enhanced phosphorus (P) management contributing to enhanced sustainability in non-ruminant (poultry, swine, and fish) production; reduced environmental impact due to reduced waste P in non-ruminant production; enhanced “global” bioavailability of minerals (iron, zinc, calcium, magnesium) for both humans and non-ruminant animals; enhancement of animal health, productivity and the quality of animal products; development of “low seed total P” crops which also can enhance management of P in agricultural production and contribute to its sustainability. Evaluations of this trait by industry and by advocates of biofortification via breeding for enhanced mineral density have been too short term and too narrowly focused. Arguments against breeding for the low-phytate trait overstate the negatives such as potentially reduced yields and field performance or possible reductions in phytic acid’s health benefits. Progress in breeding or genetically-engineering high-yielding stress-tolerant low-phytate crops continues. Perhaps due to the potential benefits of the low-phytate trait, the challenge of developing high-yielding, stress-tolerant low-phytate crops has become something of a holy grail for crop genetic engineering. While there are widely available and efficacious alternative approaches to deal with the problems posed by seed-derived dietary phytic acid, such as use of the enzyme phytase as a feed additive, or biofortification breeding, if there were an interest in developing low-phytate crops with good field performance and good seed quality, it could be accomplished given adequate time and support. Even with a moderate reduction in yield, in light of the numerous benefits of low-phytate types as human foods or animal feeds, should one not grow a nutritionally-enhanced crop variant that perhaps has 5% to 10% less yield than a standard variant but one that is substantially more nutritious? Such crops would be a benefit to human nutrition especially in populations at risk for iron and zinc deficiency, and a benefit to the sustainability of agricultural production.

scholarly journals A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Francesca Caccuri ◽  
Alberto Zani ◽  
Serena Messali ◽  
Marta Giovanetti ◽  
Antonella Bugatti ◽  
...  
Keyword(s):  
Viral Load ◽  
Selection Process ◽  
In Silico Analysis ◽  
High Viral Load ◽  
Current Approach ◽  
The One ◽  
Host Evolution ◽  
Silico Analysis ◽  
Generation Sequencing

Abstract Background Since the first outbreak of SARS-CoV-2, the clinical characteristics of the Coronavirus Disease 2019 (COVID-19) have been progressively changed. Data reporting a viral intra-host and inter-host evolution favouring the appearance of mild SARS-CoV-2 strains are since being accumulating. To better understand the evolution of SARS-CoV-2 pathogenicity and its adaptation to the host, it is therefore crucial to investigate the genetic and phenotypic characteristics of SARS-CoV-2 strains circulating lately in the epidemic. Methods Nasopharyngeal swabs have been analyzed for viral load in the early (March 2020) and late (May 2020) phases of epidemic in Brescia, Italy. Isolation of SARS-CoV-2 from 2 high viral load specimens identified on March 9 (AP66) and on May 8 (GZ69) was performed on Vero E6 cells. Amount of virus released was assessed by quantitative PCR. Genotypic characterization of AP66 and GZ69 was performed by next generation sequencing followed by an in-depth in silico analysis of nucleotide mutations. Results The SARS-CoV-2 GZ69 strain, isolated in May from an asymptomatic healthcare worker, showed an unprecedented capability of replication in Vero E6 cells in the absence of any evident cytopathic effect. Vero E6 subculturing, up to passage 4, showed that SARS-CoV-2 GZ69 infection was as productive as the one sustained by the cytopathic strain AP66. Whole genome sequencing of the persistently replicating SARS-CoV-2 GZ69 has shown that this strain differs from the early AP66 variant in 9 nucleotide positions (C2939T; C3828T; G21784T; T21846C; T24631C; G28881A; G28882A; G28883C; G29810T) which lead to 6 non-synonymous substitutions spanning on ORF1ab (P892S; S1188L), S (K74N; I95T) and N (R203K, G204R) proteins. Conclusions Identification of the peculiar SARS-CoV-2 GZ69 strain in the late Italian epidemic highlights the need to better characterize viral variants circulating among asymptomatic or paucisymptomatic individuals. The current approach could unravel the ways for future studies aimed at analyzing the selection process which favours viral mutations in the human host.

