56 research outputs found
Experimental evidence for the role of domain swapping in the evolution of the histone fold
No full textThe histone fold forms the fundamental endoskeleton of the protein core of the nucleosome and is also found in several transcription factors. We have investigated the evolutionary origins of this ubiquitous protein motif, which is found soluble exclusively as an antiparallel (handshake motif) dimer. We introduced a three amino acid insertion into the middle of a homodimeric archaeal histone fold motif. The engineered molecule was found to be a soluble and stable monomer with properties consistent with a four-helix-bundle protein. The experimental evidence presented here support the hypothesis that the handshake association motif characteristic of present-day histone dimers is the evolutionary product of domain swapping between two four-helix bundle domains, each of which derived from the tandem duplication of a primitive helix–strand–helix unit.</jats:p
Mosaic - A Cloud Platform for NGS High-Throughput Analysis
No full textExploration of the microbiome is an exciting new area of science. There has been an explosion of new tools designed for the microbiome space. Many of these tools require considerable computational resources and can prove challenging to install and run. DNAnexus has created Mosaic, a cloud platform for microbiome informatics. Mosaic allows third-party bioinformatics tools to run on cloud instances through a graphical user interface (GUI). Mosaic handles computational microbiome analysis and is bringing together the microbiome community for increased communication and collaboration. It offers tool comparison and tool usage without the need for a high-performance computing cluster or extensive programming experience.</p
Selecting One of Several Mating Types through Gene Segment Joining and Deletion in Tetrahymena thermophila
No full textThe unicellular eukaryote Tetrahymena thermophila has seven mating types. Cells can mate only when they recognize cells of a different mating type as non-self. As a ciliate, Tetrahymena separates its germline and soma into two nuclei. During growth the somatic nucleus is responsible for all gene transcription while the germline nucleus remains silent. During mating, a new somatic nucleus is differentiated from a germline nucleus and mating type is decided by a stochastic process. We report here that the somatic mating type locus contains a pair of genes arranged head-to-head. Each gene encodes a mating type-specific segment and a transmembrane domain that is shared by all mating types. Somatic gene knockouts showed both genes are required for efficient non-self recognition and successful mating, as assessed by pair formation and progeny production. The germline mating type locus consists of a tandem array of incomplete gene pairs representing each potential mating type. During mating, a complete new gene pair is assembled at the somatic mating type locus; the incomplete genes of one gene pair are completed by joining to gene segments at each end of germline array. All other germline gene pairs are deleted in the process. These programmed DNA rearrangements make this a fascinating system of mating type determination.The unicellular eukaryote Tetrahymena thermophila has seven mating types. Cells can mate only when they recognize cells of a different mating type as non-self. As a ciliate, Tetrahymena separates its germline and soma into two nuclei. During growth the somatic nucleus is responsible for all gene transcription while the germline nucleus remains silent. During mating, a new somatic nucleus is differentiated from a germline nucleus and mating type is decided by a stochastic process. We report here that the somatic mating type locus contains a pair of genes arranged head-to-head. Each gene encodes a mating type-specific segment and a transmembrane domain that is shared by all mating types. Somatic gene knockouts showed both genes are required for efficient non-self recognition and successful mating, as assessed by pair formation and progeny production. The germline mating type locus consists of a tandem array of incomplete gene pairs representing each potential mating type. During mating, a complete new gene pair is assembled at the somatic mating type locus; the incomplete genes of one gene pair are completed by joining to gene segments at each end of germline array. All other germline gene pairs are deleted in the process. These programmed DNA rearrangements make this a fascinating system of mating type determination
Correction: Selecting One of Several Mating Types through Gene Segment Joining and Deletion in Tetrahymena thermophila.
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The germline <i>mat</i> locus contains six incomplete mating type gene pairs.
No full text<p>The locus is a 91-kb tandem array of six incomplete, head-to-head mating type gene pairs, in the order II, V, VI, IV, VII, and III (order established as shown in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001518#pbio-1001518-g004" target="_blank">Figure 4</a>). Each gene pair begins to the left with the <i>MTA</i> conserved TM exon (diagonal lines) and ends with the <i>MTB</i> conserved TM exon (dark gray). Only the terminal genes (<i>MTA2</i> and <i>MTB3</i>) have full length versions of their TM exons. The mating type-specific, somatic-destined segment for each mating type gene pair, which includes the 5′ <i>MTA</i> and <i>MTB</i> segments and the intervening upstream spacer region (putative promoter), is shown as a single thick colored bar. Between the TM exon segments of adjacent gene pairs, there is a small amount of germline-limited sequence (GLS; black). Several IESs are located within the mating type-specific segments (also black). Excluding IES sequence, the mating type-specific segments are of comparable size: II, 8,673 bp; V, 9,132 bp; VI, 9,352 bp; IV, 8,450 bp; VII, 8,277 bp; and III, 8,384 bp. Exact coordinates of all these features are given in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001518#pbio.1001518.s008" target="_blank">Table S4</a>.</p
Molecular identification of the mating type locus using RNA-seq.
