Identification of Differential Drought Response Mechanisms in Medicago sativa subsp. sativa and falcata through Comparative Assessments at the Physiological, Biochemical, and Transcriptional Levels

Alfalfa (Medicago sativa L.) is an extensively grown perennial forage legume, and although it is relatively drought tolerant, it consumes high amounts of water and depends upon irrigation in many regions. Given the progressive decline in water available for irrigation, as well as an escalation in climate change-related droughts, there is a critical need to develop alfalfa cultivars with improved drought resilience. M. sativa subsp. falcata is a close relative of the predominantly cultivated M. sativa subsp. sativa, and certain accessions have been demonstrated to exhibit superior performance under drought. As such, we endeavoured to carry out comparative physiological, biochemical, and transcriptomic evaluations of an as of yet unstudied drought-tolerant M. sativa subsp. falcata accession (PI 641381) and a relatively drought-susceptible M. sativa subsp. sativa cultivar (Beaver) to increase our understanding of the molecular mechanisms behind the enhanced ability of falcata to withstand water deficiency. Our findings indicate that unlike the small number of falcata genotypes assessed previously, falcata PI 641381 may exploit smaller, thicker leaves, as well as an increase in the baseline transcriptional levels of genes encoding particular transcription factors, protective proteins, and enzymes involved in the biosynthesis of stress-related compounds. These findings imply that different falcata accessions/genotypes may employ distinct drought response mechanisms, and the study provides a suite of candidate genes to facilitate the breeding of alfalfa with enhanced drought resilience in the future.

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Transcriptional regulation of genes involved in Zn transport after foliar Zn application to Medicago sativa

10.1101/2020.05.11.088617 ◽

2020 ◽

Author(s):

Alessio Cardini ◽

Elisa Pellegrino ◽

Philip J. White ◽

Barbara Mazzolai ◽

Marco C. Mascherpa ◽

...

Keyword(s):

Medicago Sativa ◽

Agricultural Production ◽

Molecular Mechanisms ◽

Zn Deficiency ◽

Forage Crops ◽

Zn Uptake ◽

And Zn Deficiency ◽

Zn Concentration ◽

Genes Encoding ◽

Edible Tissues

ABSTRACTZinc (Zn) is an essential micronutrient for both plants and animals, and Zn deficiency is one of the most widespread problems for agricultural production. Although many studies have been performed on the biofortification of staple crops with Zn, few studies have focused on forage crops. In this study the molecular mechanisms of Zn transport-related in Medicago sativa L. were investigated following foliar Zn applications aimed at increasing the accumulation of Zn in edible tissues. Zinc uptake and redistribution between shoot and root were determined following the application of six Zn doses to leaves (0, 0.01, 0.1, 0.5, 1, 10 mg Zn plant-1). Twelve putative genes encoding proteins involved in Zn transport (MsZIP1-7, MsZIF1, MsMTP1, MsYSL1, MsHMA4 and MsNAS1) were identified and the changes in their expression following foliar Zn application were quantified using newly designed RT-qPCR assays. Shoot and root Zn concentration was increased following foliar Zn applications ≥ 0.1 mg plant-1. Increased expression of MsZIP2, MsHMA4 and MsNAS1 in shoots, and of MsZIP2 and MsHMA4 in roots, was observed with the largest Zn dose. By contrast, MsZIP3 was downregulated in shoots at Zn doses ≥ 0.1 mg plant-1. Three functional modules were identified in the M. sativa response to foliar Zn application: genes involved in Zn uptake by cells, genes involved in vacuolar Zn sequestration and genes involved in Zn redistribution within the plant. These results will inform genetic engineering strategies aimed at increasing the efficiency of crop Zn biofortification.One-sentence summaryUpregulation of ZIP2, NASI and HMA4 and downregulation of ZIP3 are associated with Zn sequestration and shoot-to-root translocation in Medicago sativa following foliar Zn biofortification

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Transcriptional Regulation of Genes Involved in Zinc Uptake, Sequestration and Redistribution Following Foliar Zinc Application to Medicago sativa

Plants ◽

10.3390/plants10030476 ◽

2021 ◽

Vol 10 (3) ◽

pp. 476

Author(s):

Alessio Cardini ◽

Elisa Pellegrino ◽

Philip J. White ◽

Barbara Mazzolai ◽

Marco C. Mascherpa ◽

...

