Journal of Plant Biochemistry and Biotechnology最新文献

{"title":"Inadequate lysine content of wheat endosperm proteins - possibility of correcting it by CRISPR-Cas system of genome editing","authors":"Hirendra Kumar Das, Megha Kaushik, Pranab Kumar Mandal","doi":"10.1007/s13562-024-00881-5","DOIUrl":"https://doi.org/10.1007/s13562-024-00881-5","url":null,"abstract":"<p>Proteins in endosperms of mature wheat seeds contain ~ 2.5% lysine. Proteins in endosperms of immature wheat seeds after 8 days of anthesis, interestingly contain ~ 8% lysine. Wheat endosperm proteins collected 15 days after anthesis, when treated with proteases isolated from endosperms 20 days after anthesis, released 10.2% lysine and 5.6% leucine. In contrast, the same proteins, when treated with proteases isolated from endosperms 8 days after anthesis, released 7.0% lysine and 12.0% leucine. The protease C, that could cleave polylysine, but could not cleave polyaspartic acid and polyglutamic acid, appeared only at 16 days after anthesis and continued to be present till 28 days after anthesis. Soybean trypsin inhibitor inhibited the activity of protease C completely. Transcriptome analysis of developing wheat seeds has revealed the presence of three major transcripts containing trypsin-like domains. The amounts of these three transcripts increased from 2 weeks after anthesis to 4 weeks after anthesis and decreased thereafter. If a wheat variety could be created which is devoid of protease C or the above mentioned trypsin like proteases, the lysine content of endosperm proteins of that variety would possibly be higher. This could today be achieved by using the CRISPR-Cas systems of genome editing.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"10 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140115719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular differentiation of the green and purple Tulsi (Ocimum tenuiflorum L.) and its application in authentication of market samples","authors":"Mohamed Shaibi, Raju Balaji, Madasamy Parani","doi":"10.1007/s13562-024-00883-3","DOIUrl":"https://doi.org/10.1007/s13562-024-00883-3","url":null,"abstract":"<p>Tulsi (Holi Basil, <i>Ocimum tenuiflorum</i>) is extensively used in herbal medicine, and it includes two distinct subtypes; namely green Tulsi and purple Tulsi. Both types have similar medicinal properties. However, purple Tulsi contains a significantly higher amount of methyleugenol, which is genotoxic, and its daily intake is restricted. We developed a polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) method to identify purple Tulsi. For this purpose, we selected a C &gt; T single nucleotide polymorphism (SNP) in the <i>ycf1</i> gene of the chloroplast genome that overlapped with a <i>Dde</i>I restriction site. The primers and PCR conditions were optimized to amplify a 797 bp DNA encompassing the C &gt; T SNP, specifically from <i>O. tenuiflorum</i>. After restriction digestion of the PCR product with <i>Dde</i>I, green Tulsi was identified by two fragments (539 bp and 258 bp), and purple Tulsi was recognized by a single fragment (797 bp). Analysis of 40 Tulsi market samples revealed that only 36 (90%) were derived from <i>O. tenuiflorum</i>. The majority of the market samples were purple Tulsi (60%) or a mixture of green and purple Tulsi (27.5%), with some mixed samples containing up to 50% purple Tulsi.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"50 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140115566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CRISPR/Cas system for the traits enhancement in potato (Solanum tuberosum L.): present status and future prospectives","authors":"","doi":"10.1007/s13562-024-00878-0","DOIUrl":"https://doi.org/10.1007/s13562-024-00878-0","url":null,"abstract":"<h3>Abstract</h3> <p>The increasing global population projected to reach 9.7 billion by 2050 from the current 7.7 billion, which is going to significantly impact food availability. Therefore, current global agricultural production needs to be increased to feed the unconstrained growing population. The changing climatic condition due to anthropogenic activities also makes the conditions more challenging to meet the required crop productivity in the future. Potato is third most consumed staple food. The current cultivation and demand of potato is particularly more in developing countries with high levels of poverty, hunger, and malnutrition because it is cheap source of nutrition and easily available. Potato is severely infected by a number of diseases, insect pests, and abiotic environmental conditions. Amidst the backdrop of climate change, the situation is deteriorating. Projections indicate that the average potato productivity in India's primary potato-growing states, responsible for approximately 90% of the nation's total potato output, is expected to decline by 2.0% in the 2050s and a more substantial 6.4% in the 2080s. Therefore to develop tolerance in plants to cope with changing environmental condition is need of hour to feed the overgrowing population. In this review, we discussed the application of CRISPR to enhance the crop productivity and develop biotic and abiotic stress-tolerant in potato to face the current changing climatic conditions is also discussed. The review also sheds light on the future prospects of CRISPR/Cas technology for potato breeding, including potential challenges and opportunities.