scholarly journals Whole Genome Sequencing and Analysis of Chlorimuron-Ethyl Degrading Bacteria Klebsiella pneumoniae 2N3

2019 ◽  
Vol 20 (12) ◽  
pp. 3053 ◽  
Author(s):  
Cheng Zhang ◽  
Qingkai Hao ◽  
Zhengyi Zhang ◽  
Xianghui Zhang ◽  
Hongyu Pan ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Gene Knockout ◽  
Scientific Evidence ◽  
Gc Content ◽  
Open Reading Frames ◽  
Degradation Rates ◽  
Degrading Bacteria ◽  
High Throughput Dna Sequencing ◽  
Chlorimuron Ethyl ◽  
Reading Frames

Klebsiella pneumoniae 2N3 is a strain of gram-negative bacteria that can degrade chlorimuron-ethyl and grow with chlorimuron-ethyl as the sole nitrogen source. The complete genome of Klebsiella pneumoniae 2N3 was sequenced using third generation high-throughput DNA sequencing technology. The genomic size of strain 2N3 was 5.32 Mb with a GC content of 57.33% and a total of 5156 coding genes and 112 non-coding RNAs predicted. Two hydrolases expressed by open reading frames (ORFs) 0934 and 0492 were predicted and experimentally confirmed by gene knockout to be involved in the degradation of chlorimuron-ethyl. Strains of ΔORF 0934, ΔORF 0492, and wild type (WT) reached their highest growth rates after 8–10 hours in incubation. The degradation rates of chlorimuron-ethyl by both ΔORF 0934 and ΔORF 0492 decreased in comparison to the WT during the first 8 hours in culture by 25.60% and 24.74%, respectively, while strains ΔORF 0934, ΔORF 0492, and the WT reached the highest degradation rates of chlorimuron-ethyl in 36 hours of 74.56%, 90.53%, and 95.06%, respectively. This study provides scientific evidence to support the application of Klebsiella pneumoniae 2N3 in bioremediation to control environmental pollution.

scholarly journals Hydrolase CehA and Monooxygenase CfdC Are Responsible for Carbofuran Degradation inSphingomonassp. Strain CDS-1

2018 ◽  
Vol 84 (16) ◽  
Author(s):  
Xin Yan ◽  
Wen Jin ◽  
Guang Wu ◽  
Wankui Jiang ◽  
Zhangong Yang ◽  
...  
Keyword(s):  
Benzene Ring ◽  
Gene Knockout ◽  
Degradation Mechanism ◽  
Draft Genome ◽  
Open Reading Frames ◽  
Flavin Mononucleotide ◽  
Genetic Determinants ◽  
Content Type ◽  
Degrading Bacteria ◽  
Reading Frames

ABSTRACTCarbofuran, a broad-spectrum systemic insecticide, has been extensively used for approximately 50 years. Diverse carbofuran-degrading bacteria have been described, among which sphingomonads have exhibited an extraordinary ability to catabolize carbofuran; other bacteria can only convert carbofuran to carbofuran phenol, while all carbofuran-degrading sphingomonads can degrade both carbofuran and carbofuran phenol. However, the genetic basis of carbofuran catabolism in sphingomonads has not been well elucidated. In this work, we sequenced the draft genome ofSphingomonassp. strain CDS-1 that can transform both carbofuran and carbofuran phenol but fails to grow on them. On the basis of the hypothesis that the genes involved in carbofuran catabolism are highly conserved among carbofuran-degrading sphingomonads, two such genes,cehACDS-1andcfdCCDS-1, were predicted from the 84 open reading frames (ORFs) that share ≥95% nucleic acid similarities between strain CDS-1 and another sphingomonadNovosphingobiumsp. strain KN65.2 that is able to mineralize the benzene ring of carbofuran. The results of the gene knockout, genetic complementation, heterologous expression, and enzymatic experiments reveal thatcehACDS-1andcfdCCDS-1are responsible for the conversion of carbofuran and carbofuran phenol, respectively, in strain CDS-1. CehACDS-1hydrolyzes carbofuran to carbofuran phenol. CfdCCDS-1, a reduced flavin mononucleotide (FMNH2)- or reduced flavin adenine dinucleotide (FADH2)-dependent monooxygenase, hydroxylates carbofuran phenol at the benzene ring in the presence of NADH, FMN/FAD, and the reductase CfdX. It is worth noting that we found that carbaryl hydrolase CehAAC100, which was previously demonstrated to have no activity toward carbofuran, can actually convert carbofuran to carbofuran phenol, albeit with very low activity.IMPORTANCEDue to the extensive use of carbofuran over the past 50 years, bacteria have evolved catabolic pathways to mineralize this insecticide, which plays an important role in eliminating carbofuran residue in the environment. This study revealed the genetic determinants of carbofuran degradation inSphingomonassp. strain CDS-1. We speculate that the close homologuescehAandcfdCare highly conserved among other carbofuran-degrading sphingomonads and play the same roles as those described here. These findings deepen our understanding of the microbial degradation mechanism of carbofuran and lay a foundation for the better use of microbes to remediate carbofuran contamination.

