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Genome biology of Actinobacillus pleuropneumoniae JL03, an isolate of serotype 3 prevalent in China.

Xu Z, Zhou Y, Li L, Zhou R, Xiao S, Wan Y, Zhang S, Wang K, Li W, Li L, Jin H, Kang M, Dalai B, Li T, Liu L, Cheng Y, Zhang L, Xu T, Zheng H, Pu S, Wang B, Gu W, Zhang XL, Zhu GF, Wang S, Zhao GP, Chen H - PLoS ONE (2008)

Bottom Line: Preliminary analysis of the genomic sequence and the functions of the encoded proteins not only confirmed the present physiological and pathological knowledge but also offered new insights into the metabolic and virulence characteristics of this important pathogen.In addition to confirming the lack of ApxI toxin, identification of a nonsense mutation in apxIVA and a 5'-proximal truncation of the flp operon deleting both its promoter and the flp1flp2tadV genes have provided convincing scenarios for the low virulence property of JL03.Comparative genomic analysis using the available sequences of other serotypes, probable strain (serotype)-specific genomic islands related to capsular polysaccharides and lipopolysaccharide O-antigen biosyntheses were identified in JL03, which provides a foundation for future research into the mechanisms of serotypic diversity of A. pleuropneumoniae.

View Article: PubMed Central - PubMed

Affiliation: Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.

ABSTRACT
Actinobacillus pleuropneumoniae is the etiologic agent of porcine contagious pleuropneumonia, a cause of considerable world wide economic losses in the swine industry. We sequenced the complete genome of A. pleuropneumoniae, JL03, an isolate of serotype 3 prevalent in China. Its genome is a single chromosome of 2,242,062 base pairs containing 2,097 predicted protein-coding sequences, six ribosomal rRNA operons, and 63 tRNA genes. Preliminary analysis of the genomic sequence and the functions of the encoded proteins not only confirmed the present physiological and pathological knowledge but also offered new insights into the metabolic and virulence characteristics of this important pathogen. We identified a full spectrum of genes related to its characteristic chemoheterotrophic catabolism of fermentation and respiration with an incomplete TCA system for anabolism. In addition to confirming the lack of ApxI toxin, identification of a nonsense mutation in apxIVA and a 5'-proximal truncation of the flp operon deleting both its promoter and the flp1flp2tadV genes have provided convincing scenarios for the low virulence property of JL03. Comparative genomic analysis using the available sequences of other serotypes, probable strain (serotype)-specific genomic islands related to capsular polysaccharides and lipopolysaccharide O-antigen biosyntheses were identified in JL03, which provides a foundation for future research into the mechanisms of serotypic diversity of A. pleuropneumoniae.

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The characterizations of A. pleuropneumoniae JL03's genome and the oriC region.(A) Circular genome representation of JL03. Circles are numbered from 1 (outer circle) to 10 (inner circle). The circles 1/2 shows predicted CDSs on the plus and minus strand in JL03 color-coded by COG categories. All genes are colored according to biological functions: gold for translation, ribosomal structure and biogenesis; orange for RNA processing and modification; light orange for transcription; dark orange for DNA replication, recombination and repair; antique white for cell division and chromosome partitioning; pink for defense mechanisms; tomato for signal transduction mechanisms; peach for cell envelope biogenesis and outer membrane; deep pink for intracellular trafficking, secretion and vesicular transport; pale green for posttranslational modification, protein turnover and chaperones; royal blue energy production and conversion; blue for carbohydrate transport and metabolism; dodger blue for amino acid transport and metabolism; sky blue for nucleotide transport and metabolism; light blue for coenzyme metabolism; cyan for lipid metabolism; medium purple for inorganic ion transport and metabolism; aquamarine for secondary metabolites biosynthesis, transport and catabolism; gray for function unknown. Circle 3/4, the putative horizontal transferred genes in deep pink identified by SIGI-HMM on the forward and reverse strand. Circle 5, repetitive elements in yellow, above 200nt and cutoff value 1e-10. Circle 6, transposases in green and potential prophage genes in dark orange. Circle 7, mean centered GC content of JL03 genes (red: above mean, blue-below mean). Circle 8, tRNA genes in orange. Circle 9, rRNA genes in red. Circle 10, GC Skew plot (windowsize: 1000, windowoverlap: 500). (B) Genetic organization of the oriC regions in three representative organisms within the family of Pasteurellaceae: JL03, A. pleuropneumoniae; 35000HP, H. ducreyi; and Pm70, P. multocida.
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pone-0001450-g001: The characterizations of A. pleuropneumoniae JL03's genome and the oriC region.(A) Circular genome representation of JL03. Circles are numbered from 1 (outer circle) to 10 (inner circle). The circles 1/2 shows predicted CDSs on the plus and minus strand in JL03 color-coded by COG categories. All genes are colored according to biological functions: gold for translation, ribosomal structure and biogenesis; orange for RNA processing and modification; light orange for transcription; dark orange for DNA replication, recombination and repair; antique white for cell division and chromosome partitioning; pink for defense mechanisms; tomato for signal transduction mechanisms; peach for cell envelope biogenesis and outer membrane; deep pink for intracellular trafficking, secretion and vesicular transport; pale green for posttranslational modification, protein turnover and chaperones; royal blue energy production and conversion; blue for carbohydrate transport and metabolism; dodger blue for amino acid transport and metabolism; sky blue for nucleotide transport and metabolism; light blue for coenzyme metabolism; cyan for lipid metabolism; medium purple for inorganic ion transport and metabolism; aquamarine for secondary metabolites biosynthesis, transport and catabolism; gray for function unknown. Circle 3/4, the putative horizontal transferred genes in deep pink identified by SIGI-HMM on the forward and reverse strand. Circle 5, repetitive elements in yellow, above 200nt and cutoff value 1e-10. Circle 6, transposases in green and potential prophage genes in dark orange. Circle 7, mean centered GC content of JL03 genes (red: above mean, blue-below mean). Circle 8, tRNA genes in orange. Circle 9, rRNA genes in red. Circle 10, GC Skew plot (windowsize: 1000, windowoverlap: 500). (B) Genetic organization of the oriC regions in three representative organisms within the family of Pasteurellaceae: JL03, A. pleuropneumoniae; 35000HP, H. ducreyi; and Pm70, P. multocida.