No full text<p>(A) RNA-seq data from mt VI and mt V cells <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001518#pbio.1001518-Xiong1" target="_blank">[18]</a> mapped to a ∼300-kb region of the SB210 macronuclear reference genome (mt VI) (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001518#pbio.1001518.s002" target="_blank">Figure S2</a>). The graph shows the number of RNA-seq reads (<i>y</i>-axis) from growing mt VI cells (orange, positive values), 3-h starved mt VI cells (blue, positive values) and 3-h starved mt V cells (red, shown as negative values) that mapped to the ∼300-kb region. Orange overlays blue. The box encloses a segment containing two genes with mating type-specific expression in starved cells and no expression in growing cells. <i>x</i>-axis: position within the 300-kb segment. (B) Transcripts (mt VI, blue) and transcript segments (mt V, red) were assembled from RNA-seq reads mapping to the boxed region in (A) and, for mt VI, from sequenced RT-PCR products. 5′ and 3′ untranslated regions are not included. The mt VI-derived transcripts correspond to a pair of divergently transcribed predicted genes (KC405257), now named <i>MTA6</i> and <i>MTB6</i>, respectively. Thin connecting lines represent introns. Both transcripts are drawn to scale, where each tick mark on the scale represents 1 kb. Each gene contains a TM exon and furin-like repeats (*).</p
Most assembled somatic TM exons are generated by a single, simple joining event.
No full text<p>The sequenced TM exons are from progeny that had not yet undergone their first division (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001518#pbio.1001518.s001" target="_blank">Figure S1</a>, stage 3, and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001518#s4" target="_blank">Materials and Methods</a>). The top six lines represent the germline mating type gene pairs of SB210, shown in their germline order (from top to bottom). All TM exons are drawn to scale. The darker gray bars represent intact and truncated <i>MTA</i> TM exons, while the lighter gray bars represent truncated and intact <i>MTB</i>-TM exons. The mating type-specific segments are color-coded, as labeled, and are not drawn to scale as indicated by the double slash marks. The dashes beyond <i>MTA2</i>-TM and <i>MTB3</i>-TM indicate sequence adjacent to the <i>mat</i> locus, which is identical in all nuclei. Vertical bars of mating type-specific color within <i>MTA</i> and <i>MTB</i> TM exon segments represent the location of polymorphic nucleotides relative to the germline consensus sequence of each TM exon (the consensus sequence is shown in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001518#pbio.1001518.s017" target="_blank">Text S6</a> and a complete list of polymorphisms is shown in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001518#pbio.1001518.s009" target="_blank">Tables S5</a> and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001518#pbio.1001518.s010" target="_blank">S6</a>). As an example, the simplest possible germline origin of the most common somatic <i>MTA6</i>-TM and <i>MTB6</i>-TM exons is indicated by boxed regions within the germline mating type gene pairs and somatic exons. For each mating type, approximately ten <i>MTA</i>-TM exons and 30 <i>MTB</i>-TM exons were sequenced (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001518#pbio.1001518.s018" target="_blank">Texts S7</a> and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001518#pbio.1001518.s019" target="_blank">S8</a> for details). Numbers to the left of <i>MTA</i> and to the right of <i>MTB</i> TM exons represent the number of times each combination of polymorphic nucleotides was found among the sequenced TM exons. *, location of a base not present in the germline; these changes could be due to either PCR errors or replication repair errors and occurred at a rate of 1 bp in 50 Kbp (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001518#pbio.1001518.s018" target="_blank">Texts S7</a> and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001518#pbio.1001518.s019" target="_blank">S8</a> for details).</p
Only one mating type gene pair remains in the somatic nucleus.
No full text<p>Southern blot analysis was carried out using whole-cell genomic DNA from a mature strain of each mating type (SB4208, SB4211, SB4214, SB4217, SB4220, and SB4223; see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001518#pbio.1001518.s005" target="_blank">Table S1</a>). The DNA was digested with <i>PvuII</i> restriction endonuclease and separated by pulsed-field gel electrophoresis. Black segments, mating type-specific segment of each gene pair; diagonally hatched segments, conserved TM exons; arrows, <i>PvuII</i> sites; thin black bars, probes; size (kb) shown is that of the relevant <i>PvuII</i> fragment in the somatic genome (the corresponding germline <i>PvuII</i> fragments are not visible due to differences in size and copy number).</p
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