Journal: BMC Genomics

Article Title: Identification of TTAGGG-binding proteins in Neurospora crassa , a fungus with vertebrate-like telomere repeats

doi: 10.1186/s12864-015-2158-0

Figure Lengend Snippet: Experimental design and results of Neurospora telomere pull-down. a Schematic workflow of the label-free telomere interaction screen. Extracts of N. crassa were incubated with either a telomeric probe (TTAGGG) or a shuffled control sequence (TGTGAG). For each probe, four pull-downs were performed independently and measured using high resolution mass spectrometry. To identify TTAGGG repeat binding proteins the MaxLFQ algorithm was used to compare individual peptide intensities between the telomeric bait and the shuffled control sequence. b Volcano plot of the telosome of N. crassa . We identified 12 proteins (two-sided t -test, Welch, FDR = 0.05) to be enriched at the telomeric TTAGGG probe compared to the shuffled control. c Heatmap representation of z-scored enrichment values obtained from MaxLFQ intensities for the 12 significantly enriched Neurospora proteins validates reproducible binding behaviour in each replicate

Article Snippet: Fig. 2 Structure and evolutionary conservation of TTAGGG-associated proteins. a Domain structure of Neurospora proteins reported by InterPro 46.0 ( http://www.ebi.ac.uk/interpro/ ).

Techniques: Incubation, Control, Sequencing, Mass Spectrometry, Binding Assay

Journal: BMC Genomics

Article Title: Identification of TTAGGG-binding proteins in Neurospora crassa , a fungus with vertebrate-like telomere repeats

doi: 10.1186/s12864-015-2158-0

Figure Lengend Snippet: Structure and evolutionary conservation of TTAGGG-associated proteins. a Domain structure of Neurospora proteins reported by InterPro 46.0 ( http://www.ebi.ac.uk/interpro/ ). The position of the domains and length of the proteins are drawn to scale. b Overview of the corresponding homologs in S. cerevisiae , S. pombe , C. albicans and A. fumigatus as determined by sequence similarity search. The telomeric motifs are indicated for each species. Blast hits in black are true homologs whereas blast hits in white showed weak homology and the reverse blast identified a different homologous protein. The first e-value represents the search of the N. crassa protein vs. the respective species and the second e-value the reverse blast search. N. crassa names in blue are proposed based on experimental data from this study

Article Snippet: Fig. 2 Structure and evolutionary conservation of TTAGGG-associated proteins. a Domain structure of Neurospora proteins reported by InterPro 46.0 ( http://www.ebi.ac.uk/interpro/ ).

Techniques: Sequencing

Journal: BMC Genomics

Article Title: Identification of TTAGGG-binding proteins in Neurospora crassa , a fungus with vertebrate-like telomere repeats

doi: 10.1186/s12864-015-2158-0

Figure Lengend Snippet: Characterization of binding mode of Neurospora TTAGGG-binding proteins. a Western blots from pull-downs of recombinantly expressed Neurospora proteins incubated with concatemerized oligonucleotides of telomeric repeats (TTAGGG) or a shuffled control sequence (TGTGAG) to check for direct binding. b Comparative binding test for double-stranded versus single-stranded telomeric DNA. Direct TTAGGG-binding proteins from ( a ) were incubated with increasing amounts of single-stranded TTAGGG repeats. Only NCU2404 binding is decreased at higher ssTTAGGG oligonucleotide concentrations revealing the other 5 proteins as double-strand binders. c Western blot of the competition assay of NCU02404 shows that its binding can only be competed with ssTTAGGG but not with an unrelated control sequence

Article Snippet: Fig. 2 Structure and evolutionary conservation of TTAGGG-associated proteins. a Domain structure of Neurospora proteins reported by InterPro 46.0 ( http://www.ebi.ac.uk/interpro/ ).

Techniques: Binding Assay, Western Blot, Incubation, Control, Sequencing, Competitive Binding Assay

Journal: BMC Genomics

Article Title: Identification of TTAGGG-binding proteins in Neurospora crassa , a fungus with vertebrate-like telomere repeats

doi: 10.1186/s12864-015-2158-0

Figure Lengend Snippet: Model for the N. crassa telosome based on our mass spectrometric screen and the binding analysis. Neurospora has at least six double strand binding proteins (five were validated experimentally [ green ] and one was inferred from homology [ grey ]) and two single-strand binding proteins of which we have experimentally validated one [ yellow ] while the other [ grey ] was inferred from homology. Connections indicate homologs between Neurospora and the other yeast species

Article Snippet: Fig. 2 Structure and evolutionary conservation of TTAGGG-associated proteins. a Domain structure of Neurospora proteins reported by InterPro 46.0 ( http://www.ebi.ac.uk/interpro/ ).

Techniques: Binding Assay

Journal: BMC Genomics

Article Title: Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe

doi: 10.1186/s12864-024-09966-w

Figure Lengend Snippet: Structural features of the ZoPP2Cs. A Multiple sequences alignment of ZoPP2C conserved domains. B 3D structural model of PP2C structural domains. C ZoPP2C sequence logos for conserved domains, generated using Jalview (v2.10.3). The height of the symbols within the stack indicates the relative frequency of each amino acid. Logos were created by comparing multiple ZoPP2C protein sequences

Article Snippet: According to the Interpro ( https://www.ebi.ac.uk/interpro/ ) analysis, four major ZoPP2C protein structural domains including PPM-type phosphatase-like domain, PP2Cc, PP2C-SIG, PP2C_like were identified in 97 ZoPP2Cs’ amino acids.