scholarly journals The Genome Sequence of the Gram-Positive Sugarcane Pathogen Leifsonia xyli subsp. xyli

2004 ◽  
Vol 17 (8) ◽  
pp. 827-836 ◽  
Author(s):  
Claudia B. Monteiro-Vitorello ◽  
Luis E. A. Camargo ◽  
Marie A. Van Sluys ◽  
João P. Kitajima ◽  
Daniela Truffi ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gc Content ◽  
Open Reading Frames ◽  
Circular Chromosome ◽  
Free Sugars ◽  
Sugar Transporters ◽  
Living Organisms ◽  
Bacterial Plant Pathogen ◽  
Single Circular Chromosome ◽  
Reading Frames

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.

scholarly journals Characterization and Genome Sequence of Mycobacterium Phage XianYue

2020 ◽  
Vol 9 (25) ◽  
Author(s):  
Wesley D. Rhinehart ◽  
Amanda J. Laidlaw ◽  
Alexis M. O’Neal ◽  
Jessica A. Toller ◽  
Miriam Segura-Totten ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gc Content ◽  
Open Reading Frames ◽  
Nucleotide Identity ◽  
Content Type ◽  
Reading Frames

ABSTRACT Novel mycobacteriophage XianYue was isolated in Northeast Georgia and infects Mycobacteria smegmatis mc2155. Actinobacteriophages which share at least 50% nucleotide identity are grouped into clusters, with XianYue in cluster A2. Its genome is 52,907 bp with 91 open reading frames (ORFs) and 62.9% GC content, and it shares 86.51% nucleotide identity with mycobacteriophage Trixie.

scholarly journals Identification of Open Reading Frames Unique to a Select Agent: Ralstonia solanacearum Race 3 Biovar 2

2006 ◽  
Vol 19 (1) ◽  
pp. 69-79 ◽  
Author(s):  
Dean W. Gabriel ◽  
Caitilyn Allen ◽  
Mark Schell ◽  
Timothy P. Denny ◽  
Jean T. Greenberg ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
Plant Pathogens ◽  
Draft Genome ◽  
Gc Content ◽  
Gene Organization ◽  
Open Reading Frames ◽  
United States Department ◽  
Detection And Identification ◽  
Reading Frames ◽  
Unique Genes

An 8× draft genome was obtained and annotated for Ralstonia solanacearum race 3 biovar 2 (R3B2) strain UW551, a United States Department of Agriculture Select Agent isolated from geranium. The draft UW551 genome consisted of 80,169 reads resulting in 582 contigs containing 5,925,491 base pairs, with an average 64.5% GC content. Annotation revealed a predicted 4,454 protein coding open reading frames (ORFs), 43 tRNAs, and 5 rRNAs; 2,793 (or 62%) of the ORFs had a functional assignment. The UW551 genome was compared with the published genome of R. solanacearum race 1 biovar 3 tropical tomato strain GMI1000. The two phylogenetically distinct strains were at least 71% syntenic in gene organization. Most genes encoding known pathogenicity determinants, including predicted type III secreted effectors, appeared to be common to both strains. A total of 402 unique UW551 ORFs were identified, none of which had a best hit or >45% amino acid sequence identity with any R. solanacearum predicted protein; 16 had strong (E < 10-13) best hits to ORFs found in other bacterial plant pathogens. Many of the 402 unique genes were clustered, including 5 found in the hrp region and 38 contiguous, potential prophage genes. Conservation of some UW551 unique genes among R3B2 strains was examined by polymerase chain reaction among a group of 58 strains from different races and biovars, resulting in the identification of genes that may be potentially useful for diagnostic detection and identification of R3B2 strains. One 22-kb region that appears to be present in GMI1000 as a result of horizontal gene transfer is absent from UW551 and encodes enzymes that likely are essential for utilization of the three sugar alcohols that distinguish biovars 3 and 4 from biovars 1 and 2.

scholarly journals Synthesis of a Klebsiella pneumoniae O-Antigen Heteropolysaccharide (O12) Requires an ABC 2 Transporter

2003 ◽  
Vol 185 (5) ◽  
pp. 1634-1641 ◽  
Author(s):  
Luis Izquierdo ◽  
Susana Merino ◽  
Miguel Regué ◽  
Florencia Rodriguez ◽  
Juan M. Tomás
Keyword(s):  
Klebsiella Pneumoniae ◽  
Genomic Library ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
Complete Analysis ◽  
E Coli ◽  
O Antigen ◽  
High Level ◽  
K 12 ◽  
Reading Frames

