Genome-wide superior alleles, haplotypes and candidate genes associated with tolerance on sodic-dispersive soils in wheat (Triticum aestivum L.)

Key message The pleiotropic SNPs/haplotypes, overlapping genes (metal ion binding, photosynthesis), and homozygous/biallelic SNPs and transcription factors (HTH myb-type and BHLH) hold great potential for improving wheat yield potential on sodic-dispersive soils. Abstract Sodic-dispersive soils have multiple subsoil constraints including poor soil structure, alkaline pH and subsoil toxic elemental ion concentration, affecting growth and development in wheat. Tolerance is required at all developmental stages to enhance wheat yield potential on such soils. An in-depth investigation of genome-wide associations was conducted using a field phenotypic data of 206 diverse Focused Identification of Germplasm Strategy (FIGS) wheat lines for two consecutive years from different sodic and non-sodic plots and the exome targeted genotyping by sequencing (tGBS) assay. A total of 39 quantitative trait SNPs (QTSs), including 18 haplotypes were identified on chromosome 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 5A, 5D, 6B, 7A, 7B, 7D for yield and yield-components tolerance. Among these, three QTSs had common associations for multiple traits, indicating pleiotropism and four QTSs had close associations for multiple traits, within 32.38 Mb. The overlapping metal ion binding (Mn, Ca, Zn and Al) and photosynthesis genes and transcription factors (PHD-, Dof-, HTH myb-, BHLH-, PDZ_6-domain) identified are known to be highly regulated during germination, maximum stem elongation, anthesis, and grain development stages. The homozygous/biallelic SNPs having allele frequency above 30% were identified for yield and crop establishment/plants m−2. These SNPs correspond to HTH myb-type and BHLH transcription factors, brassinosteroid signalling pathway, kinase activity, ATP and chitin binding activity. These resources are valuable in haplotype-based breeding and genome editing to improve yield potential on sodic-dispersive soils.

Comprehensive Genome-wide Identification, Characterization, and Expression Analysis of CCHC Zinc Finger Gene Family in Wheat (Triticum aestivum L.)

Background: The CCHC zinc finger proteins (CCHC-ZFPs) are transcription factors that play versatile roles in plant growth, development, and responses to biotic/abiotic stress. However, little is known about the CCHC-ZF genes in bread wheat (Triticum aestivum), an important food crop.Results: In this study, 50 TaCCHC-ZF genes were identified and distributed unevenly on 21 wheat chromosomes. According to the phylogenetic features, the 50 TaCCHC-ZF genes were classified into eight groups with specific motifs and gene structures. 43 TaCCHC-ZF genes were identified as segmentally duplicated genes that formed 36 segmental duplication gene pairs. Additionally, the collinearity analyses between wheat and eight other representative plant species showed that wheat had closer phylogenetic relationships with monocots compared to dicots. A total of 636 cis-elements related to environmental stress and phytohormone responsiveness were identified in the promoter of TaCCHC-ZF genes. Moreover, GO enrichment results revealed that all 50 TaCCHC-ZF genes were annotated under metal ion binding and nucleic acid binding. 91 miRNA binding sites within the 34 TaCCHC-ZF genes were identified by miRNA targets analyses, indicating that the expression of TaCCHC-ZF genes could be regulated by the miRNAs. Based on published transcriptome data, 38 TaCCHC-ZF genes were identified as DEGs, and 15 TaCCHC-ZF genes among them were verified by qRT-PCR assays, which showed response to drought, heat, or simultaneous response of them.Conclusions: This study systematically explored the gene structures, evolutionary characteristics, and potential roles during environmental responses of TaCCHC-ZF genes, providing a foundation for further investigation and application of TaCCHC-ZF genes in the molecular breeding of T. aestivum.

Analysis of Overexpressed miRNA in Circulation and Cancer Tissue to Develop a Potential microRNA Panel for the Diagnosis of Colorectal Cancer

Background: Colorectal cancer (CRC) represents the world’s fourth deadly cancer, but its early diagnosis can be curative with considerable success rates. This study was aimed to identify CRC specific microRNAs (miRNAs) in tissue and serum samples to develop a miRNA-based diagnostics panel for the minimal invasive detection of CRC in early condition. Methods: By integrating four microarrays in tissue and serum samples of CRC from Gene Expression Omnibus (GEO) database, we screened out the highly expressed miRNAs in each dataset by using limma R package. Two important upregulated miRNAs namely hsa-miR-1246 and hsa-miR-1825 were overlapped in both tissue and serum samples of CRC, and were investigated to target identification, followed by functional annotation and protein- protein interaction (PPI) study for the target genes through DAVID and STRING respectively. Finally, hub target genes were retrieved by Cytoscape analysis. Results: It was shown that target genes of hsa-miR-1246 and hsa-miR-1825 were involved with core KEGG pathways (such as cAMP, PI3K-Akt and calcium signaling pathway). In addition, biological processes (such as cell adhesion and cell proliferation), cellular components (such as plasma membrane and cytosol), molecular functions (such as protein binding and metal ion binding), were mostly associated with the target genes. Their top 5 target genes were retrieved and their biological function towards tumor progression was shown using Cancer Hallmarks Analytics Tool. Conclusion: This study suggested that hsa-miR-1246 and hsa-miR-1825, as overlapped upregulated tissue and circulating miRNAs might have a vital role in the development of CRC and their five hub target genes were identified.

