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1.  Sequence Analysis of Staphylococcus hyicus ATCC 11249T, an Etiological Agent of Exudative Epidermitis in Swine, Reveals a Type VII Secretion System Locus and a Novel 116-Kilobase Genomic Island Harboring Toxin-Encoding Genes 
Genome Announcements  2015;3(1):e01525-14.
Staphylococcus hyicus is the primary etiological agent of exudative epidermitis in swine. Analysis of the complete genome sequence of the type strain revealed a locus encoding a type VII secretion system and a large chromosomal island harboring the genes encoding exfoliative toxin ExhA and an EDIN toxin homolog.
doi:10.1128/genomeA.01525-14
PMCID: PMC4335327
2.  Genome Sequence of Actinobacillus suis Type Strain ATCC 33415T 
Genome Announcements  2014;2(5):e00926-14.
The assembled and annotated genome of Actinobacillus suis ATCC 33415T is reported here. The 2,501,598-bp genome encodes 2,246 open reading frames (ORFs) with strain variable incursion of an integrative conjugative element into a tRNA locus. Comparative analysis of the deduced gene set should inform our understanding of pathogenesis, genomic plasticity, and serotype variation.
doi:10.1128/genomeA.00926-14
PMCID: PMC4172276  PMID: 25237027
3.  Draft Genome Sequence of Bovine Mastitis Isolate Staphylococcus agnetis CBMRN 20813338 
Genome Announcements  2014;2(5):e00883-14.
Presented here is a draft genome sequence for Staphylococcus agnetis CBMRN 20813338, isolated from a lactating dairy cow with subclinical mastitis. The genome is approximately 2,416 kb and has 35.79% G+C content. Analysis of the deduced open reading frame (ORF) set identified candidate virulence attributes in addition to potential molecular targets for species identification.
doi:10.1128/genomeA.00883-14
PMCID: PMC4155595  PMID: 25189590
4.  Draft Genome Sequence of Staphylococcus chromogenes Strain MU 970, Isolated from a Case of Chronic Bovine Mastitis 
Genome Announcements  2014;2(4):e00835-14.
Coagulase-negative staphylococcal species are a common cause of subclinical bovine mastitis, with Staphylococcus chromogenes being one of the most frequently identified species in these cases. The draft genome sequence of an S. chromogenes isolate (MU 970) recovered from the milk of a cow with a chronic intramammary infection is reported here.
doi:10.1128/genomeA.00835-14
PMCID: PMC4132628  PMID: 25125652
5.  Complete Genome Sequence of the Bovine Mastitis Pathogen Mycoplasma californicum Strain ST-6T (ATCC 33461T) 
Genome Announcements  2014;2(4):e00648-14.
Mycoplasma californicum is one of several mycoplasmal species associated with bovine mastitis. The complete genome sequence of 793,841 bp has been determined and annotated for the M. californicum ST-6 type strain, providing a resource for the identification of surface antigens and putative pathoadaptive features.
doi:10.1128/genomeA.00648-14
PMCID: PMC4081997  PMID: 24994797
6.  Draft Genome Sequence of Moraxella bovoculi Strain 237T (ATCC BAA-1259T) Isolated from a Calf with Infectious Bovine Keratoconjunctivitis 
Genome Announcements  2014;2(3):e00612-14.
Moraxella bovoculi is a recently identified species, recovered from the bovine eye, which is under investigation as an etiological agent of infectious bovine keratoconjunctivitis. A draft genome sequence of the Moraxella bovoculi type strain 237T has been determined to identify features that may be important during host colonization.
doi:10.1128/genomeA.00612-14
PMCID: PMC4073114  PMID: 24970830
7.  Draft Genome Sequence of Fusobacterium necrophorum subsp. funduliforme Bovine Liver Abscess Isolate B35 
Genome Announcements  2014;2(2):e00412-14.
Fusobacterium necrophorum is a Gram-negative anaerobic bacterium that causes foot rot and liver abscesses in cattle. F. necrophorum subsp. necrophorum and the less virulent organism F. necrophorum subsp. funduliforme are recognized. We present here a draft genome sequence of the bovine liver abscess isolate F. necrophorum subsp. funduliforme strain B35, which affords a genomic perspective of virulence and bovine adaptation.
doi:10.1128/genomeA.00412-14
PMCID: PMC4007993  PMID: 24786958
8.  Complete Genome Sequence of Mycoplasma bovoculi Strain M165/69T (ATCC 29104) 
Genome Announcements  2014;2(1):e00115-14.
