Multiple sequence alignment of three zinc fingers of select KLF proteins and Wilms’ tumor proteins.

<p>Two new KLF groups (predicted KLF18 proteins and Zfp352/Zfp352l/Zfp353) are shown above the red line. Known KLF members below the red line are grouped according to frequently well-supported clusters found in separate phylogenetic studies. Conserved cysteines and histidines involved in metal binding are on black background. Three conserved DNA base-interacting arginines are shaded in magenta. Three negatively charged residues interacting with the three arginines are shaded in grey, with connections for interaction pairs shown above the alignment. Negatively charged residues (aspartate and glutamate) and positively charged residues (lysine, arginine, and histidine) are colored red and blue, respectively. Insertion and deletion events are highlighted in cyan. Species name abbreviations are: bt, <i>Bos taurus</i> (cow); cf, <i>Canis familaiaris</i> (domestic dog); ch, <i>Choloepus hoffmanni</i> (two-toed sloth); cj, <i>Callithrix jacchus</i> (common marmoset); cp, <i>Cavia porcellus</i> (guinea pig); dn, <i>Dasypus novemicinctus</i> (nine-banded armadillo); dr, <i>Danio rerio</i> (zebrafish); ec, <i>Equus caballus</i> (horse); hs, <i>Homo sapiens</i> (human); la, <i>Loxodonta Africana</i> (African Savannah elephant); mm, <i>Mus musculus</i> (mouse); oc, <i>Oryctolagus cuniculus</i> (rabbit); rn, <i>Rattus norvegicus</i> (rat); sa, <i>Sorex araneus</i> (common shrew); tb, <i>Tupaia belangeri</i> (tree shrew); tm, <i>Trichechus manatus latirostris</i> (the Floirida manatee); xt, <i>Xenopus tropicalis</i> (Western clawed frog). Species names are colored as follows - black: Euarchontoglires; red: Laurasiatheria; green: Afrotheria; magenta: Xenarthra; and blue: non-mammalian vertebrates.</p

Chromosome localization and gene synteny of <i>KLF17</i> and <i>KLF18</i> in vertebrate genomes.

<p>Chromosome (Chr) or scaffold (Sca.) numbers are shown to the left of the gene order diagrams, with ‘r’ after the chromosome number denoting the reverse strand. In most of the placental mammalian genomes, <i>KLF17</i> and <i>KLF18</i> are neighbors arranged in a tail-to-tail fashion, and they are sandwiched by three upstream genes (abbreviations: <i>B</i>: <i>B4GALT2</i>; <i>C</i>: <i>CCDC24</i>; and <i>S</i>: <i>SLC6A9</i>) and three downstream genes (abbreviations: <i>D</i>: <i>DMAP1</i>; <i>E</i>: <i>ERI3</i>; and <i>R</i>: <i>RNF220</i>). Such a gene context for <i>KLF17</i> is largely preserved in non-mammalian vertebrates including chicken, frog, and zebrafish. Copy number expansions of <i>KLF18</i> (the number of expanded genes shown beside the brackets) were observed in rat, guinea pig, and rabbit. The aardvark <i>KLF18</i> with pseudogene evidence is shown with dashed outline. The tree on the left shows the relationships of mammals and other vertebrates. Roots of four major groups (superorders) of placental mammals are shown in circles - E: Euarchontoglires; L: Laurasiatheria; A: Afrotheria; and X: Xenarthra.</p

Gene synteny and a model of evolution for <i>Zfp352</i>, <i>Zfp352l</i>, and <i>Zfp353</i>.

<p>(A) Gene synteny of <i>Zfp352</i>, <i>Zfp352l</i>, and <i>Zfp353</i> in the mouse and rat genomes. (B) A model of expansion of mouse KLF members. LGD and RT are abbreviations for local gene duplication and retrotransposition, respectively. <i>UrZfp352</i> represents the ancestor gene of extant <i>Zfp352</i> and <i>Zfp352l</i>.</p

A phylogenetic tree of SP/KLF proteins with the human Wilms’ tumor protein (human_WT1) as an out-group.