Mentions: The genome of A. pleuropneumoniae strain JL03 is composed of 2,242,062 base pairs (bps) with a single circular chromosome (Figure 1A). Referring to genomic coordinates of strain L20, the dnaA gene, designated APJL0001, was selected as the first gene of the JL03 genome. The putative replication origin (oriC) of JL03 chromosome was identified between two genes, gidA (APJL1688) and cof (APJL1689), based on GC skew and the presence of DnaA protein recognition sequences (DnaA-boxes) [12], [13] with typical gamma proteobacterium oriC features as what found in other genera of the Pasteurellaceae family (Figure 1B and Table 1).


Genome biology of Actinobacillus pleuropneumoniae JL03, an isolate of serotype 3 prevalent in China.

Xu Z, Zhou Y, Li L, Zhou R, Xiao S, Wan Y, Zhang S, Wang K, Li W, Li L, Jin H, Kang M, Dalai B, Li T, Liu L, Cheng Y, Zhang L, Xu T, Zheng H, Pu S, Wang B, Gu W, Zhang XL, Zhu GF, Wang S, Zhao GP, Chen H - PLoS ONE (2008)

The characterizations of A. pleuropneumoniae JL03's genome and the oriC region.(A) Circular genome representation of JL03. Circles are numbered from 1 (outer circle) to 10 (inner circle). The circles 1/2 shows predicted CDSs on the plus and minus strand in JL03 color-coded by COG categories. All genes are colored according to biological functions: gold for translation, ribosomal structure and biogenesis; orange for RNA processing and modification; light orange for transcription; dark orange for DNA replication, recombination and repair; antique white for cell division and chromosome partitioning; pink for defense mechanisms; tomato for signal transduction mechanisms; peach for cell envelope biogenesis and outer membrane; deep pink for intracellular trafficking, secretion and vesicular transport; pale green for posttranslational modification, protein turnover and chaperones; royal blue energy production and conversion; blue for carbohydrate transport and metabolism; dodger blue for amino acid transport and metabolism; sky blue for nucleotide transport and metabolism; light blue for coenzyme metabolism; cyan for lipid metabolism; medium purple for inorganic ion transport and metabolism; aquamarine for secondary metabolites biosynthesis, transport and catabolism; gray for function unknown. Circle 3/4, the putative horizontal transferred genes in deep pink identified by SIGI-HMM on the forward and reverse strand. Circle 5, repetitive elements in yellow, above 200nt and cutoff value 1e-10. Circle 6, transposases in green and potential prophage genes in dark orange. Circle 7, mean centered GC content of JL03 genes (red: above mean, blue-below mean). Circle 8, tRNA genes in orange. Circle 9, rRNA genes in red. Circle 10, GC Skew plot (windowsize: 1000, windowoverlap: 500). (B) Genetic organization of the oriC regions in three representative organisms within the family of Pasteurellaceae: JL03, A. pleuropneumoniae; 35000HP, H. ducreyi; and Pm70, P. multocida.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2175527&req=5

