Genes involved in degradation of para-nitrophenol are differentially arranged in form of non-contiguous gene clusters in Burkholderia sp. strain SJ98.

Biodegradation of para-Nitrophenol (PNP) proceeds via two distinct pathways, having 1,2,3-benzenetriol (BT) and hydroquinone (HQ) as their respective terminal aromatic intermediates. Genes involved in these pathways have already been studied in different PNP degrading bacteria. Burkholderia sp. strain SJ98 degrades PNP via both the pathways. Earlier, we have sequenced and analyzed a ~41 kb fragment from the genomic library of strain SJ98. This DNA fragment was found to harbor all the lower pathway genes; however, genes responsible for the initial transformation of PNP could not be identified within this fragment. Now, we have sequenced and annotated the whole genome of strain SJ98 and found two ORFs (viz., pnpA and pnpB) showing maximum identity at amino acid level with p-nitrophenol 4-monooxygenase (PnpM) and p-benzoquinone reductase (BqR). Unlike the other PNP gene clusters reported earlier in different bacteria, these two ORFs in SJ98 genome are physically separated from the other genes of PNP degradation pathway. In order to ascertain the identity of ORFs pnpA and pnpB, we have performed in-vitro assays using recombinant proteins heterologously expressed and purified to homogeneity. Purified PnpA was found to be a functional PnpM and transformed PNP into benzoquinone (BQ), while PnpB was found to be a functional BqR which catalyzed the transformation of BQ into hydroquinone (HQ). Noticeably, PnpM from strain SJ98 could also transform a number of PNP analogues. Based on the above observations, we propose that the genes for PNP degradation in strain SJ98 are arranged differentially in form of non-contiguous gene clusters. This is the first report for such arrangement for gene clusters involved in PNP degradation. Therefore, we propose that PNP degradation in strain SJ98 could be an important model system for further studies on differential evolution of PNP degradation functions

Chemotaxis gene clusters in <i>Burkholderia</i> strains SJ98, YI23, CCGE 1001, CCGE 1002 and CCGE 1003.

<p>Chemotaxis gene clusters in <i>Burkholderia</i> strains SJ98, YI23, CCGE 1001, CCGE 1002 and CCGE 1003.</p

Characterization of <i>Burkholderia</i> sp. SJ98, <i>Burkholderia</i> sp. YI23, <i>Burkholderia</i> sp. CCGE 1001, <i>Burkholderia</i> sp. CCGE 1002 and <i>Burkholderia</i> sp. CCGE 1003.

<p>Characterization of <i>Burkholderia</i> sp. SJ98, <i>Burkholderia</i> sp. YI23, <i>Burkholderia</i> sp. CCGE 1001, <i>Burkholderia</i> sp. CCGE 1002 and <i>Burkholderia</i> sp. CCGE 1003.</p

Genome alignment of <i>Burkholderia</i> sp.

<p>SJ98 and <i>Burkholderia</i> sp. YI23.<b> </b></p

Genome assembly results of <i>Burkholderia</i> sp. SJ98.

*<p>Scaffolds produced by assembly of Roche’s 454 FLX data.</p>**<p>Sequences (16 contigs and 1 scaffold) produced after gap filling of Assembly-1 by Illumina GA IIX data.</p>***<p>Contigs produced after the finishing of Assembly-3 (Sanger’s sequencing and manually by BLAST), final assembly.</p

Number of <i>che</i> gene homologs in <i>E.coli</i>, <i>B</i>. sp. SJ98, <i>B</i>. sp.YI23, <i>B</i>. sp. CCGE 1001, <i>B</i>. sp. CCGE 1002 and <i>B</i>. sp. CCGE 1003.

