Journal of Plant Biochemistry and Biotechnology最新文献

{"title":"Genome sequencing of Mesorhizobium Spp. NI-7, an efficient nitrogen-fixing microsymbiont of chickpea with potential to unravel the molecular mechanisms of symbiotic nitrogen fixation in legumes","authors":"Deevita Srivastava, Asim K Ghosh, Aashish Ranjan, Senjuti Sinharoy","doi":"10.1007/s13562-024-00917-w","DOIUrl":"https://doi.org/10.1007/s13562-024-00917-w","url":null,"abstract":"<p>Root nodule symbiosis is a major pillar of sustainable agriculture. The newly formed symbiotic organ in the legume root harbours rhizobacteria, which can fix atmospheric nitrogen into a bioavailable and reduced form, ammonia. Previously, we reported the isolation of an efficient <i>Mesorhizobium spp.</i> NI-7, from the interior of chickpea nodules. Here, we report the draft genome sequence of the <i>Mesorhizobium spp.</i> NI-7 and the comparative genomics among different Mesorhizobium strains that have adopted symbiosis during chickpea domestication. The draft genome of <i>Mesorhizobium spp.</i> NI-7 consists of a single 4.28 Mbp chromosome and a 359 Kbp plasmid. The 16 S rDNA sequence based phylogenetic analysis highlighted that <i>Mesorhizobium spp.</i> NI-7 belongs to a diverse Mesorhizobium clade that evolved during the domestication of chickpea. Comparative genomics among several Mesorhizobium strains identified 2193 common orthologous groups and several unique orthologous groups among the different Mesorhizobium pairs. The draft genome contains the essential nitrogen fixation genes along with the genes required for the nutrient exchange from the plant to the symbiont. Additionally, part of the symbiotic NOD-factor operon and Type III secretion system were also detected in the <i>Mesorhizobium spp.</i> NI-7 draft genome. The comparative genomics among the Mesorhizobium strains identified a subset of rhizobial genes that would have evolved during chickpea-Mesorhizobium adaptation to the Indian sub-continent. These genes are unique targets that can be validated in the future to understand the chickpea and Mesorhizobium adaptation. In summary, the draft genome sequencing of <i>Mesorhizobium spp.</i> NI-7 will equip the plant-microbe community with a chickpea-compatible Mesorhizobium strain isolated from India, suitable for both fundamental and advanced research on nodulation in chickpea, as well as for promoting sustainable agriculture in a comprehensive manner.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260433","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 characterization of functional microRNAs and their significant targets in maize plants","authors":"Abdul Baqi, Samiullah, Ghulam Mustafa Khan, Asadullah, Naqeebullah Khan, Attiq-Ur-Rehman, Alia Ahmed","doi":"10.1007/s13562-024-00918-9","DOIUrl":"https://doi.org/10.1007/s13562-024-00918-9","url":null,"abstract":"<p>Various metabolic and cell signaling processes influence the function of maize plant cells. miRNAs play numerous regulatory roles in regulating yield and protecting against various stressors. This study aims to identify and partially characterize some novel miRNAs in maize using in silico tools and provide a preliminary evaluation of their role. In this research, 20 novel conserved maize miRNAs belonging to 20 miRNA families were predicted using in silico tools and validated through RT-PCR. Consequently, 5850 different protein targets of these newly predicted miRNAs were identified via the psRNA Target approach. These targets included 20 significant ones involved in regulating metabolism, structural proteins, cell signaling proteins, and transportation factors. Moreover, the miRNA zma-miR5068 was predicted to be involved in the ubiquitin fusion protein process. Overall, this study examines novel maize miRNAs targeting several significant genes that could help manage the environment for better maize tolerance.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260436","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":"Phytosynthesis of copper nanoparticles using curcuma aromatica and its application in medical fabrics for antibacterial activity","authors":"Vardhana Janakiraman, Reethiga, B. Sampathkumar, N. K. Udaya Prakash","doi":"10.1007/s13562-024-00919-8","DOIUrl":"https://doi.org/10.1007/s13562-024-00919-8","url":null,"abstract":"<p>Antimicrobial textiles are crucial in various industries for combating contamination and improving hygiene. Copper's potent antimicrobial properties enhance infection control in medical fabrics. This study aims to synthesize copper in the form of nanoparticles CuNPs using <i>Curcuma aromatica</i>, to provide an effective, eco-friendly solution for antimicrobial medical textiles. The powder of the rhizome of <i>Curcuma aromatica</i> was boiled in sterile distilled water and the extract was used in the synthesis of CuNPs. The resulting CuNPs were characterized by