Gao Y et al. (2012), Comparative Analysis of SWIRM Domain-Containing...

ECB-ART-42549

Comp Funct Genomics 2012 Jan 01;2012:310402. doi: 10.1155/2012/310402.

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Comparative Analysis of SWIRM Domain-Containing Proteins in Plants.

Gao Y , Yang S , Yuan L , Cui Y , Wu K .

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Chromatin-remodeling complexes affect gene expression by using the energy of ATP hydrolysis to locally disrupt or alter the association of histones with DNA. SWIRM (Swi3p, Rsc8p, and Moira) domain is an alpha-helical domain of about 85 residues in chromosomal proteins. SWIRM domain-containing proteins make up large multisubunit complexes by interacting with other chromatin modification factors and may have an important function in plants. However, little is known about SWIRM domain-containing proteins in plants. In this study, 67 SWIRM domain-containing proteins from 6 plant species were identified and analyzed. Plant SWIRM domain proteins can be divided into three distinct types: Swi-type, LSD1-type, and Ada2-type. Generally, the SWIRM domain forms a helix-turn-helix motif commonly found in DNA-binding proteins. The genes encoding SWIRM domain proteins in Oryza sativa are widely expressed, especially in pistils. In addition, OsCHB701 and OsHDMA701 were downregulated by cold stress, whereas OsHDMA701 and OsHDMA702 were significantly induced by heat stress. These observations indicate that SWIRM domain proteins may play an essential role in plant development and plant responses to environmental stress.

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Genes referenced: LOC115925415 LOC583082 LOC590215

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	Figure 1. Phylogenetic analysis of SWIRM domain-containing proteins in plants. The neighbor joining phylogenetic tree constructed by MEGA4 summarizes the evolutionary relationships among the 67 members of the SWIRM domain-containing proteins from Arabidopsis thaliana (At), Medicago truncatula (Mt), Oryza sativa L. ssp. Japonica (Os), Physcomitrella patens (Pp), Populus trichocarpa (Pt), and Zea mays (Zm).
	Figure 2. Structure-base sequence alignment of SWIRM domain subtypes. The sequence alignment was produced using Cluatal X. Resulting sequences were then adjusted manually using the GeneDoc software. The secondary structure was predicted by Jpred and PSIPRED. (a) Alignment of the SWIRM domain sequences in Oryza sativa. The coloring represents the conservation profile of amino acid residues distinguished by the following amino acid classes: hydrophobic residues are indicated by shaded black, charged residues (ED) by shaded blue, positive residues (RK) by shaded red, polar residues (YNRDTK) by shaded light green, amphoteric residues (RQ) by shaded green, small residues (NDSTPASV) by shaded yellow, aliphatic residues (LIAV) by shaded gray, and aromatic residues (YHWH) by shaded pink. (b) Alignment of the Swi3-type SWIRM domain sequences. The shaded blocks indicate several highly conserved residues by the alignment of SWIRM domain in Oryza sativa and Arabidopsis thaliana. (c) Alignment of the LSD1-type SWIRM domain sequences. The shaded blocks indicate several highly conserved residues by the alignment of SWIRM domains in Oryza sativa and Arabidopsis thaliana. (d) Alignment of the Ada2-type SWIRM domain sequences.
	Figure 3. Conserved domains of SWIRM domain-containing proteins in Oryza sativa. (a) The neighbor joining phylogenetic tree constructed by MEGA4 summarizes the evolutionary relationships among the 11 members of the SWIRM domain-containing proteins from Oryza sativa. (b) The conserved domains of SWIRMs in Oryza sativa were drawn by DOG 2.0 with their corresponding amino acid lengths.
	Figure 4. Expression patterns of genes encoding SWIRM family proteins in Oryza sativa based on Genevestigator. (a)-(b) Expression patterns of SWIRM genes in different developmental stages and different anatomical parts. The darkest blue color represents the maximum level of expression for a given gene across all measurements available in the database for this gene. This means that color intensities can only be compared between elements from the same gene but not with those from other genes. The expression potential of a gene is a robust measure for the maximum of the expression level for this gene. The expression potential is defined as the average of the top 1% signal values across all samples for a given probe set in a given platform. (c) Expression patterns of SWIRM genes induced by abiotic stress. Green-red color coding bar represents ratios of treatment versus control values. Gray is used to indicate that both treatment and control are in the background range and that therefore the ratio is not robust. The background threshold B(x) is a probe set specific expression level. It is defined as B(x) ≤ 50% quantile of all signals measured of probe set x having “absent” calls (P value > 0.05) according to MAS5.

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