<?xml version="1.0" encoding="ISO-8859-1"?><article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<front>
<journal-meta>
<journal-id>0121-3709</journal-id>
<journal-title><![CDATA[ORINOQUIA]]></journal-title>
<abbrev-journal-title><![CDATA[Orinoquia]]></abbrev-journal-title>
<issn>0121-3709</issn>
<publisher>
<publisher-name><![CDATA[Instituto de Investigaciones de la Orinoquia Colombiana]]></publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id>S0121-37092013000100008</article-id>
<title-group>
<article-title xml:lang="es"><![CDATA[Análisis genómico al azar de Edwardsiella tarda ETSJ54: anotación de genes relacionados con virulencia]]></article-title>
<article-title xml:lang="en"><![CDATA[A random genome analysis of Edwardsiella tarda ETSJ54: annotation of putative virulence - related genes]]></article-title>
<article-title xml:lang="pt"><![CDATA[A análise do genoma aleatória de Edwardsiella tarda ETSJ54: anotação de genes de virulência relacionados ao putativos]]></article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Verjan - García]]></surname>
<given-names><![CDATA[Noel]]></given-names>
</name>
<xref ref-type="aff" rid="A01"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Iregui - Castro]]></surname>
<given-names><![CDATA[Carlos A.]]></given-names>
</name>
<xref ref-type="aff" rid="A02"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Hirono]]></surname>
<given-names><![CDATA[Ikuo]]></given-names>
</name>
<xref ref-type="aff" rid="A03"/>
</contrib>
</contrib-group>
<aff id="A01">
<institution><![CDATA[,Universidad del Tolima Facultad de Medicina Veterinaria y Zootecnia Departamento de Sanidad Animal]]></institution>
<addr-line><![CDATA[ ]]></addr-line>
</aff>
<aff id="A02">
<institution><![CDATA[,Universidad Nacional de Colombia Facultad de Medicina Veterinaria y Zootecnia Laboratorio de Patobiología]]></institution>
<addr-line><![CDATA[Bogotá ]]></addr-line>
<country>Colombia</country>
</aff>
<aff id="A03">
<institution><![CDATA[,University of Marine Science and Technology Laboratory of Genome Science ]]></institution>
<addr-line><![CDATA[Tokyo ]]></addr-line>
<country>Japan</country>
</aff>
<pub-date pub-type="pub">
<day>00</day>
<month>06</month>
<year>2013</year>
</pub-date>
<pub-date pub-type="epub">
<day>00</day>
<month>06</month>
<year>2013</year>
</pub-date>
<volume>17</volume>
<numero>1</numero>
<fpage>69</fpage>
<lpage>83</lpage>
<copyright-statement/>
<copyright-year/>
<self-uri xlink:href="http://www.scielo.org.co/scielo.php?script=sci_arttext&amp;pid=S0121-37092013000100008&amp;lng=en&amp;nrm=iso"></self-uri><self-uri xlink:href="http://www.scielo.org.co/scielo.php?script=sci_abstract&amp;pid=S0121-37092013000100008&amp;lng=en&amp;nrm=iso"></self-uri><self-uri xlink:href="http://www.scielo.org.co/scielo.php?script=sci_pdf&amp;pid=S0121-37092013000100008&amp;lng=en&amp;nrm=iso"></self-uri><abstract abstract-type="short" xml:lang="es"><p><![CDATA[Como un paso inicial para comprender los mecanismos de patogenicidad usados por Edwardsiella tarda durante la infección en peces, se llevo a cabo un secuenciamiento genómico parcial y al azar de librerias de ADN construidas en vectores cosmido y plasmido generadas a partir de una cepa (ETSJ54) virulenta de E. tarda para identificar genes presumiblemente relacionados con su virulencia. Los genes relacionados con virulencia de acuerdo a la semejanza en las secuencias de nucleotides con otras especies bacterianas fueron agrupados en nueve categorías que incluyeron quimiotaxis y motilidad, endotoxina (LPS), secreción de toxinas por los sistemas scretorios I y III, adquisición de hierro, proteasas y sobreviviencia dentro de macrófagos. Los resultados indican que E. tarda posee un amplio rango de genes involucrados en la virulencia y en la patogenicidad de generos bacterianos diversos y especies como Salmonella, Yersinia and Vibrios. Los resultados también indican que existe un alto flujo de genes en el genoma de E. tarda que podrían explicar en algún grado su potencial de infectar y causar enfermedad en varias especies animales.]]></p></abstract>
<abstract abstract-type="short" xml:lang="en"><p><![CDATA[As an initial step to understand the pathogenic mechanisms displayed by Edwardsiella tarda during infection in fish, we conducted a random genome sequencing of cosmid and plasmid DNA libraries generated from a virulent E. tarda strain (ETSJ54) to identify putative virulence-related genes. The assumed virulence-related genes of E. tarda were grouped into nine categories including chemotaxis and motility, adhesion and invasion, endotoxin (LPS), toxin secretion by type I and type III secretion systems, iron uptake, proteases, and intra-macrophage survival. The results reveal that E. tarda is equipped with a wide range of genes involved in virulence and pathogenesis of diverse bacterial genera and species including Salmonella, Yersinia and Vibrios species. The results also indicate a high genetic flux in the E. tarda genome that could explain in some extent its potential to infect and to cause disease in a number of animal species.]]></p></abstract>
