Erratum to: Molecular dynamics simulation reveals DNA-specific recognition mechanism via c-Myb in pseudo-palindromic consensus of promoter.

The original version of this article (Weng et al., 2023) unfortunately contained a mistake. In Acknowledgments, the number (No.

ZmNRT1.1B (ZmNPF6.6) determines nitrogen use efficiency via regulation of nitrate transport and signalling in maize.

Nitrate (NO ) is crucial for optimal plant growth and development and often limits crop productivity under low availability. In comparison with model plant Arabidopsis, the molecular mechanisms underlying NO acquisition and utilization remain largely unclear in maize. In particular, only a few genes have been exploited to improve nitrogen use efficiency (NUE).

Molecular dynamics simulation reveals DNA-specific recognition mechanism via c-Myb in pseudo-palindromic consensus of promoter.

This study aims to gain insight into the DNA-specific recognition mechanism of c-Myb transcription factor during the regulation of cell early differentiation and proliferation. Therefore, we chose the chicken myeloid gene, mitochondrial import protein 1 (), as a target to study the binding specificity between potential dual-Myb-binding sites. The c-Myb-binding site in is a pseudo-palindromic sequence AACGGTT, which contains two AACNG consensuses.

Engineered chimeric insecticidal crystalline protein improves resistance to lepidopteran insects in rice (Oryza sativa L.) and maize (Zea mays L.).

The insecticidal crystalline proteins (Crys) are a family of insect endotoxin functioning in crop protection. As insects keep evolving into tolerance to the existing Crys, it is necessary to discover new Cry proteins to overcome potential threatens. Crys possess three functional domains at their N-termini, and the most active region throughout evolution was found at the domain-III.

Phylogenetic analyses of the 19 STR loci in X chromosome revealed discriminant forensic characteristics for Chinese Daur and Oroqen minorities.

In respect of forensic genetics, X-STRs are widely applied for deficiency paternity cases. Given the popularization of AGCU-X19 STR Kit in China, there has been investigation conducted into the genetic data and forensic parameters of 19 X-STR loci in many of the Chinese ethnic groups, which makes it possible to perform nationwide phylogenetic comparation. To evaluate the allele and haplotype diversity of 19 X-STR loci and to explore their forensic efficiency in the Daur and Oroqen minorities, unrelated healthy Daur (n = 86) and Oroqen (n = 165) individuals were recruited from Heilongjiang province, so as to reveal the phylogenetic relationship between the two minorities and other Chinese ethnic groups.

Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks.

The limited knowledge of genomic diversity and functional genes associated with the traits of soybean varieties has resulted in slow progress in breeding. In this study, we sequenced the genomes of 250 soybean landraces and cultivars from China, America, and Europe, and investigated their population structure, genetic diversity and architecture, and the selective sweep regions of these accessions. Five novel agronomically important genes were identified, and the effects of functional mutations in respective genes were examined.

Potential interaction between autophagy and auxin during maize leaf senescence.

Leaf senescence is important for crop yield as delaying it can increase the average yield. In this study, population genetics and transcriptomic profiling were combined to dissect its genetic basis in maize. To do this, the progenies of an elite maize hybrid Jidan27 and its parental lines Si-287 (early senescence) and Si-144 (stay-green), as well as 173 maize inbred lines were used.

QTL Mapping of Fusarium Ear Rot Resistance in Maize.

Ear rot is a globally prevalent class of disease in maize, of which Fusarium ear rot (FER), caused by the fungal pathogen , is the most commonly reported. In this study, three F populations, namely F-C, F-D, and F-J, and their corresponding F families were produced by crossing three highly FER-resistant inbred lines, Cheng351, Dan598, and JiV203, with the same susceptible line, ZW18, for quantitative trait locus (QTL) mapping of FER resistance. The individual crop plants were inoculated with a spore suspension of the pathogen injected into the kernels of the maize ears.

