Fragmentation Patterns in Ten Genes among Three H. acinonychis Strains

<p>Ten genes that are intact in 26695 but are fragmented in the Sheeba genome (subgroup B) were re-sequenced from strains t1 and HA5141 of subgroup B and BombayA of subgroup A. Black lines indicate sequenced fragments and thick blue arrows indicate CDSs of ≥140 bp. Designations at the top indicate CDS designations in 26695 whereas designations above the Sheeba sequences indicate both the protein name and the CDS designations in Sheeba (Hac0035, Hac0036, etc.).</p

Neighbor-Joining Tree Based on the GTR+G+I Evolutionary Model for 3,406 bp Sequences from 58 Strains of H. pylori and Four Strains of H. acinonychis

<p>The tree shows the phylogenetic relationships between H. acinonychis and populations within <i>H. pylori,</i> and arrows indicate the three strains, J99, 26695, and Sheeba, from which genome sequences are currently available. This phylogenetic tree indicates that H. pylori (lines) and H. acinonychis (lines plus red dots) are closely related but cannot resolve the direction of ancestor-descendent relationships. Genetic distance scale bar at bottom.</p

Cohesin Rings Devoid of Scc3 and Pds5 Maintain Their Stable Association with the DNA

<div><p>Cohesin is a protein complex that forms a ring around sister chromatids thus holding them together. The ring is composed of three proteins: Smc1, Smc3 and Scc1. The roles of three additional proteins that associate with the ring, Scc3, Pds5 and Wpl1, are not well understood. It has been proposed that these three factors form a complex that stabilizes the ring and prevents it from opening. This activity promotes sister chromatid cohesion but at the same time poses an obstacle for the initial entrapment of sister DNAs. This hindrance to cohesion establishment is overcome during DNA replication via acetylation of the Smc3 subunit by the Eco1 acetyltransferase. However, the full mechanistic consequences of Smc3 acetylation remain unknown. In the current work, we test the requirement of Scc3 and Pds5 for the stable association of cohesin with DNA. We investigated the consequences of Scc3 and Pds5 depletion <em>in vivo</em> using degron tagging in budding yeast. The previously described DHFR–based N-terminal degron as well as a novel Eco1-derived C-terminal degron were employed in our study. Scc3 and Pds5 associate with cohesin complexes independently of each other and require the Scc1 “core” subunit for their association with chromosomes. Contrary to previous data for Scc1 downregulation, depletion of either Scc3 or Pds5 had a strong effect on sister chromatid cohesion but not on cohesin binding to DNA. Quantity, stability and genome-wide distribution of cohesin complexes remained mostly unchanged after the depletion of Scc3 and Pds5. Our findings are inconsistent with a previously proposed model that Scc3 and Pds5 are cohesin maintenance factors required for cohesin ring stability or for maintaining its association with DNA. We propose that Scc3 and Pds5 specifically function during cohesion establishment in S phase.</p> </div

ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, -2

<p><b>Copyright information:</b></p><p>Taken from "ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, "</p><p>http://www.biomedcentral.com/1471-2164/8/269</p><p>BMC Genomics 2007;8():269-269.</p><p>Published online 8 Aug 2007</p><p>PMCID:PMC1994688.</p><p></p>fied according to molecular function or biological process. The group of others includes about 3000 ESTs with hits whose E-value was not better than 10Red: number of different ESTs, blue: number of total ESTs

ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, -1

<p><b>Copyright information:</b></p><p>Taken from "ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, "</p><p>http://www.biomedcentral.com/1471-2164/8/269</p><p>BMC Genomics 2007;8():269-269.</p><p>Published online 8 Aug 2007</p><p>PMCID:PMC1994688.</p><p></p>mosomes of , according to their best hits. Relative length of each chromosome (blue) and number of guppy markers (red) are plotted. Of 387 significant hits, 136 (38%) were assigned to the fraction of the genomic sequences not yet annotated by chromosome number

Gene Fragmentation, Duplication, and Import

<div><p>(A) Fragmentation of the <i>vacA</i> (vacuolating cytotoxin) gene (red) into 13 fragments and import of <i>neuACB, cst, cst</i> (blue-green) within Sheeba. <i>neuACB</i> encode acylneuraminate cytidyltransferases and <i>cst</i> encodes a sialyltransferase.</p><p>(B) Translocation of a duplicate of the fragmented <i>vacA</i> gene to a different genomic location. The duplicated <i>vacA</i> gene (red) contains the same fragmentation pattern and differs by only one sequence polymorphism in 3,815 bp from that in part A, indicating that the duplication is recent and occurred after the fragmentation event. Next to the duplicated <i>vacA</i> gene are located three genes (light blue) that are unique to H. acinonychis.</p><p>(C) Homologies of the <i>neuACB, cst, cst</i> gene cluster from part A with syntenic clusters in C. jejuni NCTC11168 and the B. cereus virulence plasmid pBC218.</p></div

Similarities between the Genomes of H. acinonychis Sheeba and H. pylori 26695 and J99

<div><p>(A) Venn diagram of genomic properties. Numbers in red within each arc represent numbers of genes, each of which may contain multiple CDSs if the corresponding gene is fragmented.</p><p>(B) Age calculations since a common ancestor (LCA) based on synonymous pair-wise distances for 612 conserved genes according to the methods of Li et al., 1985 and the modified Nei-Gojobori method.</p><p>(C) Frequencies of normalized blast scores in pair-wise comparisons between Sheeba and three other genomes.</p></div

Interaction of Pds5, Scc3 and Wpl1 with cohesin ring.