<abstract abstract-type="short" xml:lang="pt"><p><![CDATA[Como um passo inicial para entender os mecanismos patogenéticos expostos por Edwardsiella tarda durante a infecção no peixe, conduzimos uma genoma sequencing de cosmid e plasmad ADN bibliotecas geradas de um virulento E. tarda tensão (ETSJ54) para identificar genes putativos relacionados com virulência. Os genes relacionados com virulência assumidos de E. tarda foram agrupados em ocho categorias inclusive chemotaxis e motility, endotoxin (LPS), tipo I e tipo III sistemas de substância segreda, compreensão de ferro, procaçoadores, e intra-macrophage sobrevivência. Os resultados revelam que E. tarda é equipado com uma larga variedade de genes implicados na virulência e pathogenesis de gêneros bacterianos diversos e espécie inclusive Salmonella, Yersinia e espécie Vibrios. Os resultados também indicam um alto fluxo genético no E. tarda genoma que pode explicar em alguma extensão o seu potencial para infeccionar e causar a doença em um número de espécie dos animais.]]></p></abstract>
<kwd-group>
<kwd lng="es"><![CDATA[Edwardsiellosis]]></kwd>
<kwd lng="es"><![CDATA[secuenciamiento genómico]]></kwd>
<kwd lng="es"><![CDATA[virulencia]]></kwd>
<kwd lng="es"><![CDATA[patogénesis]]></kwd>
<kwd lng="en"><![CDATA[Edwardsiellosis]]></kwd>
<kwd lng="en"><![CDATA[genome sequencing]]></kwd>
<kwd lng="en"><![CDATA[virulence]]></kwd>
<kwd lng="en"><![CDATA[pathogenesis]]></kwd>
<kwd lng="pt"><![CDATA[Edwardsiellosis]]></kwd>
<kwd lng="pt"><![CDATA[genoma sequencing]]></kwd>
<kwd lng="pt"><![CDATA[virulência]]></kwd>
<kwd lng="pt"><![CDATA[pathogenesis]]></kwd>
</kwd-group>
</article-meta>
</front><body><![CDATA[  <font face="verdana" size="2">          <p align="center"><font size="4"><b>An&aacute;lisis gen&oacute;mico al azar de <i>Edwardsiella tarda</i> ETSJ54: anotaci&oacute;n de genes relacionados con virulencia</b></font></p>     <p align="center"><font size="3"><b>A random genome analysis of <i>Edwardsiella tarda</i> ETSJ54: annotation of putative virulence - related genes</b></font></p>     <p align="center"><font size="3"><b>A an&aacute;lise do genoma aleat&oacute;ria de <i>Edwardsiella tarda</i> ETSJ54: anota&ccedil;&atilde;o de genes de virul&ecirc;ncia relacionados ao putativos</b></font></p>     <p align="right"><b>Noel Verjan - Garc&iacute;a<a href="#1" name="nr1"><sup>1</sup></a><sup>,<a href="#2" name="nr2">2</a>,<a href="#3" name="nr3">3</a></sup>    <br>   Carlos A. Iregui - Castro<sup><a href="#2" name="nr2">2</a></sup>    <br> Ikuo Hirono<a href="#3" name="nr3"><sup>3</sup></a></b></p>     <p><a href="#nr1" name="1">1</a> MVZ, MSc, PhD, Grupo de Investigaci&oacute;n Inmunobiolog&iacute;a y Patog&eacute;nesis, Departamento de Sanidad Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad del Tolima, Ibagu&eacute; Colombia.    <br>   Email: <a href="mailto:nverjang@ut.edu.co">nverjang@ut.edu.co</a>.    <br>   <a href="#nr2" name="2">2</a> MV, PhD, Laboratorio de Patobiolog&iacute;a, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional de Colombia, Bogot&aacute; Colombia.    ]]></body>
<body><![CDATA[<br>   <a href="#nr3" name="3">3</a> PhD, Laboratory of Genome Science, Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato, Tokyo 108-8477, Japan.</p>     <p>Recibido: marzo 5 de 2012. Aceptado: mayo 11 de 2013</p> <hr size="1" />              <p><b>Resumen</b></p>     <p>Como un paso inicial para comprender los mecanismos de patogenicidad usados por <i>Edwardsiella tarda</i> durante la infecci&oacute;n   en peces, se llevo a cabo un secuenciamiento gen&oacute;mico parcial y al azar de librerias de ADN construidas en vectores   cosmido y plasmido generadas a partir de una cepa (ETSJ54) virulenta de <i>E. tarda</i> para identificar genes presumiblemente   relacionados con su virulencia. Los genes relacionados con virulencia de acuerdo a la semejanza en las secuencias de   nucleotides con otras especies bacterianas fueron agrupados en nueve categor&iacute;as que incluyeron quimiotaxis y motilidad,   endotoxina (LPS), secreci&oacute;n de toxinas por los sistemas scretorios I y III, adquisici&oacute;n de hierro, proteasas y sobreviviencia   dentro de macr&oacute;fagos. Los resultados indican que <i>E. tarda</i> posee un amplio rango de genes involucrados en la virulencia   y en la patogenicidad de generos bacterianos diversos y especies como <i>Salmonella</i>, <i>Yersinia</i> and <i>Vibrios</i>. Los resultados   tambi&eacute;n indican que existe un alto flujo de genes en el genoma de <i>E. tarda</i> que podr&iacute;an explicar en alg&uacute;n grado su potencial de infectar y causar enfermedad en varias especies animales.</p>          <p><b>Palabras clave</b>: <i>Edwardsiellosis</i>, secuenciamiento gen&oacute;mico, virulencia, patog&eacute;nesis.</p>      <p><b>Abstract</b></p>     <p>As an initial step to understand the pathogenic mechanisms displayed by <i>Edwardsiella tarda</i> during infection in fish, we   conducted a random genome sequencing of cosmid and plasmid DNA libraries generated from a virulent <i>E. tarda</i> strain   (ETSJ54) to identify putative virulence-related genes. The assumed virulence-related genes of <i>E. tarda</i> were grouped into   nine categories including chemotaxis and motility, adhesion and invasion, endotoxin (LPS), toxin secretion by type I and   type III secretion systems, iron uptake, proteases, and intra-macrophage survival. The results reveal that <i>E. tarda</i> is equipped with a wide range of genes involved in virulence and pathogenesis of diverse bacterial genera and species including <i>Salmonella</i>, <i>Yersinia</i> and <i>Vibrios</i> species. The results also indicate a high genetic flux in the <i>E. tarda</i> genome that could explain in some extent its potential to infect and to cause disease in a number of animal species.