UV–Vis spectroscopy, SEM, FTIR analysis, and XRD. The antibacterial efficacy of the synthesized CuNPs was tested against <i>Staphylococcus aureus</i> and <i>Escherichia coli</i> using the well diffusion method. The Cotton fabrics was embedded with synthesized CuNPs and again evaluated for its anti-bacterial property. The UV–VIS Spectroscopy showed absorption peaks above 554 nm due to the plasmon resonance of CuNPs. The size range of CuNPs was from 54 to 69 nm which was confirmed by SEM. FTIR analysis indicated the presence of various organic molecules associated with CuNPs. XRD analysis revealed the face-centered cubic crystal structure of the CuNPs. The CuNPs and CuNPs embedded cotton fabrics exhibited significant antibacterial activity against both <i>Staphylococcus aureus</i> and <i>Escherichia coli</i>. These findings support the use of <i>Curcuma aromatica</i> as a suitable source for CuNP synthesis and emphasize the significance of CuNPs in the development of effective antimicrobial fabrics for medical applications.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142227722","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 study of free amino acids at metabolite and gene expression levels in Triticeae during cold acclimation","authors":"Kalpita Singh, Zsolt Gulyás, Benedikt Athmer, Bettina Kovács, Zsuzsanna Mednyánszky, Gábor Galiba, Nils Stein, Lívia Simon-Sarkadi, Gábor Kocsy","doi":"10.1007/s13562-024-00912-1","DOIUrl":"https://doi.org/10.1007/s13562-024-00912-1","url":null,"abstract":"<p>This study investigates the freezing tolerance and cold-induced changes in amino acid metabolism in three <i>Triticeae</i> species (rye, wheat, and barley) with varying levels of freezing tolerance. Freezing tests confirmed that rye exhibited the highest tolerance, while barley showed the highest sensitivity. Cold acclimation significantly increased total free amino acid levels, with wheat and barley showing nearly twice the accumulation compared to rye. The glutamate family of amino acids, particularly proline (Pro), γ-aminobutyric acid (GABA), and glutamine (Gln), displayed substantial increase during cold treatment. Pro levels were notably higher in freezing-tolerant wheat and barley genotypes, suggesting its role in osmotic stress mitigation. However, this correlation was absent in rye. Gene expression analysis revealed that cold-induced proline accumulation is likely regulated at the post-transcriptional level, particularly involving the <i>P5CS</i> gene. These findings highlight the species-specific metabolic adjustments and regulatory mechanisms underlying freezing tolerance in <i>Triticeae</i> species, emphasizing the central role of proline and glutamate family amino acids in cold acclimation.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226516","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":"Morpho-physiological and molecular responses of an ecologically important mangrove Kandelia candel (L.) Druce under salinity stress","authors":"Malini Bhattacharyya, Suraj Prasannakumari Meera, Ashifa Nizam, Ajay Kumar","doi":"10.1007/s13562-024-00904-1","DOIUrl":"https://doi.org/10.1007/s13562-024-00904-1","url":null,"abstract":"<p>Mangroves are ecologically important model plants for understanding their tolerance mechanisms to stresses. This research investigates the growth, survival performance, photosynthetic functioning, physiological, and molecular responses of <i>Kandelia candel</i> (L.) Druce under varying salinity regimes (10, 20, 30, 40, and 50 PPT NaCl) at two time points (15 and 24 DAT). The salinity-induced growth variations indicate early responses in seedlings<i>,</i> which begin at 10–20 PPT. Most leaf and stem-specific morphological parameters showed a decreasing trend with increasing salinity, leading to leaf shedding beyond 20 PPT. On the other hand, the root system showed better response, and the root-specific parameters increased up to 10–20 PPT. The salinity tolerance level of <i>K. candel</i> hardly reaches the seawater salinity range (~ 35 PPT). Beyond this, salinity hampers growth, ultimately leading to plant mortality at 50 PPT. The concentration of the photosystem pigments was higher in freshwater-grown plants, emphasising the facultative halophytic nature of <i>K</i>. <i>candel</i>. The photosynthetic performance completely ceased, initiating the progressive death of the above-ground plant tissues at 20 PPT, leading to root hydraulic failure and plant death at higher salinities. This study further explores the expression of key genes crucial for proper photosynthesis and water uptake. The RT-qPCR results show that the genes encoding photosystem proteins (<i>PsaA</i>, <i>PsaB</i>, and <i>PsbA</i>) and membrane transporters (<i>AKT1</i>, <i>NHX</i>, <i>NIP,</i> and <i>TIP</i>) are downregulated. In contrast, other photosynthetic genes (<i>RbcS</i>, <i>RbcL</i>, <i>Ycf3,</i> and <i>LHCB</i>) are upregulated under salinity stress. These results provide an understanding of the physiological and molecular basis of mangrove ecological responses to salinity stress.