Keyword(s):

Medicago Sativa ◽

Molecular Mechanisms ◽

Zinc Uptake ◽

Zn Deficiency ◽

And Zn Deficiency ◽

Zn Concentration ◽

Genes Encoding ◽

Gene Modules ◽

Medicago Sativa L ◽

Foliar Zinc Application

Zinc (Zn) is an essential micronutrient for plants and animals, and Zn deficiency is a widespread problem for agricultural production. Although many studies have been performed on biofortification of staple crops with Zn, few studies have focused on forages. Here, the molecular mechanisms of Zn transport in alfalfa (Medicago sativa L.) were investigated following foliar Zn applications. Zinc uptake and redistribution between shoot and root were determined following application of six Zn doses to leaves. Twelve putative genes encoding proteins involved in Zn transport (MsZIP1-7, MsZIF1, MsMTP1, MsYSL1, MsHMA4, and MsNAS1) were identified and changes in their expression following Zn application were quantified using newly designed RT-qPCR assays. These assays are the first designed specifically for alfalfa and resulted in being more efficient than the ones already available for Medicago truncatula (i.e., MtZIP1-7 and MtMTP1). Shoot and root Zn concentration was increased following foliar Zn applications ≥ 0.1 mg plant−1. Increased expression of MsZIP2, MsHMA4, and MsNAS1 in shoots, and of MsZIP2 and MsHMA4 in roots was observed with the largest Zn dose (10 mg Zn plant−1). By contrast, MsZIP3 was downregulated in shoots at Zn doses ≥ 0.1 mg plant−1. Three functional gene modules, involved in Zn uptake by cells, vacuolar Zn sequestration, and Zn redistribution within the plant, were identified. These results will inform genetic engineering strategies aimed at increasing the efficiency of crop Zn biofortification.

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Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

Nature Communications ◽

10.1038/s41467-021-23922-2 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Karolina Stępniak ◽

Magdalena A. Machnicka ◽

Jakub Mieczkowski ◽

Anna Macioszek ◽

Bartosz Wojtaś ◽

...

Keyword(s):

Gene Expression ◽

Chromatin Structure ◽

Molecular Mechanisms ◽

Genome Mapping ◽

Malignant Gliomas ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Multiple Tumor ◽

Genes Encoding ◽

Methylation Patterns

AbstractChromatin structure and accessibility, and combinatorial binding of transcription factors to regulatory elements in genomic DNA control transcription. Genetic variations in genes encoding histones, epigenetics-related enzymes or modifiers affect chromatin structure/dynamics and result in alterations in gene expression contributing to cancer development or progression. Gliomas are brain tumors frequently associated with epigenetics-related gene deregulation. We perform whole-genome mapping of chromatin accessibility, histone modifications, DNA methylation patterns and transcriptome analysis simultaneously in multiple tumor samples to unravel epigenetic dysfunctions driving gliomagenesis. Based on the results of the integrative analysis of the acquired profiles, we create an atlas of active enhancers and promoters in benign and malignant gliomas. We explore these elements and intersect with Hi-C data to uncover molecular mechanisms instructing gene expression in gliomas.

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EMS Derived Wheat Mutant BIG8-1 (Triticum aestivum L.)—A New Drought Tolerant Mutant Wheat Line

International Journal of Molecular Sciences ◽

10.3390/ijms22105314 ◽

2021 ◽

Vol 22 (10) ◽

pp. 5314

Author(s):

Marlon-Schylor L. le Roux ◽

Nicolas Francois V. Burger ◽

Maré Vlok ◽

Karl J. Kunert ◽

Christopher A. Cullis ◽

...