</p>     <p><b>Key words</b>: <i>Edwardsiellosis</i>, genome sequencing, virulence, pathogenesis.</p>     <p><b>Resumo</b></p>     <p>Como um passo inicial para entender os mecanismos patogen&eacute;ticos expostos por <i>Edwardsiella tarda</i> durante a infec&ccedil;&atilde;o no   peixe, conduzimos uma genoma sequencing de cosmid e plasmad ADN bibliotecas geradas de um virulento <i>E. tarda</i> tens&atilde;o   (ETSJ54) para identificar genes putativos relacionados com virul&ecirc;ncia. Os genes relacionados com virul&ecirc;ncia assumidos de   <i>E. tarda</i> foram agrupados em ocho categorias inclusive chemotaxis e motility, endotoxin (LPS), tipo I e tipo III sistemas de   subst&acirc;ncia segreda, compreens&atilde;o de ferro, proca&ccedil;oadores, e intra-macrophage sobreviv&ecirc;ncia. Os resultados revelam que   <i>E. tarda</i> &eacute; equipado com uma larga variedade de genes implicados na virul&ecirc;ncia e pathogenesis de g&ecirc;neros bacterianos   diversos e esp&eacute;cie inclusive <i>Salmonella</i>, <i>Yersinia</i> e esp&eacute;cie <i>Vibrios</i>. Os resultados tamb&eacute;m indicam um alto fluxo gen&eacute;tico   no <i>E. tarda</i> genoma que pode explicar em alguma extens&atilde;o o seu potencial para infeccionar e causar a doen&ccedil;a em um n&uacute;mero de esp&eacute;cie dos animais.</p>     ]]></body>
<body><![CDATA[<p><b>Palavras chave</b>: <i>Edwardsiellosis</i>, genoma sequencing, virul&ecirc;ncia, pathogenesis.</p>  <hr size="1" />           <p><b><font size="3">Introduction</font></b></p>     <p><i>Edwardsiellosis</i> is a systemic suppurative disease caused   by the Gram-negative bacterium <i>Edwardsiella tarda</i>,   a member of the family enterobacteriaceae (Ewing   <i>et al</i>., 1965). <i>E. tarda</i> is usually found in water-living animals,   causing disease in cultured marine and fresh-water   fishes around the world (Miyazaki and Kaige 1985).   The bacterium may also cause sporadic infections in   birds, frogs, reptiles, marine and terrestrial mammals   including humans (Verjan <i>et al</i>., 2012). The infection in   man often occurs accidentally during manipulation of   aquatic animals and range from self-limited gastrointestinal   and extraintestinal infections up to lethal septicemia (Wang <i>et al</i>., 2005; Spencer <i>et al</i>., 2008).</p>     <p>Multiple proteins appear to be involved in the virulence   and pathogenesis of <i>E. tarda</i> infections, some of   them are hemolysins (Hirono <i>et al</i>., 1997), siderophore   production, resistance to serum killing, motility mediated   by the flagella, and phosphate uptake (Mathew <i>et al</i>., 2001), a sialidase Nan A that increase colonization   of fish tissues (Jin <i>et al</i>., 2012), a type III secretion   system that allow survival and replication of <i>E. tarda</i> within macrophages (Okuda <i>et al</i>., 2006), a DNA adenine   methylase (Dam) that reduce UV radiation and   H2O2 sensibility (Sun <i>et al</i>., 2010), an iron-cofactored   superoxide dismutase (FeSOD) that inhibits macrophage-   mediated immune responses (Cheng <i>et al</i>., 2010),   and plasmids coding antibiotic resistance genes, transposases   and conjugal transfer genes have also been associated with <i>E. tarda</i> virulence (Yu <i>et al</i>., 2012).</p>     <p>The above studies have contributed substantially to understand   the pathogenic mechanisms used by <i>E. tarda</i> during the infection process in fish, and the information   gathered from the whole genome sequence of <i>E. tarda</i> EIB202 strain showed that a substantial proportion   of the genome is devoted to the growth and survival   under diverse conditions including intracellular niches   (Wang <i>et al</i>., 2009). We initially reported the identification   of seven antigenic protein coding genes of <i>E. tarda</i> ETSJ54 strain (Verjan <i>et al</i>., 2005), and subsequent   studies by others reported the usefulness and protective   effects of some of those proteins in vaccinated fish   (Hou <i>et al</i>., 2009). Our group also performed a partial   genome sequencing of the <i>E. tarda</i> ETSJ54 genome and   deposited in the Gene Bank database a number of virulent-   related genes (Verjan, 2005). Here, we present   the annotation and a discussion of the putative roles   of those genes that were available since 2005, before   the whole genome of <i>E. tarda</i> was published. By that   time there were no many sequenced genes of <i>E. tarda</i> available and by using the basic local alignment search   tool (BlastX, version 2.2.28+), the obtained nucleotide   sequences resembled those from many Gram-negative   enteropathogens, however, an up-to-date BlastP (BlastP,   version 2.2.28+) results is presented here and indicate   that almost all the coded proteins of the <i>E. tarda</i> ETSJ54   genome correspond to those of the <i>E. tarda</i> EIB202 strain   (Wang <i>et al</i>., 2009). The results shows that <i>E. tarda</i> ETSJ54, is equipped with the genes coding for major   surface structures involved in motility, lipopolysaccharides   and capsular polysaccharides, endo and exo-toxin   secretion, iron uptake, intramacrophage survival and   proteases among others. The presence of a variety of   insertion sequence elements not only indicates a high   genetic flux in the <i>E. tarda</i> genome but also suggests this   bacterium has a highly dynamic and potentially rapidly   evolving genome that could explain in some extent its   potential to infect and to cause disease in a number of animal species.