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207705","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":"Genome-wide identification and characterization of PGIP gene family in Vigna radiata L. Wilczek and its expression in wild non-progenitor, Vigna umbellata L. Thunb. modulate bruchid resistance","authors":"Ramesh Kumar, Rakesh Pandey, Shalini Purwar, Mukesh Kumar Mishra, Ashutosh Rai, Chandra Mohan Singh","doi":"10.1007/s13562-024-00915-y","DOIUrl":"https://doi.org/10.1007/s13562-024-00915-y","url":null,"abstract":"<p>Mungbean [<i>Vigna radiata</i> (L.) R. Wilczek] is an important short duration grain legume. The huge demand of mungbean around the world creates a substantial export potential. Pulse beetles (<i>Callosobruchus</i> spp.) are a key issue of concern among the several threats that limit the production of mungbean, particularly under storage conditions. An investigation was carried out to analyze the polygalacturonase inhibiting protein (PGIP) gene family in mungbean and their possible role in bruchid resistance. A pulse beetle resistant wild ricebean genotype belongs to <i>Vigna umbellata</i> (PRR 2008-2) and a susceptible cultivar from <i>V. radiata</i> (Shikha) were used in present study for gene expression profiling. Total of 41 VrPGIP genes were identified in the mungbean genome. All the genes were randomly distributed over the chromosomes. All the 41 VrPGIP genes were grouped into 06 major clades and had single exon except <i>VrPGIP-37</i>. All the genes comprised of Glyco_Hydro_18 domain. Four candidate genes <i>VrPGIP-17, VrPGIP-18, VrPGIP-21</i> and <i>VrPGIP-23</i> were found significantly up-regulated in the PRR 2008-2. These genes may be utilized in the development of resistant varieties against pulse beetle in breeding programme.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207707","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":"Single-cell multi-omics in the medicinal plant Catharanthus roseus: a new era of next generation therapeutics","authors":"Meenakshi Dangwal, Gurparsad Singh Suri, Gurleen Kaur","doi":"10.1007/s13562-024-00913-0","DOIUrl":"https://doi.org/10.1007/s13562-024-00913-0","url":null,"abstract":"<p>Developments in single-cell omics have enormous potential to revolutionize plant metabolic engineering and gene discovery. Additionally, this might pave a new path for next-generation therapeutics and stress alleviation in plants. The medicinal plant species <i>Catharanthus roseus</i> produces the natural product monoterpene indole alkaloid (MIAs), through a multistep biochemical activity. The high-throughput single-cell RNA-sequencing followed by semi-quantitative single-cell metabolomics showed MIA biosynthesis with distinct metabolite profiles across the organs. Therefore, understanding the function of gene/s and their product is necessary to find all the candidates in a complex metabolic circuit. In this commentary, we focused on the advances in single-cell multi-omic technologies in <i>C. roseus</i> about the methods illustrating cell states and the metabolites.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207708","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":"Alternative transcriptomes and plant resilience: technological innovations and biological insights","authors":"Ashish Kumar Pathak, Raja Jeet, Mathilde Moens, Yogesh Gupta, Vani Sharma, Kaushal Kumar Bhati","doi":"10.1007/s13562-024-00909-w","DOIUrl":"https://doi.org/10.1007/s13562-024-00909-w","url":null,"abstract":"<p>The development of advanced high-throughput sequencing approaches has revealed the biomolecular diversity associated with central genetic dogmas like never before. Big genomics data highlight the hidden complexity of the genetic regulation of cellular machinery and physiological responses to environmental stimuli. The investigation and identification of alternative mRNA forms and protein diversity as adaptation mechanisms to environmental stimuli is one such case of unparallel genetic complexity in plant cells. Alternative splicing and selection of alternative start and stop sites during and after transcription lead to conditional variants across protein families. The biological importance of many such proteins is well understood, especially during reprogramming of plant stress responses and development. Interestingly, valuable methodologies and technical leads in the genome and alternative transcriptome sequencing from animals and model plants are now laying the groundwork for similar studies in crops. However, identifying alternative transcriptomes remains a major challenge for higher plants. Therefore, there is a need for improved library preparation methods and data analysis pipelines. We sought to examine the status of alternative transcriptome-associated studies on plant physiological regulation in response to environmental adaptation. In addition, we evaluated the recent technological advances available for studying alternative transcriptomes in plants.