<p>Lysates of nocodazole/benomyl arrested yeast cultures were incubated with IgG sepharose to precipitate Scc1-TAP or Smc3-TAP. The presence of different proteins on the IgG beads was analysed by Western blot probed with anti-HA (12CA5), anti-MYC (71D10) and PAP (P1291, Sigma). The strains were in (A): 1771 (<i>SCC3-MYC18, PDS5-HA6</i>), 1829 (<i>SCC3-MYC18, PDS5-HA6</i>-degron, <i>SCC1-TAP</i>), 1958 (<i>SCC3-MYC18, PDS5-HA6, SCC1-TAP</i>); in (B): 1734 (<i>PDS5-MYC18, SCC3-HA6</i>), 1834 (<i>PDS5-MYC18, SCC3-HA6</i>-degron, <i>SCC1-TAP</i>), 1956 (<i>PDS5-MYC18, SCC3-HA6, SCC1-TAP</i>); in (C): 1882 (<i>WPL1-MYC18, PDS5-HA6</i>), 2014 (<i>WPL1-MYC18, PDS5-HA6, SCC1-TAP</i>), 2016 (<i>WPL1-MYC18, PDS5-HA6</i>-degron, <i>SCC1-TAP</i>); in (D): 1880 (<i>WPL1-MYC18, SCC3-HA6</i>), 2012 (<i>WPL1-MYC18, SCC3-HA6, SCC1-TAP</i>), 2018 (<i>WPL1-MYC18, SCC3-HA6</i>-degron, <i>SCC1-TAP</i>); in (E): 1771 (<i>SCC3-MYC18, PDS5-HA6</i>), 2251 (<i>SCC3-MYC18, PDS5-HA6, SMC3-TAP</i>), 2290 (<i>SCC3-MYC18, PDS5-HA6</i>-degron, <i>SMC3-TAP</i>); in (F): 1734 (<i>PDS5-MYC18, SCC3-HA6</i>), 2249 (<i>PDS5-MYC18, SCC3-HA6, SMC3-TAP</i>), 2264 (<i>PDS5-MYC18, SCC3-HA6</i>-degron, <i>SMC3-TAP</i>); in (G): 1882 (<i>WPL1-MYC18, PDS5-HA6</i>), 2253 (<i>WPL1-MYC18, PDS5-HA6, SMC3-TAP</i>), 2265 (<i>WPL1-MYC18, PDS5-HA6</i>-degron, <i>SMC3-TAP</i>); in (H): 1882 (<i>WPL1-MYC18, PDS5-HA6</i>), 2261 (<i>WPL1-MYC18, SCC3-HA6, SMC3-TAP</i>), 2271 (<i>WPL1-MYC18, SCC3-HA6</i>-degron, <i>SMC3-TAP</i>).</p

ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, -0

<p><b>Copyright information:</b></p><p>Taken from "ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, "</p><p>http://www.biomedcentral.com/1471-2164/8/269</p><p>BMC Genomics 2007;8():269-269.</p><p>Published online 8 Aug 2007</p><p>PMCID:PMC1994688.</p><p></p>fied according to molecular function or biological process. The group of others includes about 3000 ESTs with hits whose E-value was not better than 10Red: number of different ESTs, blue: number of total ESTs

Depletion of Scc3 and Pds5 with a “conventional” temperature-sensitive degron.

<p>(A–C) Strains 2395 (<i>SCC1-HA6</i>), 2452 (<i>SCC1-HA6</i>, degron-<i>MYC18-PDS5</i>), 2455 (<i>SCC1-HA6</i>, degron-<i>MYC18</i>-<i>SCC3</i>) and 2456 (<i>SCC1-HA6</i>, degron-<i>MYC18- PDS5, degron-MYC18-SCC3</i>) were arrested with nocodazole in YEP raffinose at 30°C for 2 hours, resuspended in YEP galactose containing nocodazole and incubated for 45 minutes at 30°C to induce the expression of Ubr1. Cells were shifted to 37°C in YEP galactose containing nocodazole and doxycycline to deplete Pds5 and/or Scc3. (A) Chromosomal spreads were prepared at the indicated time points and stained with DAPI for DNA, anti-HA (mouse, 16B12) and anti-MYC (rabbit, 71D10) antibodies. The secondary antibodies were Alexa Fluor 488 anti-mouse and Alexa Fluor 568 anti-rabbit. Protein fluorescence was quantified using Metamorph software. At every time point fluorescence of 50 nuclei was determined. Error bars represent standard deviation. (B) Western blot of TCA protein extracts probed with anti-HA (16B12), anti-MYC (71D10) and anti-Cdc28 (sc-28550, Santa Cruz). (C) FACS analysis of cellular DNA content. (D–F) Strains were staged in G1 with <i>α</i>-factor in YEP raffinose at 30°C, resuspended in YEP galactose containing <i>α</i>-factor and incubated for 45 minutes at 30°C to induce the expression of Ubr1. Cells were then shifted to 37°C in YEP galactose containing doxycycline and <i>α</i>-factor, incubated for 90 minutes to deplete Pds5 and/or Scc3 and subsequently released in YEP galactose containing nocodazole and doxycycline at 37°C. Chromosomal spreads (D), Western blot (E), and FACS analysis of cellular DNA content (F) are shown.</p