</p>     <p><b><font size="3">Material and methods</font></b></p>     <p><b><i>Bacterial strains and culture conditions</i></b></p>     <p><i>E. tarda</i> SJ54 (ETSJ54) was isolated from an outbreak of   disease in Japanese flounder (<i>Paralichthys olivaceus</i>) in   Shizuoka, Japan. The bacterium was grown on heart infusion   medium (Difco Laboratories, Detroit, MI, USA) at   30 &deg;C. All bacterial strains and plasmids used in this study   are described in <a href="#tab1">Table 1</a>. Escherichia coli strains XL1-   Blue MR and JM109 were grown in Luria-Bertani (LB) or   2 &times; YT medium at 37 &deg;C and when required, ampicillin   at concentrations of 50 &micro;g/ml and chloramphenicol at   20 &micro;g/ml were added (Sambrook and Russell 2001).</p>       <p align="center"><a href="img/revistas/rori/v17n1/v17n1a08tab1.gif" target="_blank">Table 1</a><a name="tab1"></a></p>     <p><b><i>Construction of genomic DNA libraries</i></b></p>     ]]></body>
<body><![CDATA[<p>Genomic DNA from ETSJ54 was isolated by the method   of Ausubel (Ausubel <i>et al</i>., 1994), and partially digested   with a fixed concentration of Sau3A1 enzyme at the   indicated time-lapses (30s, 60s, 90s, 2', 3', 5', 7', 10'   and 15'). Genomic DNA fragments obtained at each   digestion period were separated in 1% agarose by pulsed   field gel electrophoresis (PFGE), with pulse times of   5s to 20s at 6 volts for 8 hr. Genomic DNA fragments   in the 20-40 Kbp range (<a href="#fig1">Figure 1</a>) were dephosphorylated   with calf intestinal alkaline phosphatase (Promega,   Madison, WI, USA) and ligated into the BamHI site of   Supercos I vector (Stratagene, La Jolla, CA, U.S.A). The   recombinant molecules were packaged into lambda   (&lambda;) phage particles (Epicentre Technologies, Madison,   WI, USA) and used to infect <i>E. coli</i> XL1-Blue MR. Genomic   DNA from ETSJ54 was also subjected to random   mechanical shearing by using an ultrasonic disrupter   UD-21 (Tomy Digital Biology Co, Tokyo Japan), coupled   with a micro tip to produce small DNA fragments   (0.5-2 kbp) by ultrasounds. The DNA fragments were   ligated into the plasmid vector puC118 (Takara, Ohtsu,   Japan) to generate a plasmid DNA library. <i>E. coli</i>   JM109 was transformed with recombinant plasmids   by the heat shock method and all DNA, cosmid and   plasmid preparations were carried out using standard   procedures (Sambrook and Russell 2001). Cosmid and   plasmid DNA libraries were amplified and stored at -80   &deg;C until use.</p>       <p align="center"><a href="img/revistas/rori/v17n1/v17n1a08fig1.gif" target="_blank">Figure 1</a><a name="fig1"></a></p>     <p><i><b>Subcloning and nucleotide sequence determination</b></i></p>     <p>Cosmid and plasmid libraries were cultured in LB agar   plates with ampicillin and single colonies were randomly   isolated and grown in 2 x YT broth for cosmid   or plasmid DNA isolation. Sequencing of the   terminal ends of cosmid DNA was performed with   T3, 5&acute;-(ATTAACCCTCACTAAAGGGA)-3&acute; and T7,   5&acute;-TAATACGACTCACTATAGGG 3&acute; primers sets to   identify putative ORF flanking the <i>E. tarda</i> DNA fragments.   Cosmid DNA was digested with <i>EcoRI</i> restriction   enzyme to estimate the size of the inserted   DNA fragment, followed by digestion with several   restriction enzymes (i.e, <i>BamHI</i>, <i>EcoRI</i>, <i>EcoRV</i>, <i>HincII</i>,   <i>HindIII</i>, <i>PstI</i>, <i>SacI</i>, or <i>SacII</i>) and the DNA fragments   ligated into plasmid vectors (pUC118, pBluescript, or   pHSG399) for sequencing (<a href="#fig2">Figure 2</a>). Plasmid DNA   were sequenced with M13F (5&prime;-GTAAAACGACGGCCAGTACG-3&prime;) and M13R (5&prime;-ACTATCTAGAGCGGCCGCTT-3&prime;) primer sets. The nucleotide sequences   were determined by the cycle sequencing method   using Thermo sequenase fluorescent-labeled primer   cycle sequencing kit (Amersham Pharmacia Biotech,   Little Chalfont Buckinghamshire, UK). Specific oligonucleotides   primers were designed to amplify some   of the putative open reading frames (ORFs). The PCR   products were ligated into pGEM-T Easy vector (Promega,   Madison, WI, USA) and sequenced. Details for   any technique will be provided if required.