Bovine ocular infections compromise animal health and result in significant economic losses. Mycoplasma bovoculi is an etiological agent of conjunctivitis. Presented here is the 760,240-bp complete genome sequence of the M. bovoculi type strain M165/69T. An analysis of the deduced proteome provides insights into the adherence and antigenic variation mechanisms of the strain.
doi:10.1128/genomeA.00115-14
PMCID: PMC3931370  PMID: 24558249
9.  Draft Genome Sequence of Staphylococcus simulans UMC-CNS-990, Isolated from a Case of Chronic Bovine Mastitis 
Genome Announcements  2013;1(6):e01037-13.
Coagulase-negative staphylococci are frequently isolated from cases of subclinical bovine mastitis. Reported here is a draft genome sequence of Staphylococcus simulans UMC-CNS-990, an isolate recovered from a chronic intramammary infection of a Holstein cow. Unexpectedly, a cluster of genes encoding gas vesicle proteins was found within the 2,755-kb genome.
doi:10.1128/genomeA.01037-13
PMCID: PMC3861428  PMID: 24336375
10.  Genome Sequence Analysis of Staphylococcus equorum Bovine Mastitis Isolate UMC-CNS-924 
Genome Announcements  2013;1(5):e00840-13.
Intramammary infections in dairy cattle are frequently caused by staphylococci, resulting in mastitis and associated economic losses. A draft genome sequence was determined for Staphylococcus equorum UMC-CNS-924, isolated from the milk of a Holstein cow, to better understand the genetic basis of its pathogenesis and adaptation to the bovine mammary gland.
doi:10.1128/genomeA.00840-13
PMCID: PMC3798454  PMID: 24136848
11.  Complete Genome Sequences of Mycoplasma leachii Strain PG50T and the Pathogenic Mycoplasma mycoides subsp. mycoides Small Colony Biotype Strain Gladysdale 
Journal of Bacteriology  2012;194(16):4448-4449.
Mycoplasma mycoides subsp. mycoides small colony biotype (SC) is the high-consequence animal pathogen causing contagious bovine pleuropneumonia. We report the complete genome sequences of the pathogenic strain M. mycoides subsp. mycoides SC Gladysdale and a close phylogenetic relative, Mycoplasma leachii PG50T, another bovine pathogen of the M. mycoides phylogenetic clade.
doi:10.1128/JB.00761-12
PMCID: PMC3416226  PMID: 22843585
12.  Genome Sequence of Mycoplasma hyorhinis Strain GDL-1 
Journal of Bacteriology  2012;194(7):1848.
Mycoplasma hyorhinis impacts swine health and production in many countries, either as a primary pathogen or as a component of a polymicrobial infection. Isolates of this species are also common contaminants of tissue culture lines. The genome sequence of the cell culture isolate M. hyorhinis GDL-1 is presented herein.
doi:10.1128/JB.00033-12
PMCID: PMC3302467  PMID: 22408248
13.  Genome Sequence of Mycoplasma putrefaciens Type Strain KS1 
Journal of Bacteriology  2011;193(21):6094.
Mycoplasma putrefaciens is a causative agent of contagious agalactia in goats. Reported herein is the complete genome sequence of the M. putrefaciens type strain KS1.
doi:10.1128/JB.06051-11
PMCID: PMC3194915  PMID: 21994925
14.  U1 RNA Induces Innate Immunity Signaling 
Arthritis and rheumatism  2004;50(9):2891-2896.
Objective
The U1–70-kd RNP is a prominent target of autoimmunity in connective tissue diseases. In this study, we explored whether its endogenous ligand, U1 RNA, mediates a proimmune signal and may be immunogenic.
Methods
We assayed the proliferation of control and MyD88-knockout splenocytes in response to in vitro–synthesized U1 RNA, and measured interleukin-6 (IL-6) and IL-8 secretion induced by U1 RNA in a human cell line competent for signaling through Toll-like receptor 3 (TLR-3) and TLR-5.
Results
Treatment with U1 RNA or with poly(I-C), a known agonist of TLR-3, induced approximately twice as much control splenocyte proliferation as did treatment with RNase-digested U1 RNA. Proliferation in response to either poly(I-C) or U1 RNA by MyD88-knockout splenocytes was similarly attenuated. Similar to poly(I-C), U1 RNA induced significant secretion of both IL-6 and IL-8 from a TLR-3–expressing human cell line; in contrast, the TLR-5 agonist flagellin induced predominantly IL-8 secretion. Pretreatment of U1 RNA with RNase abolished IL-6 and IL-8 secretion.
Conclusion
U1 RNA is capable of inducing manifestations consistent with TLR-3 activation. The ability of U1 RNA (which has a substantial double-stranded secondary structure) to activate TLR-3 may contribute to the immunogenicity of the U1–70-kd autoantigen. Stimulation of innate immunity by native RNA molecules with a double-stranded secondary structure may help explain the high prevalence of autoimmunity to RNA binding proteins.
doi:10.1002/art.20428
PMCID: PMC1475509  PMID: 15457457
15.  Complete Genome Sequence of Mycoplasma bovis Type Strain PG45 (ATCC 25523)▿  
Infection and Immunity  2010;79(2):982-983.
