Unique feature of Fe-OM complexes for limiting Cd accumulation in grains by target-regulating gene expression in rice tissues

This study investigated the impact of soil type and rice cultivars on variations in the iron plaque formation and cadmium (Cd) accumulation by different portions of rice seedlings under the influence of Fe amendment. The experiments were performed in pots under glasshouse conditions using two typical paddy soils. Rice seedlings were exposed to three concentrations of Cd (0, 1 and 3 mg kg−1 soil) and Fe (0, 1.0 and 2.0 g kg−1 soil). The results revealed that shoot biomass decreased by 12.2–23.2% in Quest and 12.8–30.8% in Langi in the Cd1.0 and Cd3.0 treatments, while shoot biomass increased by 11.2–19.5% in Quest and 26–43.3% in Langi in Fe1.0 and Fe2.0 as compared to the Fe control. The Cd concentration in the roots and shoots of rice seedlings were in the order of Langi cultivar > Quest cultivar, but the Fe concentration in rice tissues showed the reverse order. Fe plaque formations were promoted by Fe application, which was 7.8 and 10.4 times higher at 1 and 2 g kg−1 Fe applications compared to the control Fe treatment. The Quest cultivar exhibited 13% higher iron plaque formation capacity compared to the Langi cultivar in both soil types. These results indicate that enhanced iron plaque formation on the root surface was crucial to reduce the Cd concentration in rice plants, which could be an effective strategy to regulate grain Cd accumulation in rice plants.

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Elucidation of Novel cis-Regulatory Elements and Promoter Structures Involved in Iron Excess Response Mechanisms in Rice Using a Bioinformatics Approach

Frontiers in Plant Science ◽

10.3389/fpls.2021.660303 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yusuke Kakei ◽

Hiroshi Masuda ◽

Naoko K. Nishizawa ◽

Hiroyuki Hattori ◽

May Sann Aung

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Expression Patterns ◽

Regulatory Elements ◽

High Accuracy ◽

Future Application ◽

Conserved Sequences ◽

Network Analyses ◽

Fe Excess ◽

Rice Tissues

Iron (Fe) excess is a major constraint on crop production in flooded acidic soils, particularly in rice cultivation. Under Fe excess, plants activate a complex mechanism and network regulating Fe exclusion by roots and isolation in various tissues. In rice, the transcription factors and cis-regulatory elements (CREs) that regulate Fe excess response mechanisms remain largely elusive. We previously reported comprehensive microarray analyses of several rice tissues in response to various levels of Fe excess stress. In this study, we further explored novel CREs and promoter structures in rice using bioinformatics approaches with this microarray data. We first performed network analyses to predict Fe excess-related CREs through the categorization of the gene expression patterns of Fe excess-responsive transcriptional regulons, and found four major expression clusters: Fe storage type, Fe chelator type, Fe uptake type, and WRKY and other co-expression type. Next, we explored CREs within these four clusters of gene expression types using a machine-learning method called microarray-associated motif analyzer (MAMA), which we previously established. Through a comprehensive bioinformatics approach, we identified a total of 560 CRE candidates extracted by MAMA analyses and 42 important conserved sequences of CREs directly related to the Fe excess response in various rice tissues. We explored several novel cis-elements as candidate Fe excess CREs including GCWGCWGC, CGACACGC, and Myb binding-like motifs. Based on the presence or absence of candidate CREs using MAMA and known PLACE CREs, we found that the Boruta-XGBoost model explained expression patterns with high accuracy of about 83%. Enriched sequences of both novel MAMA CREs and known PLACE CREs led to high accuracy expression patterns. We also found new roles of known CREs in the Fe excess response, including the DCEp2 motif, IDEF1-, Zinc Finger-, WRKY-, Myb-, AP2/ERF-, MADS- box-, bZIP and bHLH- binding sequence-containing motifs among Fe excess-responsive genes. In addition, we built a molecular model and promoter structures regulating Fe excess-responsive genes based on new finding CREs. Together, our findings about Fe excess-related CREs and conserved sequences will provide a comprehensive resource for discovery of genes and transcription factors involved in Fe excess-responsive pathways, clarification of the Fe excess response mechanism in rice, and future application of the promoter sequences to produce genotypes tolerant of Fe excess.