</p>       <p align="center"><a href="img/revistas/rori/v17n1/v17n1a08fig2.gif" target="_blank">Figure 2</a><a name="fig2"></a></p>     <p><b><i>Gene annotation and classification</i></b></p>     <p>The DNA sequence data of ETSJ54 were compared   with those in the GenBank (www.ncbi.nlm.nih.gov)   database using the BLASTX (Version 2.2.28+) software   (Zhang <i>et al</i>., 2000) of the National Center for   Biotechnology Information, to identify DNA sequences   that resemble our query sequence based on similarity   of the nucleotide sequence. The identified   closest homologous gene sequence in other bacterial   species allowed predicting its putative function   or the potential origin of the DNA sequence and   its classification. The functional classification of E.   tarda DNA sequences followed that used for other   pathogens such as <i>Yersinia</i> and <i>Salmonella</i> species   database of the Sanger Institute (<a href="www.sanger.ac.uk/Projects/Microbes/" target="_blank">www.sanger.ac.uk/Projects/Microbes/</a>), or those reported in the Microbial   Genome Database (<a href="http://mbgd.genome.ad.jp" target="_blank">http://mbgd.genome.ad.jp</a>). The putative virulence-related genes of <i>E. tarda</i> ETSJ54 were submitted to the GenBank data base   and the data included the closest original hits obtained   when no <i>E. tarda</i> genome was known. Here,   we provide an updated comparison of the predicted   amino acid sequence of the ETSJ54 ORFs using the   BLASTP (Version 2.2.28+) software (Altschul <i>et al</i>.,   1997).</p>     <p><b><font size="3">Results</font></b></p>     <p><b><i>Functional classification of E. tarda ETSJ54 open   reading frames (ORFs)</i></b></p>     <p>One thousand and one hundred fifty eight (1,158) putative   ORFs of the <i>Edwardsiella</i> <i>tarda</i> ETSJ54 genome   were identified from a total of 1,382 sequenced clones   (1,056 cosmid and 326 plasmid clones). The number   of putative ORFs and the coded genes revealed that   there was not significant redundancy in the sequenced   clones, and indicates these libraries are unique and   represent an important tool for further studies. The   functional classification of <i>E. tarda</i> ETSJ54 ORFs (<a href="#tab3">Table   2</a>) shows 5 major categories as follows: small molecule   metabolism (256 ORFs), which constitute 22% from   total ORFs and contain protein-coding genes involved   in degradation of carbon compound and amino acids,   energy metabolism, central intermediary metabolism,   amino acid biosynthesis, polyamine synthesis, nucleosides   and nucleotides biosynthesis, cofactors and fatty   acid biosynthesis. The other four major categories are   the broad regulatory function-related genes (65 ORFs),   macromolecule metabolism (219 ORFs), cell processes   (179 ORFs) and others (439 ORFs), which include   insertion sequence elements and hypothetical proteins.   The percentages of <i>E. tarda</i> ETSJ54 ORFs in each   subcategory are shown in <a href="#fig3">Figure 3</a>.</p>     ]]></body>
<body><![CDATA[<p align="center"><a href="img/revistas/rori/v17n1/v17n1a08tab2.gif" target="_blank">Table 2</a><a name="tab2"></a></p>     <p><b><i>Virulence-related genes in the E. tarda ETSJ54   strain</i></b></p>     <p>A total of one hundred and five (105) putative virulence-   related genes of <i>E. tarda</i> ETSJ54 were annotated   and deposited in the Gene Bank database. Identification   was made by comparison of their nucleotide   sequence with those in other bacterial pathogens, in   which virulence-related genes and the coding protein   have been characterized in some extent. Eighty (80)   putative virulence-related genes were grouped into 8   subcategories and the GeneBank accession numbers   are presented in <a href="#tab3">Table 3</a>. The subcategories in which   the <i>E. tarda</i> ETSJ54 ORFs fall into were chemotaxis and   motility conferred by the flagellum, capsular polysaccharide   and endotoxin production, exotoxin secretion   by type I and type III secretion systems, iron uptake,   proteases and intramacrophage survival. A wide range   of membrane proteins, lipoproteins and proteins   involved in peptidoglycan biosynthesis are also components   of the bacterial cell wall, and may play different   roles in the pathogenesis of the disease, they were   classified as "other virulence-related genes" and not   included in this report. The predicted amino acid sequences   coded by 80 of the ETSJ54 ORFs were compared   to those in the protein sequence database and   show that almost all coded proteins resemble those   recently reported in <i>E. tarda</i> EIB202 (Wang <i>et al</i>., 2009)   and the <i>E. tarda</i> C07-087 (Tekedar <i>et al</i>., 2013), however,   there still differences between <i>E. tarda</i> strains and   the amino acid identity may varies from 48% to 100   %. These differences may support further studies of its   characterization.</p>       <p align="center"><a href="img/revistas/rori/v17n1/v17n1a08tab3.gif" target="_blank">Table 3</a><a name="tab3"></a></p>     <p><b><font size="3">Discussion</font></b></p>     <p><b><i>Chemotaxis and motility conferred by the flagellum</i></b></p>     <p>Bacteria are able to sense, respond and adapt to environmental   signals that may be useful or detrimental to   cell survival. Chemotaxis proteins and the flagellum are   coupled to various signal transduction pathways that   modulate gene expression to drive motility, cell-to-cell   clumping or prevent chemotaxis (Bible <i>et al</i>., 2012). In   fish pathogens, those proteins may be advantageous in   a highly dynamic environment such the water, where   they may allow the bacteria to reach the host mucosal   surfaces and to find an appropriate niche for colonization.   