This complete and fully assembled genome sequence of Mycoplasma bovis type strain PG45 is the first available for this species and offers a framework for comparison with additional pathogenic isolates. The single circular chromosome of 1,003,404 bp reveals multiple gene sets and mechanisms involved in variable expression of surface antigens and the incursion of numerous and assorted mobile elements, despite its reduced size.
doi:10.1128/IAI.00726-10
PMCID: PMC3028869  PMID: 21134966
16.  A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes 
BMC Genomics  2010;11:430.
Background
Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT). Expanding genome sequence databases reveal the pattern in a widening range of bacteria, and recently among eucaryotic microbes. We examined the genomic flux and consequences of the motif by determining its distribution, predicted structural features and association with membrane-targeted proteins.
Results
Using a refined hidden Markov model, we document a 25-residue protein sequence motif tandemly arrayed in variable-number repeats in ORFs lacking assigned functions. It appears sporadically in unicellular microbes from disparate bacterial and eucaryotic clades, representing diverse lifestyles and ecological niches that include host parasitic, marine and extreme environments. Tracts of the repeats predict a malleable configuration of recurring domains, with conserved hydrophobic residues forming an amphipathic secondary structure in which hydrophilic residues endow extensive sequence variation. Many ORFs with these domains also have membrane-targeting sequences that predict assorted topologies; others may comprise reservoirs of sequence variants. We demonstrate expressed variants among surface lipoproteins that distinguish closely related animal pathogens belonging to a subgroup of the Mollicutes. DNA sequences encoding the tandem domains display dyad symmetry. Moreover, in some taxa the domains occur in ORFs selectively associated with mobile elements. These features, a punctate phylogenetic distribution, and different patterns of dispersal in genomes of related taxa, suggest that the repeat may be disseminated by HGT and intra-genomic shuffling.
Conclusions
We describe novel features of PARCELs (Palindromic Amphipathic Repeat Coding ELements), a set of widely distributed repeat protein domains and coding sequences that were likely acquired through HGT by diverse unicellular microbes, further mobilized and diversified within genomes, and co-opted for expression in the membrane proteome of some taxa. Disseminated by multiple gene-centric vehicles, ORFs harboring these elements enhance accessory gene pools as part of the "mobilome" connecting genomes of various clades, in taxa sharing common niches.
doi:10.1186/1471-2164-11-430
PMCID: PMC2996958  PMID: 20626840
18.  Distinctive Repertoire of Contingency Genes Conferring Mutation- Based Phase Variation and Combinatorial Expression of Surface Lipoproteins in Mycoplasma capricolum subsp. capricolum of the Mycoplasma mycoides Phylogenetic Cluster†  
Journal of Bacteriology  2006;188(13):4926-4941.
The generation of surface variation among many divergent species of Mollicutes (mycoplasmas) occurs through stochastic expression patterns of diverse lipoprotein genes. The size and wide distribution of such variable gene sets in minimal (∼0.6- to 1.4-Mb) mycoplasmal genomes suggest their key role in the adaptation and survival of these wall-less monoderms. Diversity through variable genes is less clearly established among phylogenetically similar mycoplasmas, such as the Mycoplasma mycoides cluster of ruminant pathogens, which vary widely in host range and pathobiology. Using (i) genome sequences from two members of this clade, Mycoplasma capricolum subsp. capricolum and M. mycoides subsp. mycoides small colony biotype (SC), (ii) antibodies to specific peptide determinants of predicted M. capricolum subsp. capricolum gene products, and (iii) analysis of the membrane-associated proteome of M. capricolum subsp. capricolum, a novel set of six genes (vmcA to vmcF) expressing distinct Vmc (variable M. capricolum subsp. capricolum) lipoproteins is demonstrated. These occur at two separate loci in the M. capricolum subsp. capricolum genome, which shares striking overall similarity and gene synteny with the M. mycoides subsp. mycoides SC genome. Collectively, Vmc expression is noncoordinate and combinatorial, subject to a single-unit insertion/deletion in a 5′ flanking dinucleotide repeat that governs expression of each vmc gene. All vmc genes share modular regions affecting expression and membrane translocation. In contrast, vmcA to vmcD genes at one locus express surface proteins with highly structured size-variable repeating domains, whereas vmcE to vmcF genes express products with short repeats devoid of predicted structure. These genes confer a distinctive, dynamic surface architecture that may represent adaptive differences within this important group of pathogens as well as exploitable diagnostic targets.
doi:10.1128/JB.00252-06
PMCID: PMC1483001  PMID: 16788201

Results 1-18 (18)