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Decision letter for "Retinal Defocus and Form‐Deprivation Induced Regional Differential Gene Expression of BMPs in Chick RPE"

10.1002/cne.24957/v1/decision1 ◽

2020 ◽

Keyword(s):

Gene Expression ◽

Differential Gene Expression ◽

Differential Gene

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Decision letter for "Early postnatal gene expression in the developing neocortex of prairie voles ( Microtus ochrogaster ) is related to parental rearing style"

10.1002/cne.24856/v2/decision1 ◽

2020 ◽

Keyword(s):

Gene Expression ◽

Microtus Ochrogaster ◽

Prairie Voles ◽

Developing Neocortex ◽

Parental Rearing

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Silica Incorporation in the Cell Wall of the Singing Cell of Urtica dioica

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100116541 ◽

1975 ◽

Vol 33 ◽

pp. 584-585

Author(s):

A. E. Sowers ◽

E. L. Thurston

Keyword(s):

Cell Wall ◽

Unique Feature ◽

Urtica Dioica ◽

Wall Material ◽

Pain Response ◽

Apical Portion ◽

Ultrastructural Investigation ◽

Plant Families ◽

Bulbous Tip

Plant stinging emergences exhibit functional similarities in that they all elicit a pain response upon contact. A stinging emergence consists of an elongated stinging cell and a multicellular pedestal (Fig. 1). A recent ultrastructural investigation of these structures has revealed the ontogeny and morphology of the stinging cells differs in representative genera in the four plant families which possess such structures. A unique feature of the stinging cell of Urtica dioica is the presence of a siliceous cell wall in the apical portion of the cell. This rigid region of the cell wall is responsible for producing the needle-like apparatus which penetrates the skin. The stinging cell differentiates the apical bulbous tip early in development and the cell continues growth by intercalary addition of non-silicified wall material until maturity.The uppermost region of the stinging cell wall is entirely composed of silica (Fig. 2, 3) and upon etching with a 3% solution of HF (5 seconds), the silica is partially removed revealing the wall consisting of individualized silica bodies (Fig. 4, 5).

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Molecular and Microscopic Analysis of Altered Gene Expression in Transgenic and Gene Targeted Mice

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100162521 ◽

1996 ◽

Vol 54 ◽

pp. 12-13

Author(s):

W. K. Jones ◽

J. Robbins

Keyword(s):

Gene Expression ◽

Pulmonary Veins ◽

Microscopic Analysis ◽

Mouse Tissue ◽

Adult Heart ◽

Heavy Chains ◽

Altered Gene Expression ◽

Altered Gene ◽

Pulmonary Myocardium

Two myosin heavy chains (MyHC) are expressed in the mammalian heart and are differentially regulated during development. In the mouse, the α-MyHC is expressed constitutively in the atrium. At birth, the β-MyHC is downregulated and replaced by the α-MyHC, which is the sole cardiac MyHC isoform in the adult heart. We have employed transgenic and gene-targeting methodologies to study the regulation of cardiac MyHC gene expression and the functional and developmental consequences of altered α-MyHC expression in the mouse.We previously characterized an α-MyHC promoter capable of driving tissue-specific and developmentally correct expression of a CAT (chloramphenicol acetyltransferase) marker in the mouse. Tissue surveys detected a small amount of CAT activity in the lung (Fig. 1a). The results of in situ hybridization analyses indicated that the pattern of CAT transcript in the adult heart (Fig. 1b, top panel) is the same as that of α-MyHC (Fig. 1b, lower panel). The α-MyHC gene is expressed in a layer of cardiac muscle (pulmonary myocardium) associated with the pulmonary veins (Fig. 1c). These studies extend our understanding of α-MyHC expression and delimit a third cardiac compartment.

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Linking transcription, RNA polymerase II elongation and alternative splicing

Biochemical Journal ◽

10.1042/bcj20200475 ◽

2020 ◽

Vol 477 (16) ◽

pp. 3091-3104 ◽

Cited By ~ 1

Author(s):

Luciana E. Giono ◽

Alberto R. Kornblihtt

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Rna Polymerase Ii ◽

Environmental Changes ◽

Transcription Elongation ◽

Single Gene ◽

Regulation Of Gene Expression ◽

Regulation Of Transcription ◽

Stepping Stones ◽

Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

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