scholarly journals Cloning and characterization of novel human SLC4A8 gene products encoding Na+-driven Cl−/HCO3− exchanger variants NDCBE-A, -C, and -D

2008 ◽  
Vol 34 (3) ◽  
pp. 265-276 ◽  
Author(s):  
Mark D. Parker ◽  
Patrice Bouyer ◽  
Christopher M. Daly ◽  
Walter F. Boron
Keyword(s):  
In Silico Analysis ◽  
Functional Expression ◽  
Inhibitory Effect ◽  
Functional Difference ◽  
The Novel ◽  
Equivalent Position ◽  
Rapid Amplification ◽  
Novel Exon ◽  
Silico Analysis

The reported sequences of the human and mouse Na+-driven Cl−/HCO3− exchangers (NDCBEs) differ greatly in their extreme cytosolic COOH termini (Ct). In human NDCBE (NDCBE-B), a 17-amino acid (aa) sequence replaces 66 aa at the equivalent position in mouse NDCBE (NDCBE-A). We performed 5′- and 3′-rapid amplification of cDNA ends (RACE) on human brain cDNA, followed by PCR of full-length cDNAs to determine whether the human SLC4A8 gene was capable of producing the mouselike Ct sequence. Our study confirmed the presence in human cDNA of mouse NDCBE-like transcripts (human NDCBE-A) and also disclosed the existence of three further novel NDCBE transcripts that we have called NDCBE-C, NDCBE-D, and NDCBE-D′. The novel NDCBE-C/D/D′ transcripts initiate at a novel “exon 0” positioned ∼35 kb upstream of the first exon of NDCBE-A/B. NDCBE-C/D/D′ protein products are predicted to be truncated by 54 aa in the cytosolic NH2 terminus (Nt) compared with NDCBE-A/B. Our data, combined with a new in silico analysis of partial transcripts reported by others in the region of the human SLC4A8 gene, increase the known extent of the SLC4A8 gene by 49 kb, to 124 kb. A functional comparison of NDCBE-A/B/C/D expressed in Xenopus oocytes demonstrates that the Nt variation does not affect the basal functional expression of NDCBE, but those with the shorter Ct have a 25–50% reduced functional expression compared with those with the longer Ct. By comparison with an artificially truncated NDCBE that contains neither 17-aa nor 66-aa Ct cassette, we determined that the functional difference is unrelated to the 66-aa cassette of NDCBE-A/C, but is instead due to an inhibitory effect of the 17-aa cassette of NDCBE-B/D.

In silico, Physico-chemical characterization and analysis of Sandalwood proteins

2018 ◽  
Vol 3 (02) ◽  
pp. 150-157
Author(s):  
Asad Amir ◽  
Neelesh Kapoor ◽  
Hirdesh Kumar ◽  
Mohd. Tariq ◽  
Mohd. Asif Siddiqui
Keyword(s):  
Secondary Structure ◽  
In Silico ◽  
Chemical Characterization ◽  
In Silico Analysis ◽  
Chemical Parameters ◽  
Physico Chemical ◽  
In Silico Studies ◽  
The Family ◽  
Silico Analysis

Sandalwood is a commercially and culturally important plant species belonging to the family Santalaceae and the genus Santalum. In Indian sandalwood is renowned for its oil, which is highly rated for its sweet, fragrant, persistent aroma and the fixative property which is highly demanded by the perfume industry. For better production and varieties, requires to understanding the functions of proteins, their analysis and characterization of proteins sequences and their structures, their localizations in cell and their interaction with other functional partner. Due to limited number of in silico studies on sandalwood, in the present study we have performed in silico analysis by characterization of sandalwood proteins. Total 23 proteins were obtained and characterization using UniProtKB, identifying their physico-chemical parameters using ProtParam tool and prediction of their secondary structure elements using GOR of all 23 proteins.

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