Keyword(s):

Amino Acids ◽

Water Deficit ◽

Triticum Aestivum L ◽

Water Deficit Stress ◽

Drought Response ◽

Fibrous Root ◽

Wheat Varieties ◽

Breeding Programs ◽

Response Characteristics ◽

Drought Tolerant

Drought response in wheat is considered a highly complex process, since it is a multigenic trait; nevertheless, breeding programs are continuously searching for new wheat varieties with characteristics for drought tolerance. In a previous study, we demonstrated the effectiveness of a mutant known as RYNO3936 that could survive 14 days without water. In this study, we reveal another mutant known as BIG8-1 that can endure severe water deficit stress (21 days without water) with superior drought response characteristics. Phenotypically, the mutant plants had broader leaves, including a densely packed fibrous root architecture that was not visible in the WT parent plants. During mild (day 7) drought stress, the mutant could maintain its relative water content, chlorophyll content, maximum quantum yield of PSII (Fv/Fm) and stomatal conductance, with no phenotypic symptoms such as wilting or senescence despite a decrease in soil moisture content. It was only during moderate (day 14) and severe (day 21) water deficit stress that a decline in those variables was evident. Furthermore, the mutant plants also displayed a unique preservation of metabolic activity, which was confirmed by assessing the accumulation of free amino acids and increase of antioxidative enzymes (peroxidases and glutathione S-transferase). Proteome reshuffling was also observed, allowing slow degradation of essential proteins such as RuBisCO during water deficit stress. The LC-MS/MS data revealed a high abundance of proteins involved in energy and photosynthesis under well-watered conditions, particularly Serpin-Z2A and Z2B, SGT1 and Calnexin-like protein. However, after 21 days of water stress, the mutants expressed ABC transporter permeases and xylanase inhibitor protein, which are involved in the transport of amino acids and protecting cells, respectively. This study characterizes a new mutant BIG8-1 with drought-tolerant characteristics suited for breeding programs.

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Genes encoding putative bicarbonate transporters as a missing molecular link between molt and mineralization in crustaceans

Scientific Reports ◽

10.1038/s41598-021-91155-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shai Abehsera ◽

Shmuel Bentov ◽

Xuguang Li ◽

Simy Weil ◽

Rivka Manor ◽

...

Keyword(s):

Calcium Carbonate ◽

Molecular Mechanisms ◽

Ph Control ◽

Functional Genomic ◽

Single Event ◽

Tight Coupling ◽

Molt Cycle ◽

Mineral Deposition ◽

Bicarbonate Transporters ◽

Genes Encoding

AbstractDuring their life, crustaceans undergo several molts, which if theoretically compared to the human body would be equivalent to replacing all bones at a single event. Such a dramatic repetitive event is coupled to unique molecular mechanisms of mineralization so far mostly unknown. Unlike human bone mineralized with calcium phosphate, the crustacean exoskeleton is mineralized mainly by calcium carbonate. Crustacean growth thus necessitates well-timed mobilization of bicarbonate to specific extracellular sites of biomineralization at distinct molt cycle stages. Here, by looking at the crayfish Cherax quadricarinatus at different molting stages, we suggest that the mechanisms of bicarbonate ion transport for mineralization in crustaceans involve the SLC4 family of transporters and that these proteins play a key role in the tight coupling between molt cycle events and mineral deposition. This discovery of putative bicarbonate transporters in a pancrustacean with functional genomic evidence from genes encoding the SLC4 family—mostly known for their role in pH control—is discussed in the context of the evolution of calcium carbonate biomineralization.

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Improved response of human gingival fibroblasts to titanium coated with micro-/nano-structured tantalum

International Journal of Implant Dentistry ◽

10.1186/s40729-021-00316-z ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Chu-nan Zhang ◽

Lin-yi Zhou ◽

Shu-jiao Qian ◽

Ying-xin Gu ◽

Jun-yu Shi ◽

...