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226517","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":"Evaluating the dynamics of physical, proximate, mineral and antioxidant compositions during dragon fruit development","authors":"Rahul Sen, Ananta Madhab Baruah","doi":"10.1007/s13562-024-00916-x","DOIUrl":"https://doi.org/10.1007/s13562-024-00916-x","url":null,"abstract":"<p>Current study investigates the changes in physical, nutritional, and antioxidant compositions of two dragon fruit species <i>H. costaricensis</i> (HC) and <i>H. udantus</i> (HU) from 7 days after fruit set (DAFS) to maturity. In both species during development, physical parameters such as length, diameter, weight, volume, and pulp percentage increased, while peel percentage decreased. Mature HC fruits have a spherical shape with a length of 7.91 ± 0.14 cm, while HU fruits were oval, measuring 9.13 ± 0.19 cm. Moisture content declined during maturation, with mature HC and HU fruits containing 82.91 ± 1.23% and 80.53 ± 0.46% moisture, respectively. In both HC and HU, ash content remained around 1%, and dietary fiber content decreased significantly, while crude protein levels increased, reaching 4.04 ± 0.03% in HC and 4.64 ± 0.05% in HU at maturity. Chemical composition analysis indicated increases in total soluble sugars, reducing sugars, and total soluble solids (TSS) during maturation, with mature HC fruits having higher TSS (13.59 ± 0.92 ºBrix) compared to HU fruits (11.91 ± 0.04 ºBrix). Antioxidant activity and total phenolic content peaked during the early developmental stages and in the peel of mature fruits for both species, then decreased as the fruits matured. This study enhances the understanding of dragon fruit's maturation process and nutritional benefits, offering crucial information for optimizing cultivation, postharvest handling, and consumption practices. By identifying key stages for nutrient and antioxidant maximization, these findings may contribute to improved agricultural practices and the development of value-added products from dragon fruit.</p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207709","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":"Proteomic, biochemical and peptidomics based analysis reveals heat responsive changes in the seedlings of Brassica juncea","authors":"Reema Rani, Ibandalin Mawlong, Balbeer Balbeer, M.S. Sujith Kumar , Pramod Kumar Rai, Vijay Veer Singh","doi":"10.1007/s13562-024-00914-z","DOIUrl":"https://doi.org/10.1007/s13562-024-00914-z","url":null,"abstract":"<p>Heat stress at seedling stage has a crucial impact on Indian mustard growth and productivity. Identifying heat stress responsive proteins can be crucial to understand the heat stress adaptive mechanisms. In this work, biochemical, proteomic, and peptidomics response of the thermotolerant genotype, BPR 543-2 was investigated in the early seedlings of mustard under heat stress treatment. A total of 403, 328 and 369 number of proteins were identified to be expressed exclusively during 0, 4 and 8 h of heat-stress while 89, 119 and 81 were differentially accumulated during 0–4 h, 4 h-8 h and 0–8 h using LC–MS/MS based analysis. Notably, BPR 543-2 expressed elevated levels of heat shock proteins, chaperones, enzymes involved in the metabolism of carbohydrate and energy, cell wall modifications and transcription factors. In addition, using MALDI-TOF-MS, overexpressed proteins involved in DNA repair, signal transduction and metabolic adaptation were identified during different time point of heat stress. Moreover, biochemical analysis revealed high TAC, TF and less turbulence in photosynthetic pigments in stressed samples. Through combined analysis of biochemical, proteomics and peptidomics approaches, it was observed that BPR 543-2 was more resilient to heat stress and experienced fewer significant metabolic disruptions in stressed samples, demonstrating its adaptability to heat stress at early seedling stage. The proteins with differential abundance were functionally annotated <i>in-silico</i> for their subcellular localization, biological and molecular functions. This work demonstrates the usefulness of proteomics and peptidomics-based approaches by providing fresh insights into the mechanism behind the heat-stress adaption mechanisms in Indian mustard. The identified critical proteins provide intriguing targets for developing stress tolerance in heat-sensitive brassica crops. </p>","PeriodicalId":16835,"journal":{"name":"Journal of Plant Biochemistry and Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142207749","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}