ABSTRACT A recombinant clone encoding enzymes for Klebsiella pneumoniae O12-antigen lipopolysaccharide (LPS) was found when we screened for serum resistance of a cosmid-based genomic library of K. pneumoniae KT776 (O12:K80) introduced into Escherichia coli DH5α. A total of eight open reading frames (ORFs) (wb O12 gene cluster) were necessary to produce K. pneumoniae O12-antigen LPS in E. coli K-12. A complete analysis of the K. pneumoniae wb O12 cluster revealed an interesting coincidence with the wb O4 cluster of Serratia marcescens from ORF5 to ORF8 (or WbbL to WbbA). This prompted us to generate mutants of K. pneumoniae strain KT776 (O12) and to study complementation between the two enterobacterial wb clusters using mutants of S. marcescens N28b (O4) obtained previously. Both wb gene clusters are examples of ABC 2 transporter-dependent pathways for O-antigen heteropolysaccharides. The wzm-wzt genes and the wbbA or wbbB genes were not interchangeable between the two gene clusters despite their high level of similarity. However, introduction of three cognate genes (wzm-wzt-wbbA or wzm-wzt-wbbB) into mutants unable to produce O antigen allowed production of the specific O antigen. The K. pneumoniae O12 WbbL protein performs the same function as WbbL from S. marcescens O4 in either the S. marcescens O4 or E. coli K-12 genetic background.

scholarly journals Genome Analysis of the Meat Starter Culture Bacterium Staphylococcus carnosus TM300

2008 ◽  
Vol 75 (3) ◽  
pp. 811-822 ◽  
Author(s):  
Ralf Rosenstein ◽  
Christiane Nerz ◽  
Lalitha Biswas ◽  
Alexandra Resch ◽  
Guenter Raddatz ◽  
...  
Keyword(s):  
Starter Culture ◽  
Gc Content ◽  
Open Reading Frames ◽  
Genomic Islands ◽  
Nitrite Reduction ◽  
Staphylococcus Carnosus ◽  
Natural Tendency ◽  
Sugar Degradation ◽  
Species Specific ◽  
Reading Frames

ABSTRACT The Staphylococcus carnosus genome has the highest GC content of all sequenced staphylococcal genomes, with 34.6%, and therefore represents a species that is set apart from S. aureus, S. epidermidis, S. saprophyticus, and S. haemolyticus. With only 2.56 Mbp, the genome belongs to a family of smaller staphylococcal genomes, and the ori and ter regions are asymmetrically arranged with the replichores I (1.05 Mbp) and II (1.5 Mbp). The events leading up to this asymmetry probably occurred not that long ago in evolution, as there was not enough time to approach the natural tendency of a physical balance. Unlike the genomes of pathogenic species, the TM300 genome does not contain mobile elements such as plasmids, insertion sequences, transposons, or STAR elements; also, the number of repeat sequences is markedly decreased, suggesting a comparatively high stability of the genome. While most S. aureus genomes contain several prophages and genomic islands, the TM300 genome contains only one prophage, ΦTM300, and one genomic island, νSCA1, which is characterized by a mosaic structure mainly composed of species-specific genes. Most of the metabolic core pathways are present in the genome. Some open reading frames are truncated, which reflects the nutrient-rich environment of the meat starter culture, making some functions dispensable. The genome is well equipped with all functions necessary for the starter culture, such as nitrate/nitrite reduction, various sugar degradation pathways, two catalases, and nine osmoprotection systems. The genome lacks most of the toxins typical of S. aureus as well as genes involved in biofilm formation, underscoring the nonpathogenic status.

scholarly journals Complete Genome Analysis of a Novel Alcaligenes Faecalis Phage vB_Af_QDWS595

2021 ◽  
Author(s):  
Yujie Jing ◽  
Hong Lin ◽  
Houqi Ning ◽  
Jingxue Wang
Keyword(s):  
Genome Analysis ◽  
Gc Content ◽  
Alcaligenes Faecalis ◽  
Open Reading Frames ◽  
Lytic Phage ◽  
Double Stranded Dna ◽  
Phylogeny Analysis ◽  
The Family ◽  
Complete Genome Analysis ◽  
Reading Frames

Abstract A novel lytic phage named vB_Af_QDWS595 against Alcaligenes faecalis was isolated and characterized in this study. The genome of phage vB_Af_QDWS595 was sequenced and analyzed, and the result revealed that the phage contained a 88,795 bp of circular double-stranded DNA with 41.12% of GC content. There were 74 putative open reading frames (ORFs) and 11 tRNAs predicted in genome of phage vB_Af_QDWS595. Phenotype and phylogeny analysis indicated that this phage might be a new member within the family Schitoviridae. Phage vB_Af_QDWS595 is the first sequenced phage against Alcaligenes faecalis to the best of our knowledge.