Keyword(s):

Molecular Mechanisms ◽

Underlying Mechanism ◽

Cell Number ◽

Human Gingival Fibroblasts ◽

Superior Performance ◽

Control Group ◽

Human Gingival Fibroblast ◽

Gingival Fibroblast ◽

Gingival Fibroblasts ◽

Integrin Β1

Abstract Objectives This study aims to evaluate the ability of tantalum-coated titanium to improve human gingival fibroblasts’ adhesion, viability, proliferation, migration performance, and the potential molecular mechanisms. Materials and methods Titanium plates were divided into two groups: (1) no coating (Ti, control), (2) Tantalum-coated titanium (Ta-coated Ti). All samples were characterized by scanning electronic microscopy, surface roughness, and hydrophilicity. Fibroblasts’ performance were analyzed by attached cell number at 1 h, 4 h, and 24 h, morphology at 1 h and 4 h, viability at 1 day, 3 days, 5 days, and 7 days, recovery after wounding at 6 h, 12 h, and 24 h. RT-PCR, western blot were applied to detect attachment-related genes’ expression and protein synthesis at 4 h and 24 h. Student’s t test was used for statistical analysis. Results Tantalum-coated titanium demonstrates a layer of homogeneously distributed nano-grains with mean diameter of 25.98 (± 14.75) nm. It was found that after tantalum deposition, human gingival fibroblasts (HGFs) adhesion, viability, proliferation, and migration were promoted in comparison to the control group. An upregulated level of Integrin β1 and FAK signaling was also detected, which might be the underlying mechanism. Conclusion In the present study, adhesion, viability, proliferation, migration of human gingival fibroblasts are promoted on tantalum-coated titanium, upregulated integrin β1 and FAK might contribute to its superior performance, indicating tantalum coating can be applied in transmucosal part of dental implant. Clinical significance Tantalum deposition on titanium surfaces can promote human gingival fibroblast adhesion, accordingly forming a well-organized soft tissue sealing and may contribute to a successful osseointegration.

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Transcriptome Changes Reveal the Molecular Mechanisms of Humic Acid-Induced Salt Stress Tolerance in Arabidopsis

Molecules ◽

10.3390/molecules26040782 ◽

2021 ◽

Vol 26 (4) ◽

pp. 782

Author(s):

Joon-Yung Cha ◽

Sang-Ho Kang ◽

Myung Geun Ji ◽

Gyeong-Im Shin ◽

Song Yi Jeong ◽

...

Keyword(s):

Salt Stress ◽

Abiotic Stress ◽

Humic Acid ◽

Stress Tolerance ◽

Plant Development ◽

Molecular Mechanisms ◽

Abiotic Stress Tolerance ◽

Principal Component ◽

Salt Stress Tolerance ◽

Genes Encoding

Humic acid (HA) is a principal component of humic substances, which make up the complex organic matter that broadly exists in soil environments. HA promotes plant development as well as stress tolerance, however the precise molecular mechanism for these is little known. Here we conducted transcriptome analysis to elucidate the molecular mechanisms by which HA enhances salt stress tolerance. Gene Ontology Enrichment Analysis pointed to the involvement of diverse abiotic stress-related genes encoding HEAT-SHOCK PROTEINs and redox proteins, which were up-regulated by HA regardless of salt stress. Genes related to biotic stress and secondary metabolic process were mainly down-regulated by HA. In addition, HA up-regulated genes encoding transcription factors (TFs) involved in plant development as well as abiotic stress tolerance, and down-regulated TF genes involved in secondary metabolic processes. Our transcriptome information provided here provides molecular evidences and improves our understanding of how HA confers tolerance to salinity stress in plants.

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Analysis of saponins detoxification genes in Ilyonectria mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

Archives of Microbiology ◽

10.1007/s00203-021-02502-4 ◽

2021 ◽

Author(s):

Guohong Zeng ◽

Jin Li ◽

Yuxiu Ma ◽

Qian Pu ◽

Tian Xiao ◽

...

Keyword(s):

Root Rot ◽

Molecular Mechanisms ◽

Management Strategies ◽

Panax Notoginseng ◽

Glycoside Hydrolases ◽

Rna Seq ◽

Host Interaction ◽

Excellent Starting Point ◽

Starting Point ◽

Genes Encoding

AbstractSaponins are kinds of antifungal compounds produced by Panax notoginseng to resist invasion by pathogens. Ilyonectria mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4H (Hours) and 12H (Hours) compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4H and 12H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation–reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen–Host Interaction) genes out of those 93 up-regulated genes. In this report, we analyzed virulence-associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

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In silico identification of Capsicum type III polyketide synthase genes and expression patterns in Capsicum annuum