<p>Branch support values 80 or above are in bold. Each protein node is denoted by the species name followed by the protein name.</p

Sequence logo of the repeated segments in the N-terminal regions of predicted KLF18 proteins.

<p>Four-residue sequence segments matching the pattern “[YC]x[sE][QH]” are extracted from predicted KLF18 proteins. These segments were extended by five residues both N-terminally and C-terminally to obtain segments of 14 residues. Sequence logo was generated for the expanded segments by the program WebLogo [44].</p

Conceptual example of our multiple regression method applied to a single column (Y465 of AMHR2; full result in Table S2).

<p>(left) Characters shown ordered by species MLS. For each non-human species, we calculate the similarity score (";BLOSUM80";) for the species’ amino acid character versus the human character (here Y); e.g., this score for Tursiops would be the similarity score for H versus Y, which is 2. (right) We then fit the MLS of all non-human species to their similarity scores; e.g., Tursiops’ contribution to this fit is the point (52, 2). Not shown are the steps to correct for mutation rate and shared phylogeny, and the simultaneous fit of body mass. For this column, the data provide relatively strong support for a nonzero slope in the fit of similarity to MLS, even given trends in mutation rate, phylogeny, and body mass, and so this position is assigned a relatively significant p-value (<i>p_MLS</i><0.01).</p

Predicted secondary structure in all positions of the human proteome and in two subsets of longevity-selected positions.

<p>Predicted secondary structure in all positions of the human proteome and in two subsets of longevity-selected positions.</p

A New Family of Predicted Krüppel-Like Factor Genes and Pseudogenes in Placental Mammals

<div><p>Krüppel-like factors (KLF) and specificity proteins (SP) constitute a family of zinc-finger-containing transcription factors that play important roles in a wide range of processes including differentiation and development of various tissues. The human genome possesses 17 KLF genes (<i>KLF1</i>–<i>KLF17</i>) and nine SP genes (<i>SP1</i>–<i>SP9</i>) with diverse functions. We used sequence similarity searches and gene synteny analysis to identify a new putative KLF gene/pseudogene named <i>KLF18</i> that is present in most of the placental mammals with sequenced genomes. <i>KLF18</i> is a chromosomal neighbor of the <i>KLF17</i> gene and is likely a product of its duplication. Phylogenetic analyses revealed that mammalian predicted KLF18 proteins and KLF17 proteins experienced elevated rates of evolution and are grouped with KLF1/KLF2/KLF4 and non-mammalian KLF17. Predicted KLF18 proteins maintain conserved features in the zinc fingers of the SP/KLF family, while possessing repeats of a unique sequence motif in their N-terminal regions. No expression data have been reported for <i>KLF18</i>, suggesting that it either has highly restricted expression patterns and specialized functions, or could have become a pseudogene in extant placental mammals. Besides <i>KLF18</i> genes/pseudogenes, we identified several <i>KLF18</i>-like genes such as <i>Zfp352</i>, <i>Zfp352</i>-like, and <i>Zfp353</i> in the genomes of mouse and rat. These <i>KLF18</i>-like genes do not possess introns inside their coding regions, and gene expression data indicate that some of them may function in early embryonic development. They represent further expansions of KLF members in the murine lineage, most likely resulted from several events of retrotransposition and local gene duplication starting from an ancient spliced mRNA of <i>KLF18</i>. </p> </div

OrthoMaM alignment of the C-terminal regions of AMHR2 ortholog kinase domains.

<p>Orthologs are ordered by species MLS. The five longevity-selected positions in this region (Y465, T469, F473, E513, and H515) are highlighted in gray. ";X"; indicates regions that we masked due to excessive divergence (Section 2.1). Long regions of gaps are not necessarily real genome deletions, but are more likely to have been missed during genome assembly or annotation.</p

AMHR2 kinase domain mapped onto experimental structure of BMPR2 kinase domain.

<p>All eight longevity-selected positions found in this domain are shown as black sticks and are further described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038595#pone.0038595.s003" target="_blank">Table S2</a>. The five longevity-selected positions discussed in the text are labeled; they are found on the αG–αH loop (Y465, T469, and F473) and the C-terminal loop following αI (E513 and H515).</p