A NaCO-Responsive Chitinase Gene From Improve Pathogen Resistance and Saline-Alkali Stress Tolerance in Transgenic Tobacco and Maize.

Salinity and microbial pathogens are the major limiting factors for crop production. Although the manipulation of many genes could improve plant performance under either of these stresses, few genes have reported that could improve both pathogen resistance and saline-alkali stress tolerance. In this study, we identified a new chitinase gene () that encodes a class II chitinase from , which grows naturally on alkaline-sodic soil.

The defective effect of starch branching enzyme IIb from weak to strong induces the formation of biphasic starch granules in amylose-extender maize endosperm.

Biphasic starch granules in maize ae mutant underwent the weak to strong SBEIIb-defective effect during endosperm development, leading to no birefringence in their exterior due to extended long branch-chains of amylopectin. Biphasic starch granules are usually detected regionally in cereal endosperm lacking starch branching enzyme (SBE). However, their molecular structure, formation mechanism, and regional distribution are unclear.

Development of dwarfish and yield-effective GM maize through passivation of bioactive gibberellin.

During the Green Revolution in the 1960s, breeding dwarf cultivars turned out to be a landmark, leading to a significant increase in the global production of wheat and rice. The most direct and effective strategy for breeding dwarf crops, among others, would be to control endogenous gibberellin (GA) levels of the crops. GA 2-oxidases are a group of 2-oxoglutarate-dependent dioxygenases that catalyze the deactivation of bioactive GAs.

Sweet Sorghum Originated through Selection of , a Plant-Specific NAC Transcription Factor Gene.

Sorghum () is the fifth most popular crop worldwide and a C model plant. Domesticated sorghum comes in many forms, including sweet cultivars with juicy stems and grain sorghum with dry, pithy stems at maturity. The locus, which controls the pithy/juicy stem trait, was discovered over a century ago.

ZmCOL3, a CCT gene represses flowering in maize by interfering with the circadian clock and activating expression of ZmCCT.

Flowering time is a trait vital to the adaptation of flowering plants to different environments. Here, we report that CCT domain genes play an important role in flowering in maize (Zea mays L.).

Identification of Drought Tolerant Mechanisms in Maize Seedlings Based on Transcriptome Analysis of Recombination Inbred Lines.

Zea mays is an important crop that is sensitive to drought stress, but survival rates and growth status remain strong in some drought-tolerant lines under stress conditions. Under drought conditions, many biological processes, such as photosynthesis, carbohydrate metabolism and energy metabolism, are suppressed, while little is known about how the transcripts of genes respond to drought stress in the genome-wide rang in the seedling stage. In our study, the transcriptome profiles of two maize recombination inbred lines (drought-tolerant RIL70 and drought-sensitive RIL93) were analyzed at different drought stages to elucidate the dynamic mechanisms underlying drought tolerance in maize seedlings during drought conditions.

Affinity chromatography revealed insights into unique functionality of two 14-3-3 protein species in developing maize kernels.

Unlabelled: The 14-3-3 proteins are a group of regulatory proteins of divergent functions in plants. However, little is known about their roles in maize kernel development. Using publically available gene expression profiling data, we found that two 14-3-3 species genes, zmgf14-4 and zmgf14-6, exhibited prominent expression profiles over other 14-3-3 protein genes during maize kernel development.

Genome-wide patterns of large-size presence/absence variants in sorghum.

The presence/absence variants (PAVs) are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum (Sorghum bicolour L.

Early transcriptomic adaptation to Na₂CO₃ stress altered the expression of a quarter of the total genes in the maize genome and exhibited shared and distinctive profiles with NaCl and high pH stresses.

Sodium carbonate (Na₂CO₃) presents a huge challenge to plants by the combined damaging effects of Na⁺, high pH, and CO₃²⁻. Little is known about the cellular responses to Na₂CO₃ stress. In this study, the transcriptome of maize (Zea mays L.

Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis.

Background: Identification of the novel genes relevant to plant cell-wall (PCW) synthesis represents a highly important and challenging problem. Although substantial efforts have been invested into studying this problem, the vast majority of the PCW related genes remain unknown.