Techniques: Sequencing, Generated

Journal: BMC Genomics

Article Title: Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe

doi: 10.1186/s12864-024-09966-w

Figure Lengend Snippet: Phylogenetic analysis of the PP2C genes. Phylogenetic trees for A. thaliana and ginger PP2C gene families were modelled using maximum likelihood (ML) and 1000 bootstrap replicates were selected. Bootstrap levels are indicated by different colored circles. Red stars specifically indicate the ginger ZoPP2C sequences

Article Snippet: According to the Interpro ( https://www.ebi.ac.uk/interpro/ ) analysis, four major ZoPP2C protein structural domains including PPM-type phosphatase-like domain, PP2Cc, PP2C-SIG, PP2C_like were identified in 97 ZoPP2Cs’ amino acids.

Techniques:

Journal: BMC Genomics

Article Title: Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe

doi: 10.1186/s12864-024-09966-w

Figure Lengend Snippet: Phylogenetic relationships and gene structure of the ZoPP2Cs. A The Motif pattern of ZoPP2Cs. The protein was comprised of motifs labelled 1–20 and featured in varied, colored boxes. Sequences for each motif can be found in Fig. S . Phylogenetic analysis was conducted on the complete sequence of the ginger ZoPP2C proteins using MEGA X software. B PP2C domains of ZoPP2Cs. The blue color represented the PP2C domain. C The exon–intron structures of ZoPP2Cs. Blue boxes indicated the 5' and 3' untranslated regions, while red boxes indicated the exons. Black lines represent the introns. The length of the protein can be estimated using the scale located at the bottom

Article Snippet: According to the Interpro ( https://www.ebi.ac.uk/interpro/ ) analysis, four major ZoPP2C protein structural domains including PPM-type phosphatase-like domain, PP2Cc, PP2C-SIG, PP2C_like were identified in 97 ZoPP2Cs’ amino acids.

Techniques: Sequencing, Software

Journal: BMC Genomics

Article Title: Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe

doi: 10.1186/s12864-024-09966-w

Figure Lengend Snippet: Schematic diagram of ZoPP2Cs collinearity in ginger. The red lines indicated ZoPP2C gene pair duplications in ginger

Article Snippet: According to the Interpro ( https://www.ebi.ac.uk/interpro/ ) analysis, four major ZoPP2C protein structural domains including PPM-type phosphatase-like domain, PP2Cc, PP2C-SIG, PP2C_like were identified in 97 ZoPP2Cs’ amino acids.

Techniques:

Journal: BMC Genomics

Article Title: Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe

doi: 10.1186/s12864-024-09966-w

Figure Lengend Snippet: Cis-regulatory elements of the ZoPP2C promoters. A Box plots of ZoPP2C promoters. Box plots depicted the expression levels of ZoPP2Cs during various growth stages under different stress conditions. B Heatmap of the ZoPP2C promoters. Heatmap displayed the number of cis-elements, whereby larger numbers were highlighted in red and smaller numbers in blue. Histograms exhibited the proportion of varied cis-elements, with diverse colors denoting distinct types of cis-elements

Article Snippet: According to the Interpro ( https://www.ebi.ac.uk/interpro/ ) analysis, four major ZoPP2C protein structural domains including PPM-type phosphatase-like domain, PP2Cc, PP2C-SIG, PP2C_like were identified in 97 ZoPP2Cs’ amino acids.

Techniques: Expressing

Journal: BMC Genomics

Article Title: Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe

doi: 10.1186/s12864-024-09966-w

Figure Lengend Snippet: Expression profiles of ZoPP2C gene family. Hierarchical clustering analysis was conducted on the expression profiles of the ZoPP2Cs across 15 ginger samples collected from various tissues and different developmental stages. Normalized values (log2FPKM) were used to represent the expression patterns by color gradient, ranging from blue (negative expression level) to red (positive expression level). Different groups represent G: root, R1-R5: five developmental stages of ginger, S: stem, S90: 90d ginger stem, R90: 90d ginger root, L90: 90d ginger leaf, Rh90: 90d ginger rhizome, RO: red outer epidermis of ginger, RI: red outer epidermal inner tissues of stem, Ye: yellow rhizome, Gr: green rhizome

Article Snippet: According to the Interpro ( https://www.ebi.ac.uk/interpro/ ) analysis, four major ZoPP2C protein structural domains including PPM-type phosphatase-like domain, PP2Cc, PP2C-SIG, PP2C_like were identified in 97 ZoPP2Cs’ amino acids.

Techniques: Expressing

Journal: BMC Genomics

Article Title: Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe

doi: 10.1186/s12864-024-09966-w

Figure Lengend Snippet: Relative expression levels of 12 selected ZoPP2C genes under chilling treatment by qRT-PCR. Blue color represents the gene expression profile in ginger leaves. Red color represents the expression profile in ginger rhizomes. The four treatments were 26°C, 10°C, 2°C, and 2°C + melatonin (LT + MT). Error bars represent the standard deviation of three independent biological replicates

Article Snippet: According to the Interpro ( https://www.ebi.ac.uk/interpro/ ) analysis, four major ZoPP2C protein structural domains including PPM-type phosphatase-like domain, PP2Cc, PP2C-SIG, PP2C_like were identified in 97 ZoPP2Cs’ amino acids.

Techniques: Expressing, Quantitative RT-PCR, Gene Expression, Standard Deviation