The flagellum has been involved in the invasion   process of <i>Salmonella enterica</i> (Stecher <i>et al</i>., 2004)   and <i>Burkholderia pseudomallei</i> in mammals (Chua <i>et al</i>., 2003), similarly in fish, a flagellin (FliC) deficient E.   tarda showed reduced pathogenecity, motility, biofilm   formation and reduced levels of TTSS virulenceassociated   proteins (He <i>et al</i>., 2012). Flagellin is the   structural component of the flagellum, and a pathogen   associated molecular pattern (PAMP) recognized by   Toll-like receptor 5 (TLR-5), capable of activate innate   and adaptive immune responses with strong adjuvant   activity (Sanders <i>et al</i>., 2009), and overexpression of   flagellin may induce elevated immune responses and   attenuate bacterial virulence (Yang <i>et al</i>., 2012). We   identified regulators of the chemotaxis response such   as CheA and major components of the flagella structure   in <i>E. tarda</i> ETSJ54 (<a href="#tab3">Table 3</a>), including flagellin, and   previously we reported that a rabbit anti-<i>E. tarda</i> serum   reacted with the recombinant flagellin (FliC, ET46) of   ETSJ54 in Western blot analysis demonstrating its antigenic   properties (Verjan <i>et al</i>., 2005). Recently, flagellin   was found in the OMP extract of <i>E. tarda</i> where   it appears to mediates direct interaction of the bacteria   with fish epithelial cell surface proteins (Liu <i>et al</i>.,   2012), indicating not only functions in motility but also   in adhesion and invasion. The flagellum is a protein export   system structurally similar to the type III secretion   of virulence factors (TTSS), which appear to exist only   in flagellated Gram-negative species, therefore, additional   functions to this structure might be discovered in   near future. Both the flagellum and TTSS were recently   reported to be regulated by the two-component system   QseB/QseC in <i>E. tarda</i> (Wang <i>et al</i>., 2011), genes   also found in <i>E. tarda</i> ETSJ54 (<a href="#tab3">Table 3</a>).</p>     <p><b><i>Lipopolysaccharide (LPS) and capsular   polysaccharide</i></b></p>     <p>The lipopolysaccharide (LPS) is considered a major virulence   factor, and is one of the most potent microbial   initiators of inflammation by Gram-negative bacteria   Three components structure the LPS molecule, the hydrophobic   lipid moiety or lipid A, an oligosaccharide   core attached to the lipid A, and the O-antigen (Gyorfy <i>et al</i>., 2013). LPS mediates cell activation by a signaling   pathway involving the LPS binding protein (LBP) that   transfer LPS to CD14 and then to the MD-2 and TLR-4   complex (Ohto <i>et al</i>., 2007), that form a multimeric   complex on the surface of monocytic cells that lead to   cytokine production (such as TNF-&alpha;, IL-1, IL-6) and a   systemic inflammatory reaction that can result in multiple   organ failure, shock and death (Gyles 2011). The   structure of the O-polysaccharide of <i>E. tarda</i> was reported   (Vinogradov <i>et al</i>., 2005) and gives insights into the   differences and relationships with other LPS molecules   and their differential immunostimulatory activities. We   identified a number of genes involved in the synthesis   and assembly of the LPS and the capsular polysaccharide   of <i>E. tarda</i> ETSJ54; however, the mechanisms   of action in fish are yet to be recognized. Fish were   reported to be low responders or insensitivity to the   effects of LPS (Iliev <i>et al</i>., 2005), although, there had   been some reports on the immunomodulatory capacity   of various LPS preparations (Sampath <i>et al</i>., 2009;   Nayak <i>et al</i>., 2011), today the hemodynamics and vascular   changes that can be induced in mammals upon   LPS administration are considered absent in fish. It is   accepted that LPS could induce a differential immune   response in fish that appears to depend on its structure   and source (Hang <i>et al</i>., 2013; Kadowaki <i>et al</i>., 2013),   and it become necessary to evaluate the role of the   LPS in the fish model of Gram-negative sepsis, as this   might be different to that known in mammals. LPS and   the capsular polysaccharide in <i>E. tarda</i> may also be involved   in conferring additional properties to the bacterium   such as serum resistance (complement mediated   killing), intramacrophage survival or even have another   roles not yet described.</p>     <p><b><i>Secretion of toxins: Type I secretion system</i></b></p>     ]]></body>
<body><![CDATA[<p>The bacterial type I secretion system (T1SS) is involved   in the secretion of various cell toxins and adhesins such   as the giant nonfimbrial adhesin of <i>Salmonella</i> (Griessl <i>et al</i>., 2013). The pore forming toxin hemolysin (HlyA)   from <i>E. coli</i> is the example of toxins inserted into the   host cell membrane to form a pore or channel that leads   to lysis of the host cell (Chen <i>et al</i>., 1996). The <i>E. tarda</i> hemolysin (EthA) was characterized in early studies (Hirono <i>et al</i>., 1997). The protein was associated with lysis   of the phagocytic vacuole within macrophages (Janda <i>et al</i>., 1991), cytotoxicity in HEp-2 cells (Strauss <i>et al</i>.,   1997), and most recently required for cell invasion and   internalization of <i>E. tarda</i> by epithelial papilloma of carp   (EPC) cells (Wang <i>et al</i>., 2010).