Results: Here we present a computational study focused on identification of the novel PCW genes in Arabidopsis based on the co-expression analyses of transcriptomic data collected under 351 conditions, using a bi-clustering technique.

Molecular dynamics analysis reveals structural insights into mechanism of nicotine N-demethylation catalyzed by tobacco cytochrome P450 mono-oxygenase.

CYP82E4, a cytochrome P450 monooxygenase, has nicotine N-demethylase (NND) activity, which mediates the bioconversion of nicotine into nornicotine in senescing tobacco leaves. Nornicotine is a precursor of the carcinogen, tobacco-specific nitrosamine. CYP82E3 is an ortholog of CYP82E4 with 95% sequence identity, but it lacks NND activity.

Cloning and characterisation of a novel 2,4-dichlorophenol hydroxylase from a metagenomic library derived from polychlorinated biphenyl-contaminated soil.

A novel 2,4-dichlorophenol hydroxylase (TfdB, EC 1.14.13.

A cost-effective high-resolution melting approach using the EvaGreen dye for DNA polymorphism detection and genotyping in plants.

High-resolution melting (HRM) analysis relies on the use of fluorescent dyes, such as LCGreen, ResoLight, and SYTO9, which bind in a saturated manner to the double-stranded DNAs. These dyes are expensive in use and may not be affordable when dealing with a large quantity of samples. EvaGreen is a much cheaper DNA helix intercalating dye and has been used in quantitative real-time polymerase chain reaction (PCR) and post-PCR DNA melt curve analysis.

Ca2+-binding protein S100A11: a novel diagnostic marker for breast carcinoma.

To evaluate whether S100A11 could be considered to be a novel diagnostic marker in breast carcinoma, the method of differential proteomics, Western blotting, and immunohistochemistry were used to detect the expression pattern and subcellular localization of S100A11. Statistical analyses indicated that specific up-regulated of A100A11 did not correlate with other prognostic factors such as age, tumor size, grade and stage, ER, PR, HER-2 and nodal status. Our data support that S100A11 is a novel diagnostic marker in breast carcinoma.

Four divergent Arabidopsis ethylene-responsive element-binding factor domains bind to a target DNA motif with a universal CG step core recognition and different flanking bases preference.

The Arabidopsis ethylene-responsive element-binding factor (AtERF) family of transcription factors has approximately 120 members, all of which possess a highly conserved ERF domain. AtERF1, AtERF4, AtEBP and CBF1 are members from different phylogenetic subgroups within the family. Electrophoretic mobility shift assay analyses revealed that the ERF domains of these four proteins were capable of binding specifically to either GCC or dehydration-responsive element (DRE) motifs.

Molecular dynamics simulations reveal the disparity in specific recognition of GCC-box by AtERFs transcription factors super family in Arabidopsis.

Arabidopsis ethylene responsive element binding factors (AtERFs) form a transcription factor super family. While the functions of most AtERFs are unknown, a number of AtERFs appear to be involved in regulation of stress-related genes through their DNA binding domains (DBD), namely ERF domains, which recognize a consensus motif GCC-box at the regulatory region. In this study, molecular dynamics simulations were performed on the four ERF domain-GCC-box complexes, AtERF1, AtERF4, AtEBP and CFBF1, to determine disparity in specific binding to the GCC-box by the AtERFs.

A fractionation procedure for identifying novel proteins induced by chill stress in Arabidopsis thaliana.

Extraction of plant proteins using typical extraction buffers leaves insoluble debris that cannot be investigated by conventional 2-DE technologies. In this paper, we present a scalable, off-line procedure for extraction of Arabidopsis thaliana homogenates that can be used in combination with both in-gel digestion and mass spectrometry. Based on sequential NaCl gradients and strong detergent fractionation, this new strategy allowed detection of 11 novel proteins from Arabidopsis thaliana that were altered in response to chilling stress.