<p>Number of <i>che</i> gene homologs in <i>E.coli</i>, <i>B</i>. sp. SJ98, <i>B</i>. sp.YI23, <i>B</i>. sp. CCGE 1001, <i>B</i>. sp. CCGE 1002 and <i>B</i>. sp. CCGE 1003.</p

Genome Annotation of <i>Burkholderia</i> sp. SJ98 with Special Focus on Chemotaxis Genes

<div><p><i>Burkholderia</i> sp. strain SJ98 has the chemotactic activity towards nitroaromatic and chloronitroaromatic compounds. Recently our group published draft genome of strain SJ98. In this study, we further sequence and annotate the genome of stain SJ98 to exploit the potential of this bacterium. We specifically annotate its chemotaxis genes and methyl accepting chemotaxis proteins. Genome of <i>Burkholderia</i> sp. SJ98 was annotated using PGAAP pipeline that predicts 7,268 CDSs, 52 tRNAs and 3 rRNAs. Our analysis based on phylogenetic and comparative genomics suggest that <i>Burkholderia</i> sp. YI23 is closest neighbor of the strain SJ98. The genes involved in the chemotaxis of strain SJ98 were compared with genes of closely related <i>Burkholderia</i> strains (i.e. YI23, CCGE 1001, CCGE 1002, CCGE 1003) and with well characterized bacterium <i>E. coli</i> K12. It was found that strain SJ98 has 37 <i>che</i> genes including 19 methyl accepting chemotaxis proteins that involved in sensing of different attractants. Chemotaxis genes have been found in a cluster along with the flagellar motor proteins. We also developed a web resource that provides comprehensive information on strain SJ98 that includes all analysis data (<a href="http://crdd.osdd.net/raghava/genomesrs/burkholderia/" target="_blank">http://crdd.osdd.net/raghava/genomesrs/burkholderia/</a>).</p></div

Study on impact of air pollution on asthma among school going children residing in urban Agra

Background: Air pollution is one of the world's most serious environmental problems. Air pollution has many negative health effects on the general population, especially children, individuals with underlying chronic disease, and the elderly. The aims of this study were to evaluate the effects of traffic-related pollution on the exacerbation of asthma and development of respiratory infections in schoolgoing children in Agra, suffering from asthma compared with healthy subjects, and to estimate the association between incremental increases in principal pollutants and the incidence of respiratory symptoms. Materials and Methods: We enrolled 702 children aged 6–18 years in this prospective study. A total of 342 children with asthma and 360 healthy subjects were monitored for 6 months from September 2013 to February 2014. Clinical data were combined with the results obtained using an air pollution monitoring system of the five most common pollutants. A total of 328 children with asthma and 345 healthy subjects completed follow-up. Results: Children with asthma reported significantly more days of fever (P <0.001) and cough (P < 0.001), episodes of rhinitis (P = 0.087), asthma attacks (P < 0.001), episodes of pneumonia (P < 0.003), and hospitalizations (P = 0.01). In the asthma cohort, living close to the street with a high traffic density was a risk factor for asthma exacerbations (odds ratio [OR] = 1.79; 95% confidence interval [CI], 1.13–2.84), whereas living near green areas was found to be protective (OR = 0.50; 95% CI, 0.31–0.80). Conclusion: There is a significant association between traffic-related pollution and the development of asthma exacerbations and respiratory infections in children suffering from asthma. These findings suggest that environmental control may be crucial for respiratory health in children with the underlying respiratory disease

Phylogenetic tree of amino acid sequences (A) <i>p</i>-nitrophenol 4-monooxygenase (PnpM), Benzenetriol dioxygenase (BtD) from stain SJ98 was taken as outgroup for the phylogenetic tree for PNP monooxygenases and (B) p-benzoquinone reductase (BqR), nitrite reductase from <i>E. coli</i> was taken as an outgroup to create the phylogenetic tree for the benzoquinone reductases.

<p>Neighbor joining method was applied at the bootstrap value of 1000. Accession number of the proteins is written in parentheses.</p

Predicted positions for the activity of <i>pnpA</i> and <i>pnpB</i> in <i>p</i>-nitrophenol (PNP) degradation pathway of strain SJ98.

<p>Predicted positions for the activity of <i>pnpA</i> and <i>pnpB</i> in <i>p</i>-nitrophenol (PNP) degradation pathway of strain SJ98.</p