pone-0001450-g001: The characterizations of A. pleuropneumoniae JL03's genome and the oriC region.(A) Circular genome representation of JL03. Circles are numbered from 1 (outer circle) to 10 (inner circle). The circles 1/2 shows predicted CDSs on the plus and minus strand in JL03 color-coded by COG categories. All genes are colored according to biological functions: gold for translation, ribosomal structure and biogenesis; orange for RNA processing and modification; light orange for transcription; dark orange for DNA replication, recombination and repair; antique white for cell division and chromosome partitioning; pink for defense mechanisms; tomato for signal transduction mechanisms; peach for cell envelope biogenesis and outer membrane; deep pink for intracellular trafficking, secretion and vesicular transport; pale green for posttranslational modification, protein turnover and chaperones; royal blue energy production and conversion; blue for carbohydrate transport and metabolism; dodger blue for amino acid transport and metabolism; sky blue for nucleotide transport and metabolism; light blue for coenzyme metabolism; cyan for lipid metabolism; medium purple for inorganic ion transport and metabolism; aquamarine for secondary metabolites biosynthesis, transport and catabolism; gray for function unknown. Circle 3/4, the putative horizontal transferred genes in deep pink identified by SIGI-HMM on the forward and reverse strand. Circle 5, repetitive elements in yellow, above 200nt and cutoff value 1e-10. Circle 6, transposases in green and potential prophage genes in dark orange. Circle 7, mean centered GC content of JL03 genes (red: above mean, blue-below mean). Circle 8, tRNA genes in orange. Circle 9, rRNA genes in red. Circle 10, GC Skew plot (windowsize: 1000, windowoverlap: 500). (B) Genetic organization of the oriC regions in three representative organisms within the family of Pasteurellaceae: JL03, A. pleuropneumoniae; 35000HP, H. ducreyi; and Pm70, P. multocida.
Mentions: The genome of A. pleuropneumoniae strain JL03 is composed of 2,242,062 base pairs (bps) with a single circular chromosome (Figure 1A). Referring to genomic coordinates of strain L20, the dnaA gene, designated APJL0001, was selected as the first gene of the JL03 genome. The putative replication origin (oriC) of JL03 chromosome was identified between two genes, gidA (APJL1688) and cof (APJL1689), based on GC skew and the presence of DnaA protein recognition sequences (DnaA-boxes) [12], [13] with typical gamma proteobacterium oriC features as what found in other genera of the Pasteurellaceae family (Figure 1B and Table 1).

Bottom Line: Preliminary analysis of the genomic sequence and the functions of the encoded proteins not only confirmed the present physiological and pathological knowledge but also offered new insights into the metabolic and virulence characteristics of this important pathogen.In addition to confirming the lack of ApxI toxin, identification of a nonsense mutation in apxIVA and a 5'-proximal truncation of the flp operon deleting both its promoter and the flp1flp2tadV genes have provided convincing scenarios for the low virulence property of JL03.Comparative genomic analysis using the available sequences of other serotypes, probable strain (serotype)-specific genomic islands related to capsular polysaccharides and lipopolysaccharide O-antigen biosyntheses were identified in JL03, which provides a foundation for future research into the mechanisms of serotypic diversity of A. pleuropneumoniae.

View Article: PubMed Central - PubMed

Affiliation: Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.

ABSTRACT
Actinobacillus pleuropneumoniae is the etiologic agent of porcine contagious pleuropneumonia, a cause of considerable world wide economic losses in the swine industry. We sequenced the complete genome of A. pleuropneumoniae, JL03, an isolate of serotype 3 prevalent in China. Its genome is a single chromosome of 2,242,062 base pairs containing 2,097 predicted protein-coding sequences, six ribosomal rRNA operons, and 63 tRNA genes. Preliminary analysis of the genomic sequence and the functions of the encoded proteins not only confirmed the present physiological and pathological knowledge but also offered new insights into the metabolic and virulence characteristics of this important pathogen. We identified a full spectrum of genes related to its characteristic chemoheterotrophic catabolism of fermentation and respiration with an incomplete TCA system for anabolism. In addition to confirming the lack of ApxI toxin, identification of a nonsense mutation in apxIVA and a 5'-proximal truncation of the flp operon deleting both its promoter and the flp1flp2tadV genes have provided convincing scenarios for the low virulence property of JL03. Comparative genomic analysis using the available sequences of other serotypes, probable strain (serotype)-specific genomic islands related to capsular polysaccharides and lipopolysaccharide O-antigen biosyntheses were identified in JL03, which provides a foundation for future research into the mechanisms of serotypic diversity of A. pleuropneumoniae.

Show MeSH
Related in: MedlinePlus