Secondary structure pattern and sequence conservation of FLZ domain.

<p>(A) Secondary structure conservation of FLZ domain. Red color indicates alpha helix and blue color indicates beta-sheet. Confidence gradient of secondary structure formation is given on the top. (B) Sequence logo of <i>Arabidopsis</i>, <i>Medicago,</i> poplar and rice FLZ domains showing amino acid conservation.</p

Schematic representation of domain organization in FLZ protein family.

<p>The FLZ proteins are scanned by InterProScan to identify conserved domains. <i>A. thaliana</i> FLZ1 is shown as a representative model for proteins which contain FLZ domain only. Proteins which possess other domains along with FLZ are also shown. The domains are abbreviated as follows, FLZ (FCS like zinc finger, PF04570), PPR (Pentatricopeptide Repeat, PF01535), Cupin (Cupin 1, PF00190), ICF (Ion channel family, PF00520), CND (Cyclic nucleotide-binding domain, PF00027) and DUF3354 (Domain of unknown function 3354, PF11834).</p

Sub-cellular localization of FLZ1 and PFA-DSP3 in onion epidermal cells.

<p>(A) Vector alone. (B) FLZ1. (C) PFA-DSP3. Left to right, YFP only, bright field, merged. FLZ1 is localized in both nucleus and cytoplasm while PFA-DSP3 is exclusively localized in nucleus. YFP were excited at 514 nm and emission was recorded at 530 nm.</p

DUF581 Is Plant Specific FCS-Like Zinc Finger Involved in Protein-Protein Interaction

<div><p>Zinc fingers are a ubiquitous class of protein domain with considerable variation in structure and function. Zf-FCS is a highly diverged group of C₂-C₂ zinc finger which is present in animals, prokaryotes and viruses, but not in plants. In this study we identified that a plant specific domain of unknown function, DUF581 is a zf-FCS type zinc finger. Based on HMM-HMM comparison and signature motif similarity we named this domain as <u>F</u>CS-<u>L</u>ike <u>Z</u>inc finger (FLZ) domain. A genome wide survey identified that FLZ domain containing genes are bryophytic in origin and this gene family is expanded in spermatophytes. Expression analysis of selected <i>FLZ</i> gene family members of <i>A. thaliana</i> identified an overlapping expression pattern suggesting a possible redundancy in their function. Unlike the zf-FCS domain, the FLZ domain found to be highly conserved in sequence and structure. Using a combination of bioinformatic and protein-protein interaction tools, we identified that FLZ domain is involved in protein-protein interaction.</p></div

Distribution of <i>FLZ</i> gene family in sequenced genomes.

<p>Distribution of <i>FLZ</i> gene family in sequenced genomes.</p

FLZ acts as the module for protein-protein interaction.

<p>(A) FLZ1 interacts with PFA-DSP3 and STH2 in Y2H. Murine p53 and SV40 large T-antigen interaction taken as positive control and p53 and lamin interaction is taken as negative control. (B) The deletion constructs of FLZ1, N-terminal (1–88 amino acids), FLZ (89–140 amino acids) and C-terminal (141–177 amino acids). (C) Y2H with deletion constructs of FLZ1 with PFA-DSP3 and STH2 showing FLZ is essential for their interaction. (D) And (E) beta-galactosidase activity of full length FLZ1 and deletion constructs interaction with PFA-DSP3 and STH2.</p

Expression analysis of <i>Arabidopsis thaliana FLZ</i> gene family in different developmental stages and tissues using real-time PCR.

<p><i>UBQ10</i> is used as endogenous control. The absolute expression is calculated from ΔCT value. Graphs represent average and error bars represent mean ± SD of two biological replicates with three technical replicates each. X axis represent samples and Y axis represent absolute expression value. Samples are abbreviated in graph is as follows, RS, radicle emerged; CS, cotyledon stage seedling; LS, 2 leaves stage seedling; MR, mature plant root; ML, mature bolts rosette leaf; FB, flower bud; FO, flower open; SS, silique small; SM, silique mature.</p

Analysis of evolutionary pressure on <i>FLZ</i> genes (A) Ka/Ks ratio of gene pair of <i>P</i>. <i>patens</i> and <i>S</i>. <i>moellendorffii</i>, <i>P</i>. <i>abies</i> and duplicated gene pairs of <i>A</i>. <i>trichopoda</i>, <i>A</i>. <i>thaliana</i> and <i>O</i>. <i>sativa</i>. The Ka/Ks ratio of whole gene and FLZ domain region is individually calculated. (B) averaged Ka/Ks ratio of whole gene and FLZ domain region of selected species studied. (C) and (D) averaged Ka/Ks ratio between <i>A</i>. <i>thaliana</i> (C) and <i>O</i>. <i>sativa</i> (D) genes and their orthologous genes from selected species.

<p>The Ka/Ks ratio of each pair is given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134328#pone.0134328.s010" target="_blank">S2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134328#pone.0134328.s011" target="_blank">S3</a> Tables.</p

Chromosomal location and evolutionary history of <i>Oryza sativa FLZ</i> gene family.

<p>The gene duplication analysis is done using PLAZA v2.5and verified by the position of duplicates in phylogram. Solid line connects the block duplicates and dotted line connects the tandem duplicates. The numbers indicated at the top represents the chromosome number.</p

Analysis of phylogenetic origin of FLZ proteins.

<p>Phylogram of <i>P</i>. <i>patens</i>, <i>S</i>. <i>moellendorffii</i>, <i>P</i>. <i>abies</i> and <i>A</i>. <i>trichopoda</i> FLZ proteins was inferred by BI method based on JTT model. The numbers adjacent to the branches represent posteriori probability values. The tree is drawn to scale, with branch lengths measured in the number of amino acid substitutions per site.</p