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"9 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140036684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Measurement of transgene copy number in transgenic tobacco plants producing human interferon-γ (hIFN-γ) using quantitative real-time PCR","authors":"Reza Heidari Japelaghi, Raheem Haddad, Mostafa Valizadeh, Ebrahim Dorani Uliaie, Mokhtar Jalali Javaran","doi":"10.1007/s13562-024-00879-z","DOIUrl":"https://doi.org/10.1007/s13562-024-00879-z","url":null,"abstract":"<p>In transgenic plants, the transgene copy numbers can highly affect the level of expression and genetic stability of the transgene. Hence, the first step in their characterization is the estimation of transgene copy numbers integrated in the plant genome. Quantitative real-time PCR (qRT-PCR) was used to determine the copy numbers of human interferon-γ (<i>hIFN</i>-γ) and hygromycin phosphortransferase II (<i>hpt</i>II) transgenes in the genome of the T₀ generation of 18 transgenic tobacco lines using the <i>axi</i>1 gene as an endogenous control. With optimized PCR conditions, we attained highly exact estimates of one, two, three, and/or four transgene copies in the T₀ transformants. Moreover, estimation of copy numbers of the <i>hIFN</i>-γ transgene and the <i>hpt</i>II selective marker gene indicated that rearrangements of the T-DNA has regularly happened in transgenic tobacco. Transgene copy number was also estimated using Southern blot analysis of gDNA derived from transformants. The transcript level and expression amount of recombinant hIFN-γ protein were evaluated in various events using RT-PCR and enzyme-linked immunosorbent assay (ELISA) techniques. A disagreement between the transcript level and the amount of recombinant protein with an inverse correlation between transgene copy number and expression level observed in some events, probably showing translational gene silencing and co-suppression or silencing, respectively. These results were also compared with segregation ratios of hygromycin-resistant phenotype in T₁ plants of each line and found to be, in general, consistent.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"30 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140036685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of phosphorus deficiency on the expression and protein localization of ENHANCER OF TRY AND CPC3 gene in Arabidopsis roots","authors":"Juri Wakamatsu, Jun Hosokawa, Rumi Tominaga","doi":"10.1007/s13562-024-00880-6","DOIUrl":"https://doi.org/10.1007/s13562-024-00880-6","url":null,"abstract":"<p>Increased hair in <i>Arabidopsis</i> roots during phosphorus deficiency is an important adaptation mechanism. The <i>CAPRICE</i> (<i>CPC</i>) gene, along with its six homologs, plays a pivotal role in root hair formation. Our previous study indicated upregulated expression of <i>ENHANCER OF TRY AND CPC1</i> (<i>ETC1</i>) and <i>ENHANCER OF TRY AND CPC3</i> (<i>ETC3</i>) homologous genes in response to phosphorus deficiency. ETC1 translocates from the root sub-epidermis to epidermal cells, thereby increasing the number of root hairs. In this study, we specifically focused on ETC3 to explore its function in this process. Our results showed that <i>etc1</i>, <i>etc3</i>, and <i>etc1 etc3</i> mutants did not induce as much root hairs in response to phosphorus deficiency as the wild type. The upregulation of <i>ETC1</i> and <i>ETC3</i> in response to phosphorus deficiency was restricted to the roots, with no such response observed in leaves. Furthermore, examination of ETC3:GFP protein localization revealed that ETC3 expression was induced in the internal root tissues under phosphorus deficiency, without migrating to epidermal cells as observed for ETC1. This finding suggests that ETC3 may indirectly contribute to root hair formation through a different mechanism. Therefore, elucidating the complex process that governs root hair increase in phosphorus-deficient plants can lead to future advances in plant breeding and nutrient stress adaptation.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"34 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140018670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and recombinant production of a flavonoid glucosyltransferase with broad substrate specificity from Vaccinium corymbosum","authors":"","doi":"10.1007/s13562-024-00876-2","DOIUrl":"https://doi.org/10.1007/s13562-024-00876-2","url":null,"abstract":"<h3>Abstract</h3> <p>Glucosyltransferases (GTs) are enzymes that use UDP-glucose to glucosylate wide variety of substrates, including the aglycones of anthocyanins. Anthocyanins are glycosylated polyphenolic plant pigments possessing potential health benefits to humans. The berries of <em>Vaccinium</em> species plants are rich in anthocyanins. Although the flavonoid content of bilberries is well characterized, the enzymes responsible for carrying out anthocyanin modifications are not thoroughly studied. In this study, a predicted sequence of an anthocyanin glucosyltransferase was identified from the genomic data of <em>Vaccinium corymbosum</em>. The codon-optimized gene sequence of the protein was integrated into the genome of <em>P. pastoris.