bims-pisump 2018-07-08 papers

Issue of 2018–07–08
five papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Mol Plant. 2018 Jun 27. pii: S1674-2052(18)30193-X. [Epub ahead of print]

Molecular Mechanisms of Leaf Morphogenesis.

Plants maintain the ability to form lateral appendages throughout their life cycle and form leaves as the principal lateral appendages of the stem. Leaves initiate at the peripheral zone of the shoot apical meristem, then develop into flattened structures. In most plants, the leaf functions as a solar panel, where photosynthesis converts carbon dioxide and water into carbohydrates and oxygen. To produce structures that can optimally fulfil this function, plants precisely regulate the initiation, shape, and polarity of leaves. Moreover, leaf development is highly flexible, but follows common themes and involves conserved regulatory mechanisms. Leaves may have evolved from lateral branches that converted into determinate, flattened structures. Many other plant parts, such as the floral organs, are considered specialized leaves, and thus leaf development underlies their morphogenesis. Here, we review recent advances in the understanding of how three-dimensional leaf forms are established. We focus on how genes, phytohormones, and mechanical properties modulate leaf development, discussing this in the context of leaf initiation, polarity establishment and maintenance, leaf flattening, and intercalary growth.

Keywords: Leaf; blastozone; lateral organ; meristem; morphogenesis; shoot

DOI: https://doi.org/10.1016/j.molp.2018.06.006

Theor Appl Genet. 2018 Jun 30.

The early flowering trait of an emmer wheat accession (Triticum turgidum L. ssp. dicoccum) is associated with the cis-element of the Vrn-A3 locus.

Kazusa Nishimura, Ryuji Moriyama, Keisuke Katsura, Hiroki Saito, Rihito Takisawa, Akira Kitajima, Tetsuya Nakazaki.

KEY MESSAGE: We identified a novel allele of the Vrn-A3 gene that is associated with an early flowering trait in wheat. This trait is caused by a cis-element GATA box in Vrn-A3. To identify novel flowering genes in wheat, we investigated days from germination to heading (DGH) in tetraploid wheat accessions. We found that the tetraploid variety Triticum turgidum L. ssp. dicoccum (TN26) harbors unknown genes that surpass the earliness effect of the early flowering allele Ppd-A1a harbored by TN28 (T. turgidum L. ssp. turgidum conv. pyramidale). Using recombinant inbred lines resulting from a cross between TN26 and TN28, we performed a quantitative trait locus (QTL) analysis for DGH. We identified a QTL for earliness in TN26 on chromosome 7AS, the chromosome on which Vrn-A3 is located. By sequence analysis for the Vrn-A3 locus in both TN26 and TN28, we identified a 7-bp insertion that included a cis-element GATA box sequence at the promoter region of the Vrn-A3 locus of TN26. Based on an expression analysis using sister lines for Vrn-A3, we suggest that the early flowering trait of TN26 was caused by the GATA box in Vrn-A3. In addition, we identified tetraploid wheat as a useful genetic resource for wheat breeding.

DOI: https://doi.org/10.1007/s00122-018-3131-5

New Phytol. 2018 Jun 30.

Epigenetic regulation of anthocyanin biosynthesis by an antagonistic interaction between H2A.Z and H3K4me3.

Hanyang Cai, Man Zhang, Mengnan Chai, Qing He, Xinyu Huang, Lihua Zhao, Yuan Qin.

The accumulation of anthocyanins in response to specific developmental cues or environmental conditions plays a vital role in plant development and protection against stresses. Extensive research has examined the regulation of anthocyanin biosynthetic genes at the transcriptional and post-transcriptional levels, but the role of chromatin in this regulation remains unknown. Chromatin immunoprecipitation and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analyses were performed. Genetic interactions between trimethylation of lysine 4 on histone H3 (H3K4me3) and the chromatin remodeling complex SWR1 in the control of anthocyanin biosynthesis were further studied. In this study, we provide evidence that a conserved histone H2 variant, H2A.Z, negatively regulates anthocyanin accumulation through deposition at a set of anthocyanin biosynthetic genes and consequently represses their expression in Arabidopsis thaliana. Our data indicate that the accumulation of anthocyanin in H2A.Z deposition-deficient mutants is associated with increased H3K4me3, which is required for promotion of the expression of anthocyanin biosynthetic genes. We further provide evidence that H3K4me3 in anthocyanin biosynthetic genes is negatively associated with the presence of H2A.Z. Our results reveal an antagonistic relationship between H2A.Z and H3K4me3 in the regulation of the expression of anthocyanin biosynthesis genes, adding another layer of regulation to anthocyanin biosynthesis genes and highlighting the role of chromatin in gene regulation.