scholarly journals DNA Sequencing and Analysis of the Low-Ca2+-Response Plasmid pCD1 of Yersinia pestis KIM5

1998 ◽  
Vol 66 (10) ◽  
pp. 4611-4623 ◽  
Author(s):  
Robert D. Perry ◽  
Susan C. Straley ◽  
Jacqueline D. Fetherston ◽  
Debra J. Rose ◽  
Jason Gregor ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Yersinia Pestis ◽  
Yersinia Pseudotuberculosis ◽  
Gc Content ◽  
Effector Proteins ◽  
Open Reading Frames ◽  
Is Elements ◽  
Virulence Property ◽  
Leucine Rich Repeats ◽  
Reading Frames

ABSTRACT The low-Ca2+-response (LCR) plasmid pCD1 of the plague agent Yersinia pestis KIM5 was sequenced and analyzed for its genetic structure. pCD1 (70,509 bp) has an IncFIIA-like replicon and a SopABC-like partition region. We have assigned 60 apparently intact open reading frames (ORFs) that are not contained within transposable elements. Of these, 47 are proven or possible members of the LCR, a major virulence property of human-pathogenicYersinia spp., that had been identified previously in one or more of Y. pestis or the enteropathogenic yersiniaeYersinia enterocolitica and Yersinia pseudotuberculosis. Of these 47 LCR-related ORFs, 35 constitute a continuous LCR cluster. The other LCR-related ORFs are interspersed among three intact insertion sequence (IS) elements (IS100and two new IS elements, IS1616 and IS1617) and numerous defective or partial transposable elements. Regional variations in percent GC content and among ORFs encoding effector proteins of the LCR are additional evidence of a complex history for this plasmid. Our analysis suggested the possible addition of a new Syc- and Yop-encoding operon to the LCR-related pCD1 genes and gave no support for the existence of YopL. YadA likely is not expressed, as was the case for Y. pestis EV76, and the gene for the lipoprotein YlpA found in Y. enterocolitica likely is a pseudogene in Y. pestis. The yopM gene is longer than previously thought (by a sequence encoding two leucine-rich repeats), the ORF upstream of ypkA-yopJ is discussed as a potential Syc gene, and a previously undescribed ORF downstream ofyopE was identified as being potentially significant. Eight other ORFs not associated with IS elements were identified and deserve future investigation into their functions.

scholarly journals Identification and Expression of the Genes Encoding a Reactivating Factor for Adenosylcobalamin-Dependent Glycerol Dehydratase

1999 ◽  
Vol 181 (13) ◽  
pp. 4110-4113 ◽  
Author(s):  
Takamasa Tobimatsu ◽  
Hideki Kajiura ◽  
Michio Yunoki ◽  
Muneaki Azuma ◽  
Tetsuo Toraya
Keyword(s):  
Escherichia Coli ◽  
Klebsiella Pneumoniae ◽  
Open Reading Frames ◽  
Gene Products ◽  
Glycerol Dehydratase ◽  
Permeabilized Cells ◽  
Genes Encoding ◽  
Reading Frames

ABSTRACT Adenosylcobalamin-dependent glycerol dehydratase undergoes inactivation by glycerol, the physiological substrate, during catalysis. In permeabilized cells of Klebsiella pneumoniae, the inactivated enzyme is reactivated in the presence of ATP, Mg2+, and adenosylcobalamin. We identified the two open reading frames as the genes for a reactivating factor for glycerol dehydratase and designated them gdrA and gdrB. The reactivation of the inactivated glycerol dehydratase by the gene products was confirmed in permeabilized recombinant Escherichia coli cells coexpressing GdrA and GdrB proteins with glycerol dehydratase.

scholarly journals Genome Sequence of Borrelia garinii Strain NMJW1, Isolated from China

2012 ◽  
Vol 194 (23) ◽  
pp. 6660-6661 ◽  
Author(s):  
Baogui Jiang ◽  
Hongwu Yao ◽  
Yigang Tong ◽  
Xiaofeng Yang ◽  
Yong Huang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Northeastern China ◽  
Open Reading Frames ◽  
Ixodes Persulcatus ◽  
Borrelia Garinii ◽  
Linear Chromosome ◽  
Content Type ◽  
Reading Frames

ABSTRACTWe announce the draft genome sequence ofBorrelia gariniistrain NMJW1, isolated fromIxodes persulcatusin northeastern China. The 902,789-bp linear chromosome (28.4% GC content) contains 813 open reading frames, 33 tRNAs, and 4 complete rRNAs.

Sign in / Sign up

Export Citation Format

Share Document