</em> Constitutive expression in yeast extract-peptone-dextrose based media gave satisfactory amount of recombinant protein. The enzyme activity assays revealed that the <em>V. corymbosum</em> GT transferred glucosyl moieties to up to three positions of diverse flavonoids, such as naringenin, kaempferol, eriodictyol and cyanidin 3-<em>O</em>-glucoside, being therefore a rather unique enzyme among GTs described so far. The enzyme preferred cyanidin 3-<em>O</em>-glucoside, peonidin 3-<em>O</em>-glucoside and eriodictyol as substrates. This enzyme could find application in biotechnological production of glucosylated flavonoids.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"51 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140007223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identifying miRNAs and target genes associated with Allicin synthesis in Allium species","authors":"Mahsa Asadi, Farhad Nazarian-Firouzabadi, Mohammad Reza Naghavi, Ahmad Ismaili","doi":"10.1007/s13562-024-00875-3","DOIUrl":"https://doi.org/10.1007/s13562-024-00875-3","url":null,"abstract":"<p>Plants in the <i>Allium</i> genus have a significant economic impact due to their production of important food and medicinal compounds. Despite their agricultural and pharmaceutical value, breeding programs for <i>Allium</i> species are lagging behind those of other major crop plants. MicroRNAs (miRNAs) are a group of small non-coding RNAs that regulate post-transcriptional gene expression. In order to identify distinct miRNAs and their target proteins involved in Allicin biosynthesis pathways under heat-stress conditions, available <i>Allium</i> species Expressed Sequence Tags (ESTs) and miRNA databases were extensively searched and bioinformatically analyzed. Three distinct miRNA candidates targeting seven genes in garlic were identified. The real-time RT-PCR analysis results revealed that miR5021 and miR565 regulate the Alliinase and Heat shock protein 70 (HSP70) genes under cold stress (4°C), while miR5184 regulates the same genes at elevated temperatures (37 and 45°C). Based on the High-Performance Liquid Chromatography (HPLC) results, the expression of the Alliinase gene was found to be higher in both stem and leaf tissues compared to the expression of miR5021 under cold stress conditions. This indicates the potential involvement of miR5021 in the biosynthetic pathway of Allicin production. Furthermore, the results of the elevated heat-stress treatment showed that the expression of the HSP70 gene under thermal stress conditions at 37°C in both stem and leaf tissue was significantly increased compared to the expression of miR5658 and miR5184 at 45°C. However the expression of the HSP70 gene in the stem tissue was significantly decreased compared to the expression of miR5658 and miR5184 genes. This experimental study aims to identify miRNAs associated with the allicin production pathway in two tissues of garlic: leaves and cloves. Among the main findings of this research, we can mention the identification of 3 miRNAs that are likely to play a role in the allicin synthesis pathway. The results of this study suggest that environmental factors may affect the biosynthesis of allicin in plants of the <i>Allium</i> family.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"37 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139755266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomics: illuminating the molecular landscape of vegetable crops: a review","authors":"Puneeth Pattaduru Vishwanath, Vishwanath Bidaramali, Suman Lata, Ramesh Kumar Yadav","doi":"10.1007/s13562-023-00871-z","DOIUrl":"https://doi.org/10.1007/s13562-023-00871-z","url":null,"abstract":"<p>Vegetables play a crucial role in global health and nutrition. Transcriptomics, a branch of functional genomics, has emerged as a powerful tool for studying gene expression patterns in various organisms, including vegetables. It is a dynamic genomics field that studies the entire set of RNA molecules in a cell, known as the transcriptome. This review offers a thorough overview of transcriptomics applications in vegetables, covering insights gained, challenges faced and future directions. It explores experimental techniques, bioinformatics tools and key findings from transcriptomic studies in various vegetable species. We summarize influential studies in vegetable crop transcriptomics and discuss how transcriptomics enhances crop productivity, disease resistance and nutritional quality in vegetables. Recent advances in RNA-seq technology have led to significant progress in characterizing the transcriptomes of diverse cell types. Transcriptomic analyses of vegetables have unveiled the dynamic patterns of gene expression, exposing temporal and spatial regulatory mechanisms. Transcriptomics identifies differentially expressed genes, aiding in finding candidate genes for desirable traits, enabling targeted breeding and genetic engineering. This review highlights its significance in understanding complex regulatory networks in vegetable development and response to environmental cues. This overview serves as a valuable resource for researchers and practitioners interested in transcriptomic studies.