Urea Gel Electrophoresis in Studies of Conformational Changes of Transferrin on Binding and Transport of Non-Ferric Metal Ions

Transferrin (Tf) is a crucial transporter protein for Fe(III), but its biological role in binding other metal ions and their delivery into cells remain highly controversial. The first systematic exploration of the effect of non-Fe(III) metal ion binding on Tf conformation has been performed by urea-polyacrylamide gel electrophoresis (urea-PAGE), which is commonly used for nucleic acids but rarely for proteins. Closed Tf conformation, similar to that caused by Fe(III)-Tf binding, was formed for In(III), V(III) or Cr(III) binding to Tf. In all these cases, metal distribution between Tf lobes and/or the rate of metal release under acidic conditions differed from that of Fe(III)-Tf. By contrast, Ga(III) and V(IV) did not form closed Tf conformation under urea-PAGE conditions. Apart from Fe(III), only In(III) was able to increase the proportion of closed Tf conformation in whole serum. These results suggest that Tf is unlikely to act as a natural carrier of any metal ion, except Fe(III), into cells but can reduce toxicity of exogenous metal ions by binding them in serum and preventing their entry into cells.

The Advantages of EPR Spectroscopy in Exploring Diamagnetic Metal Ion Binding and Transfer Mechanisms in Biological Systems

Electron paramagnetic resonance (EPR) spectroscopy has emerged as an ideal biophysical tool to study complex biological processes. EPR spectroscopy can follow minor conformational changes in various proteins as a function of ligand or protein binding or interactions with high resolution and sensitivity. Resolving cellular mechanisms, involving small ligand binding or metal ion transfer, is not trivial and cannot be studied using conventional biophysical tools. In recent years, our group has been using EPR spectroscopy to study the mechanism underlying copper ion transfer in eukaryotic and prokaryotic systems. This mini-review focuses on our achievements following copper metal coordination in the diamagnetic oxidation state, Cu(I), between biomolecules. We discuss the conformational changes induced in proteins upon Cu(I) binding, as well as the conformational changes induced in two proteins involved in Cu(I) transfer. We also consider how EPR spectroscopy, together with other biophysical and computational tools, can identify the Cu(I)-binding sites. This work describes the advantages of EPR spectroscopy for studying biological processes that involve small ligand binding and transfer between intracellular proteins.

Cationic Peptides and their Cu(II) and Ni(II) Complexes: Coordination and Biological Characteristics

Antimicrobial peptides are a promising group of compounds used for the treatment of infections. In some cases, metal ions are essential to activate these molecules. Examples of metalloantibiotics are, for instance, bleomycin and dermcidin. This study is focused on three new pseudopeptides with potential biological activity. The coordination behavior of all ligands with Cu(II) and Ni(II) ions has been examined. Various analytical methods such as potentiometric titration, UV-Vis and CD spectroscopies, and mass spectrometry were used. All compounds are convenient chelators for metal ion-binding. Two of the ligands tested have histidine residues. Surprisingly, imidazole nitrogen is not involved in the coordination of the metal ion. The N-terminal amino group, Dab side chains, and amide nitrogen atoms of the peptide bonds coordinated Cu(II) and Ni(II) in all the complexes formed. The cytotoxicity of three pseudopeptides and their complexes was evaluated. Moreover, their other model allowed for assessing the attenuation of LPS-induced cytotoxicity and anti-inflammatory activities were also evaluated, the results of which revealed to be very promising.

Prediction of Metal Ion Binding Sites of Transmembrane Proteins

The metal ion binding of transmembrane proteins (TMPs) plays a fundamental role in biological processes, pharmaceutics, and medicine, but it is hard to extract enough TMP structures in experimental techniques to discover their binding mechanism comprehensively. To predict the metal ion binding sites for TMPs on a large scale, we present a simple and effective two-stage prediction method TMP-MIBS, to identify the corresponding binding residues using TMP sequences. At present, there is no specific research on the metal ion binding prediction of TMPs. Thereby, we compared our model with the published tools which do not distinguish TMPs from water-soluble proteins. The results in the independent verification dataset show that TMP-MIBS has superior performance. This paper explores the interaction mechanism between TMPs and metal ions, which is helpful to understand the structure and function of TMPs and is of great significance to further construct transport mechanisms and identify potential drug targets.