Keywords: Arabidopsis chromatin immunoprecipitation; H2A.Z; anthocyanins; lysine 4 on histone H3 (H3K4me3)

DOI: https://doi.org/10.1111/nph.15306

Plant Physiol Biochem. 2018 Jun 23. pii: S0981-9428(18)30282-1. [Epub ahead of print]130 43-53

Identification of jumonjiC domain containing gene family among the Oryza species and their expression analysis in FL478, a salt tolerant rice genotype.

Soni Chowrasia, Alok Kumar Panda, Hukam C Rawal, Harmeet Kaur, Tapan Kumar Mondal.

The jumonji (JMJ)-C domain containing proteins belong to histone demethylases family with the ability to demethylate the tri-methylated histone residues. They act as chromatin regulators to regulate many physiological functions in plants. The present study deals with the characterization of JMJ-C gene family members in wild as well as cultivated rice species and their expression analysis in salt tolerant rice genotype, FL478. The genome wide study identified 151 members belonging to JMJ-C gene family in 11 different Oryza species. We also studied their structure, genomic location, gene duplication events, phylogenetic relationship, in silico expression analysis and identified cis elements in their promoters. We also found a few JMJ-C gene family members in rice which underwent duplication before the whole genome duplication event of the rice. The qRT-PCR based expression profiling revealed that out of the total 15 rice JMJ-C members, two were highly expressed in the flag leaf stage of FL478 under salt treatment. These two candidate JMJ-C members were also found to render salinity tolerance when over-expressed in yeast cells. Thus, the present study helps in further structural as well as functional characterization of JMJ-C genes under salinity stress in Oryza species.

Keywords: Abiotic stress; Evolution; Histone modification; Rice; Salinity stress

DOI: https://doi.org/10.1016/j.plaphy.2018.06.031

Eur J Med Genet. 2018 Jun 27. pii: S1769-7212(18)30349-5. [Epub ahead of print]

An 18 bps in-frame deletion mutation in RUNX2 gene is a population polymorphism rather than a pathogenic variant.

Jamil Amjad Hashmi, Ahmad Almatrafi, Muhammad Latif, Abdul Nasir, Sulman Basit.

We recruited a family with an affected child exhibiting features of cleidocranial dysplasia with some phenotypic variations from reported cases. Whole exome sequencing data analysis identified an 18-bps heterozygous in-frame deletion variant (c.243-260delGGCGGCTGCGGCGGCGGC) in the RUNX2 gene. Sanger sequencing validated the presence of deletion in affected individual. Initially, we considered this variant as a causal mutation for the patient's phenotype based on previous report(s). However, further analysis of variant revealed that it is present in high frequency in variety of genome variation databases. Moreover, segregation analysis discovered the presence of variant in mother as well. Furthermore, screening of population matched control individuals revealed that the variant is present in apparently healthy individuals as well. Three-dimensional structures of the wild-type and mutant RUNX2 protein (p.Ala82_Ala87del) were analysed and it was found that both wild type and mutant protein show similar secondary structure pattern. Presence of RUNX2 deletion variant (c.243-260delGGCGGCTGCGGCGGCGGC) in control individuals, its high population frequency, benign effect on the overall protein structure lead to the argument that this variant is a population polymorphism and not a pathogenic mutation.

Keywords: Cleidocranial dysplasia; Polymorphism; RUNX2 mutation; Saudi family

DOI: https://doi.org/10.1016/j.ejmg.2018.06.013