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"50 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139755264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative analysis of transcriptome and metabolome explores the underlying mechanism of pod color variation in pea (Pisum sativum L.)","authors":"","doi":"10.1007/s13562-024-00872-6","DOIUrl":"https://doi.org/10.1007/s13562-024-00872-6","url":null,"abstract":"<h3>Abstract</h3> <p>The pea (<em>Pisum sativum</em> L.) is one of widely cultivated crops over the world, but the mechanism of pod coloration is still unclear. Understanding the underlying mechanism regulating pea pod coloration can broaden pea breeding. In this study, the comparative analysis of transcriptome and metabolome was performed to examine the changes in metabolites accumulation and gene expression at two pod developmental stages in two pea accessions with green pods (GP) and yellow pods (YP). At the two omics levels, a total of 4504 differential metabolites (DEMs) were detected in four samples, and 2709 and 3725 differential expression genes (DEGs) were detected at two pod developmental stages between GP and YP, respectively. The verification results of RT-qPCR showed that the relative expression of ten genes randomly detected showed statistically high correlations between RT-qPCR and RNA-seq. The functional analysis of DEMs and DEGs found that the flavonoid metabolism pathway was the most direct metabolic pathway for the variation of pod coloration between two pea accessions. The 34 DEMs and 21 DEGs related to flavonoid metabolism pathway exhibited different expression pattern between GP and YP samples. Additionally, the combined analysis of transcriptome and metabolome in flavonoid biosynthesis pathway revealed that a direct correlation between the decreased expression level of genes and reduction accumulation of metabolites in the delphinidin biosynthesis pathway. The obtained results of this study provided a foundation to reveal the candidate genes controlling the pod color variation, and provide new germplasm resources for genetic improvement in pea.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"2 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139755282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Meta-QTL analysis enabled identification of candidate genes and haplotypes for enhancing biotic stress resistance in chickpea","authors":"Ishita Isha, Sarvjeet Singh, Uday Jha, C. Laxuman, Himabindu Kudapa, Rajeev K. Varshney, Mahendar Thudi","doi":"10.1007/s13562-024-00873-5","DOIUrl":"https://doi.org/10.1007/s13562-024-00873-5","url":null,"abstract":"<p>Fusarium wilt, Ascochyta blight and Botrytis grey mould caused by fungal pathogens are major biotic stresses that lead to 100% yield loss in chickpea (<i>Cicer arietinum</i> L.). Several independent studies reported the genomic regions, using heterogeneous populations, that are of limited use in breeding programs for the development of enhanced disease resistance in climate change scenarios. In order to identify the consensus genomic regions, we developed a consensus integrated map and performed Meta-QTL analysis using 52 QTLs reported in 17 independent studies. The consensus integrated map spanned 1292.04 cM with 669 markers on all eight linkage groups. In total, we report 10 Meta-QTLs distributed on four linkage groups (CaLG02, CaLG03, CaLG04 and CaLG06) and 172 genes belonging to a wide range of gene-families that are involved in multiple disease resistance. Among these, the key genes such as Glutaredoxin, Reticuline oxidase-like protein, and RING-Finger proteins, which have been previously reported for disease resistance. The confidence interval of reported Meta-QTLs decreased 4.89 folds from the original QTL studies whose confidence interval ranged from 0.84 to 28.94 cM. Among these genes, <i>Ca_13066</i> and <i>Ca_05186</i> present in Meta-QTL4_6 and Meta-QTL6_8, that play major role in biotic stress resistance pathways possessed 3 and 8 haplotypes respectively. Our study provides a better understanding of the genetic mechanisms underlying these three important biotic stresses. Further, the Meta-QTLs, candidate genes and haplotypes reported in this study can be used for developing climate resilient and disease resistant chickpea cultivars.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":"245 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139755186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}