Open Life Sciences ◽

10.1515/biol-2020-0077 ◽

2020 ◽

Vol 15 (1) ◽

pp. 753-762

Author(s):

Delong Kan ◽

Di Zhao ◽

Pengfei Duan

Keyword(s):

Molecular Mechanisms ◽

Polyketide Synthase ◽

Expression Patterns ◽

Class Ii ◽

Chili Pepper ◽

Type Iii Polyketide Synthase ◽

Type Iii ◽

Genes Encoding ◽

Duplication Events ◽

Pepper Leaves

AbstractStudies have shown that abundant and various flavonoids accumulate in chili pepper (Capsicum), but there are few reports on the genes that govern chili pepper flavonoid biosynthesis. Here, we report the comprehensive identification of genes encoding type III polyketide synthase (PKS), an important enzyme catalyzing the generation of flavonoid backbones. In total, 13, 14 and 13 type III PKS genes were identified in each genome of C. annuum, C. chinense and C. baccatum, respectively. The phylogeny topology of Capsicum PKSs is similar to those in other plants, as it showed two classes of genes. Within each class, clades can be further identified. Class II genes likely encode chalcone synthase (CHS) as they are placed together with the Arabidopsis CHS gene, which experienced extensive expansions in the genomes of Capsicum. Interestingly, 8 of the 11 Class II genes form three clusters in the genome of C. annuum, which is likely the result of tandem duplication events. Four genes are not expressed in the tissues of C. annuum, three of which are located in the clusters, indicating that a portion of genes was pseudogenized after tandem duplications. Expression of two Class I genes was complementary to each other, and all the genes in Class II were not expressed in roots of C. annuum. Two Class II genes (CA00g90790 and CA05g17060) showed upregulated expression as the chili pepper leaves matured, and two Class II genes (CA05g17060 and CA12g20070) showed downregulated expression with the maturation of fruits, consistent with flavonoid accumulation trends in chili pepper as reported previously. The identified genes, sequences, phylogeny and expression information collected in this article lay the groundwork for future studies on the molecular mechanisms of chili pepper flavonoid metabolism.

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The Primary Causes of Muscle Dysfunction Associated with the Point Mutations in Tpm3.12; Conformational Analysis of Mutant Proteins as a Tool for Classification of Myopathies

International Journal of Molecular Sciences ◽

10.3390/ijms19123975 ◽

2018 ◽

Vol 19 (12) ◽

pp. 3975 ◽

Cited By ~ 5

Author(s):

Yurii Borovikov ◽

Olga Karpicheva ◽

Armen Simonyan ◽

Stanislava Avrova ◽

Elena Rogozovets ◽

...

Keyword(s):

Conformational Changes ◽

Molecular Mechanisms ◽

Fiber Type ◽

Point Mutations ◽

Nemaline Myopathy ◽

Muscle Dysfunction ◽

Thin Filaments ◽

Mutant Proteins ◽

Strong Binding ◽

Genes Encoding

Point mutations in genes encoding isoforms of skeletal muscle tropomyosin may cause nemaline myopathy, cap myopathy (Cap), congenital fiber-type disproportion (CFTD), and distal arthrogryposis. The molecular mechanisms of muscle dysfunction in these diseases remain unclear. We studied the effect of the E173A, R90P, E150A, and A155T myopathy-causing substitutions in γ-tropomyosin (Tpm3.12) on the position of tropomyosin in thin filaments, and the conformational state of actin monomers and myosin heads at different stages of the ATPase cycle using polarized fluorescence microscopy. The E173A, R90P, and E150A mutations produced abnormally large displacement of tropomyosin to the inner domains of actin and an increase in the number of myosin heads in strong-binding state at low and high Ca2+, which is characteristic of CFTD. On the contrary, the A155T mutation caused a decrease in the amount of such heads at high Ca2+ which is typical for mutations associated with Cap. An increase in the number of the myosin heads in strong-binding state at low Ca2+ was observed for all mutations associated with high Ca2+-sensitivity. Comparison between the typical conformational changes in mutant proteins associated with different myopathies observed with α-, β-, and γ-tropomyosins demonstrated the possibility of using such changes as tests for identifying the diseases.

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