The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2

Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome

-Tetrachlorodibenzo-p-dioxin: its effect on genes for mandible traits in mice

Abstract 2,3,7,8-tetrachlorodibenzo-p -dioxin (TCDD) is a powerful toxicant that exerts its effects through the aryl hydrocarbon receptor (AHR) governed by the Ahr locus that in mice is located on chromosome 12. We used single marker analyses of the offspring of female mice treated/not treated with TCDD to search for a gene (quantitative trait locus or QTL) on chromosome 12 near the site of the Ahr locus to test whether this locus appeared to affect mandible size, shape, and/or asymmetry especially in the treated mice. These mice were sampled from the F 2 generation of an original intercross of two strains (C57BL/6J and AKR/J) known to be divergent in their response to TCDD. A QTL affecting mandible shape was found on chromosome 12, but its effect on mice in the treated and control groups did not differ and it was concluded that this QTL probably was not the Ahr locus itself. We also probed a second chromosome (11) and found a QTL whose effects on asymmetry of mandible shape differed in the two environments. These results suggested that the entire genome in these mice should be scanned to search for additional QTLs that might be affected by TCDD to learn more about the potential effects of this powerful toxicant on these genes.

Comparison of Methods for DNA Isolation from Food Samples for Detection of Shiga Toxin-Producing Escherichia coli by Real-Time PCR

In this study, food samples were intentionally contaminated with Escherichia coli O157:H7, and then DNA was isolated by using four commercial kits. The isolated DNA samples were compared by using real-time PCR detection of the Shiga toxin genes. The four kits tested worked similarly

Two-Year Study Evaluating the Potential Loss of Methicillin Resistance in a Methicillin-Resistant Staphylococcus aureus Culture Collection▿

A reported loss of mecA prompted us to monitor 360 cryostocked methicillin-resistant Staphylococcus aureus strains for stability. Concurrently, 14 well-characterized strains were stored in a Microbank preservation system and subjected to multiple freeze-thaw events. There were no significant declines in the methicillin-resistant populations with either method over a two-year period

Transporter Gene Frequencies within the Genomes of <i>Thiom. crunogena</i> XCL-2 (Arrow) and Other Proteobacteria

<p><i>Nitrob. winogradskyi (Nitrobacter winogradskyi)</i> is an alphaproteobacterium, <i>Nitros. europaea (Nitrosomonas europaea)</i> is a betaproteobacterium, and <i>Nitrosoc. oceani (Nitrosococcus oceani)</i> and <i>Methylo. capsulatus (Methylococcus capsulatus)</i> are gammaproteobacteria. Bars for intracellular pathogens are lighter red than the other heterotrophic gammaproteobacteria.</p

Cell Model for <i>Thiom. crunogena</i> XCL-2, with an Emphasis on Ultrastructure, Transport, Energy, Carbon Metabolism, and Chemotaxis

<p>Genes encoding virtually all of the steps for the synthesis of nucleotides and amino acids by canonical pathways are present in the bacterium, but are omitted here for simplicity. Electron transport components are yellow, and abbreviations are as follows: bc₁, <i>bc₁</i> complex; cbb₃, <i>cbb₃</i>-type cytochrome C oxidase; cytC, cytochrome C; NDH, NADH dehydrogenase; Sox, Sox system; UQ, ubiquinone. MCPs are fuchsia, as are MCPs with PAS domains or PAS folds. Influx and efflux transporter families with representatives in this genome are indicated on the figure, with the number of each type of transporter in parentheses. ATP-dependent transporters are red, secondary transporters are sky blue, ion channels are light green, and unclassified transporters are purple. Abbreviations for transporter families are as follows: ABC, ATP-binding cassette superfamily; AGCS, alanine or glycine:cation symporter family; AMT, ammonium transporter family; APC, amino acid-polyamine-organocation family; ATP syn, ATP synthetase; BASS, bile acid:Na⁺ symporter family; BCCT, betaine/carnitine/choline transporter family; CaCA, Ca²⁺:cation antiporter family; CDF, cation diffusion facilitator family; CHR, chromate ion transporter family; CPA, monovalent cation:proton antiporter-1, −2, and −3 families; DAACS, dicarboxylate/amino acid:cation symporter family; DASS, divalent anion:Na⁺ symporter family; DMT, drug/metabolite transporter superfamily; FeoB, ferrous iron uptake family; IRT, iron/lead transporter superfamily; MATE, multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) flippase superfamily, MATE family; McsS, small conductance mechanosensitive ion channel family; MFS, major facilitator superfamily; MgtE, Mg²⁺ transporter-E family; MIT, CorA metal ion transporter family; NCS2, nucleobase:cation symporter-2 family; NRAMP, metal ion transporter family; NSS, neurotransmitter:sodium symporter family; P-ATP, P-type ATPase superfamily; Pit, inorganic phosphate transporter family; PNaS, phosphate:Na⁺ symporter family; PnuC, nicotamide mononucleotide uptake permease family; RhtB, resistance to homoserine/threonine family; RND, resistance-nodulation-cell division superfamily; SSS, solute:sodium symporter family; SulP, sulfate permease family; TRAP, tripartite ATP-independent periplasmic transporter family; TRK, K⁺ transporter family; VIC, voltage-gated ion channel superfamily.</p

Circular Map of the <i>Thiom. crunogena</i> XCL-2 Genome

<p>The outer two rings (rings 1 and 2) are protein-encoding genes, which are color-coded according to COG category. Rings 3 and 4 are tRNA and rRNA genes. Ring 5 indicates the location of a prophage (magenta), phosphonate/heavy metal resistance island (cyan), and four insertion sequences (red; two insertion sequences at 2028543 and 2035034 are superimposed on this figure). The black circle indicates the deviation from the average %GC, and the purple and green circle is the GC skew (= [G − C]/[G + C]). Both the %GC and GC skew were calculated using a sliding window of 10,000 bp with a window step of 100.</p

Prophage Genome within the <i>Thiom. crunogena</i> XCL-2 Genome

<p>Lysogenic and lytic genes are delineated, as are predicted gene functions.</p

<i>Thiom. crunogena</i> XCL-2 Phosphonate Operon

<p>The <i>DBR-1</i> genes are identical to each other, as are the <i>DBR-2</i> genes. Gene abbreviations are: <i>chp</i>, conserved hypothetical protein; <i>DBR-1</i> and -<i>2</i>, DNA breaking-rejoining enzymes; <i>hyp</i>, hypothetical protein; <i>phnFDCEGHIJKLMNP</i>, phosphonate operon. An asterisk (*) marks the location of a region (within and upstream of tRNA-phe) with a high level of similarity to the 5′ ends of the two direct repeat sequences noted in the figure. The transposase and integrase are actually a single CDS separated by a frameshift.</p