</p>     <p>Another toxin that may be involved in the pathogenesis   of <i>E. tarda</i> infections, but not yet described is the   leukotoxin or RTX (repeats in the structural toxin), an   initially described cytotoxic pore-forming toxin that   appears to have a broad spectrum of biological and   biochemical activities (Linhartova <i>et al</i>., 2010). It has   been well characterized in <i>Mannheimia haemolytica</i>,   where it shows dose-dependent activity ranging from   activation, increases respiratory burst and degranulation   of leukocytes at low dose of toxin, up to apoptosis   and necrosis at high doses (Narayanan <i>et al</i>., 2002). In   this study, we identified in the <i>E. tarda</i> ETSJ54 genome   the genes coding for the hemolysin A and the hemolysin   activator protein hlyB, and a gene coding for   the <i>Salmonella</i> <i>typhimurium</i> large repetitive protein,   also called hemagglutinin/hemolysin related protein   in <i>Ralstonia solanacearum</i> (Salanoubat <i>et al</i>., 2002) or   RTX family exoprotein of <i>E. coli</i> (Perna <i>et al</i>., 2001). A   functional characterization of this protein in <i>E. tarda</i> will allow us to understand more about the pathogenic   mechanisms displayed by the bacterium during the induction   of disease.</p>     <p><b><i>Type III secretion system</i></b></p>     <p>Plant and animal bacterial pathogens possess a type III   secretion system (TTSS) that secretes bacterial virulence   proteins into the host cells, capable of modulating   a variety of cellular pathways (Hicks <i>et al</i>., 2011), to   generate a differential antigen-specific T cell responses   (Lee <i>et al</i>., 2012). This system consists of a secretion   apparatus, regulatory proteins, toxins (effector proteins)   and chaperone proteins which protect and guide   the effector proteins to the TTS apparatus (Ehrbar and   Hardt 2005). The TTSS is used for different purposes   including attachment, internalization, invasion, multiplication   within the host cells and systemic spreading   (Abe <i>et al</i>., 2005), and appear to be switched off in   vitro, when the bacteria is not in contact with host cells   (Gaillard <i>et al</i>., 2011). In <i>E. coli</i> this system may induce   effacement of the microvilli from intestinal epithelial   cells, leading to the formation of attaching/effacing   (A/E) lesions (Abe <i>et al</i>., 2005; He <i>et al</i>., 2004). <i>Yersinia</i> species and <i>Pseudomonas aeruginosa</i> effector proteins   mediate inhibition of phagocytosis by interfering with   the host cell signaling, perturbing the dynamics of the   cytoskeleton, and blocking the production of proinflammatory   cytokines (Navarro <i>et al</i>., 2005; Sodhi <i>et al</i>., 2005), whereas in <i>Salmonella</i> <i>typhimurium</i>, TTSS appear   to mediates irreversible adhesion and invasion in   vitro (Misselwitz <i>et al</i>., 2012), as well as invasion to the   intestinal epithelial cells and trafficking to the basolateral   side <i>in vivo</i> (Muller <i>et al</i>., 2012). A type III secretion   system was previously identified and characterized in   virulent strains of <i>E. tarda</i> (Rao <i>et al</i>., 2004; Zheng <i>et al</i>., 2005), and in the course of this study we also found   several components of the <i>E. tarda</i> type III secretion   system (<a href="#tab3">Table 3</a>), however its relevance in fish cell/tissue   damage needs further studies.</p>     <p><b><i>Genes associated with the iron acquisition system</i></b></p>     <p>The genome of <i>E. tarda</i> ETSJ54 like other enteropathogens   possess a gene cluster that encode proteins involved   in biosynthesis and utilization of siderophores,   proteins that mediates iron uptake (Sudheesh <i>et al</i>.,   2012), an element involved in many biological processes   such as respiration, tricarboxylic acid cycle,   oxygen transport, gene regulation and DNA biosynthesis   (Krewulak and Vogel 2008). The concentration of   iron within the host under normal conditions is too   low to permit growth of bacteria, and the pathogens   are forced to express highly efficient mechanisms for   iron acquisition. In fact, bacteria can acquire ferrous   iron (Fe<sup>2+</sup>) and accessible host iron-binding proteins   (hemoglobin, transferrin, lactoferrin) by using receptor-   mediated transport systems such as the FeoA-interacting   G-protein-like transporter FeoB (Kim <i>et al</i>.,   2012). However, the main mechanism that contributes   to the virulence is the production of iron-chelating   compounds (siderophores) also called enterobactin   (catecholate) and ferrichrome (hydroxamate), characterized   by their high specificity and affinity towards   ferric (Fe<sup>3+</sup>) iron (Andrews <i>et al</i>., 2003; Miethke and   Marahiel 2007). Siderophore production appear to be   regulated by the iron-responsive transcriptional repressor   fur and by small RNA molecules such as RyhB (Salvail <i>et al</i>., 2010). This study identified genes involved   in the synthesis and transport of siderophores through   the bacterial cell wall in <i>E. tarda</i> ETSJ54 (<a href="#tab3">Table 3</a>), that   gives support to preliminary observations that suggested   the presence of this iron acquisition system in this   bacterium (Kokubo <i>et al</i>., 1990), however, its role in   the pathogenesis of edwardsiellosis remains to be elucidated.