Evolutionary analysis of a novel zinc ribbon in the N-terminal region of threonine synthase

<p>Threonine synthase (TS) catalyzes the terminal reaction in the biosynthetic pathway of threonine and requires pyridoxal phosphate as a cofactor. TSs share a common catalytic domain with other fold type II PALP dependent enzymes. TSs are broadly grouped into two classes based on their sequence, quaternary structure, and enzyme regulation. We report the presence of a novel zinc ribbon domain in the N-terminal region preceding the catalytic core in TS. The zinc ribbon domain is present in TSs belonging to both classes. Our sequence analysis reveals that archaeal TSs possess all zinc chelating residues to bind a metal ion that are lacking in the structurally characterized homologs. Phylogenetic analysis suggests that TSs with an N-terminal zinc ribbon likely represents the ancestral state of the enzyme while TSs without a zinc ribbon must have diverged later in specific lineages. The zinc ribbon and its N- and C-terminal extensions are important for enzyme stability, activity and regulation. It is likely that the zinc ribbon domain is involved in higher order oligomerization or mediating interactions with other biomolecules leading to formation of larger metabolic complexes.</p

Additional file 1: of A novel RING finger in the C-terminal domain of the coatomer protein Îą-COP

Methods. Methods employed in this study (DOCX 32 kb

Proliferation and apoptosis in testicular tissue after / / experimental damage

Carbohydrate-degrading enzymes, arranged by GH family. (XLS 67 kb

Comparative representation of homologous protein distribution within the genomes.

<p>Proteome dataset from each genome was subjected to BLASTp to identify homologous proteins between the genomes with an E-value cutoff of 1e-5, query coverage of 50% and identity of 35%. Protein distribution between different combinations of genomes was identified and is represented as a 3D-graph. X, Y and Z-axis respectively denote genome name, the number of proteins and the genome combination.</p

Venn diagram of comparative annotations of <i>Myxococcus xanthus</i> DK1622 using RAST, Glimmer, xBASE and the original NCBI annotation.

<p>All genome annotations were mapped to each other using BLASTp [E-value cutoff: 1e^-5]. The diagram depicts the homologous proteins shared between two or more annotations (overlapping area) along with unique proteins (yellow shade). RAST, Glimmer, xBASE and the original NCBI annotations are shown in brick red, green, orange and blue colors respectively. The number of annotated proteins using the respective annotation pipeline is shown in the box.</p

Circular representation of the <i>M</i>. <i>hansupus</i> complete genome.

<p><b>Circles</b> (from inside to outside) <b>1 and 2</b> (GC content; black line and GC skew; magenta and green lines), <b>circle 3</b> (<i>M</i>. <i>hansupus</i>; red circle); <b>circle 4</b> (mapped <i>Myxococcus fulvus</i> HW-1 genome with <i>M</i>. <i>hansupus</i> genome; green circle); <b>circle 5</b> (mapped <i>Myxococcus xanthus</i> DK1622 genome with <i>M</i>. <i>hansupus</i> genome; purple circle); <b>circle 6</b> (mapped <i>Myxococcus xanthus</i> DZF1 genome with <i>M</i>. <i>hansupus</i> genome; Orange circle); <b>circle 7</b> (mapped <i>Myxococcus xanthus</i> DZ2 genome with <i>M</i>. <i>hansupus</i> genome; blue circle); <b>circle 8</b> (mapped <i>Myxococcus stipitatus</i> genome with <i>M</i>. <i>hansupus</i> genome; yellow circle). BRIG 0.95 was used to build the circular representation [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148593#pone.0148593.ref053" target="_blank">53</a>]. Mapping studies were done using BLASTn with an E-value cut-off 1e^-5.</p

Assembly statistics for <i>M</i>. <i>hansupus</i>.

<p>Assembly statistics for <i>M</i>. <i>hansupus</i>.</p

Additional file 3: of Evolutionary relationships between heme-binding ferredoxin α + β barrels

Ferredoxin α + β barrel structures in PDB (current till 30-12-15). (DOC 57 kb

General features of genus <i>Myxococcus</i> genomes as annotated by RAST.

<p>General features of genus <i>Myxococcus</i> genomes as annotated by RAST.</p

Phylogeny based on housekeeping proteins.

<p>Twenty-eight concatenated housekeeping proteins were used to generate ML based phylogenetic tree using MEGA 6.06 [model: JTT matrix; bootstrap: 100]. <i>Corallococcus coralloides</i> DSM 2259, <i>Cystobacter fuscus</i> DSM 2262, <i>Anaeromyxobacter dehalogenans</i> 2CP-C, <i>Sorangium cellulosum</i> Soce56, and <i>Bdellovibrio exovorus</i> JSS were used as outgroup species in this study. Bootstrap values corresponding to the tree nodes are provided.</p