</p>     <p><b><i>Proteases</i></b></p>     <p>Pathogenic microorganism secretes proteolytic enzymes   that mediate tissue destruction and facilitate   colonization and infection. Proteases have cytotoxic   activities, activate cytolitic toxins, stimulate the production   of inflammatory mediators enhancing vascular permeability,   promote uptake of nutrients by pathogens,   and particularly, they appear to process and degrade   vital molecules of the innate inmune system, including   the proteins of the coagulation intrinsic pathway and   complement proteins (Potempa and Pike 2009), thus   proteolytic cleavage appears to be a mechanisms of   antibacterial activities inactivation (Potempa and Potempa   2012). The metalloproteinase produced by   <i>Staphylococcus aureus</i> (Aureolysin) is an example of   zinc-dependent metalloproteinases produced as precursor   (proAur) with autocatalytic activation properties   (Nickerson <i>et al</i>., 2008), and involved in the cleavage   of host-plasma proteins and modulation of immunological   reactions (Laarman <i>et al</i>., 2011). We identified   two proteases genes in the <i>E. tarda</i> genome, one with   nucleotide sequence identity to the zinc metalloproteinase   of <i>S. epidermidis</i> and the other had identity the   chondroitin ABC lyase of <i>Proteus vulgaris</i>, an enzyme   that has beneficial effects in reducing the chondroitin   sulphate proteoglycans-mediated inhibition of central   nervous system repair, following spinal cord injury   (Bradbury and Carter 2011). The involvement of these   proteins in the pathogenesis of the disease in fish needs   specific studies of their biological function.</p>     <p><b><i>Intramacrophage survival</i></b></p>     <p>Bacterial pathogens evolved mechanism to circumvent   the hostile environment within phagocytic cells, avoiding   phagosome-lysosome fusion, conferring survival   and an intracellular lifestyle (Grabenstein <i>et al</i>., 2006)   or enabling the bacteria to adapt to intramacrophage   stresses (Thompson <i>et al</i>., 2011). <i>S. typhimurium</i>, <i>Yersinia</i> pestis and <i>Y. pseudotuberculosis</i> survive within   macrophages by regulating the expression of several   genes of the two-component regulatory PhoP/PhoQ   system. The gene products mediate survival to the   bactericide cationic peptides, inhibit antigen processing   and presentation and therefore, inhibit induction   of specific immunity (Pujol and Bliska 2005). <i>E. tarda</i> is an intracellular pathogen, and virulent strains of E.   tarda proliferate and increase in number inside the macrophages   since 9 hr after phagocytosis, which is not   observed with low virulent strains (Ishibe <i>et al</i>., 2008).   The intracellular life style and replication of <i>E. tarda</i> within murine macrophages depend on the expression   of the type III secretion system, which induces an   NF&kappa;B-mediated anti-apoptotic response in the infected   macrophages (Okuda <i>et al</i>., 2006). Mutations in the   TTSS apparatus, chaperones, effectors and regulators   of <i>E. tarda</i> were found to have decreased survival and   growth within fish phagocytes (Tan <i>et al</i>., 2005). In   addition to the genes involved in survival of <i>E. tarda</i> within macrophage reported previously (Srinivasa Rao <i>et al</i>., 2001), we identified mgtC, mgtB, molecules involved   in intramacrophage survival and growth under   Mg<sup>2+</sup> deprived media (Alix and Blanc-Potard 2007),   and pagC, another molecule regulated by the PhoPPhoQ   two-component system, found to be required   to serum resistance in <i>Salmonella enterica</i> (Nishio <i>et al</i>., 2005), that may also contribute, although at lower   levels, to this particular life style (Alix <i>et al</i>., 2008).</p>     ]]></body>
<body><![CDATA[<p><b><font size="3">Conclusions</font></b></p>     <p>Preliminary studies reported that <i>E. tarda</i> produce   several virulence-related factors involved in the   pathogenesis of edwardsiellosis. Some of the above   virulence related factors were corroborated in recent   studies using transposon mutagenesis. Moreover, in   this study, we contribute to the understanding of the   pathogenesis of <i>Edwardsiella</i> <i>tarda</i> infections by annotating   a number of genes coding for several virulence-   related factors, supporting previous observations   about its virulence. This preliminary study reveals this   bacterium possess a number of putative virulence-related   genes associated with mobile genetic elements   that mirror a high genetic flux and horizontal gene   transfer, and pathogenic mechanisms similar to those   displayed by <i>Salmonella</i> and <i>Yersinia</i> species in mammals.   This information will be useful to initiate specific   studies on the role of each gene-protein in the   pathogenesis induced by this bacterium in fish and   mammals.</p>     <p><b><font size="3">Acknowledgements</font></b></p>     <p>This study was supported in part by Grants-in-Aid for   Scientific Research from the Ministry of Education,   Science, Sports and Culture of Japan.</p>     <p><b><font size="3">References</font></b></p>     <!-- ref --><p>Ewing WH, McWhorter AC, Escobar MR, Lubin AH. <i>Edwardsiella</i>, a   new genus of Enterobacteriaceae based on a new species, <i>E.   tarda</i>. 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