Betsy Martinez-Vaz
, Saint Paul

Bioinformatics, Biotechnology, Microbiology

Ph.D. in Biochemistry
18.71

Publications

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    ABSTRACT: Leafy green vegetables have been identified as a source of foodborne illnesses worldwide over the past decade. Human enteric pathogens, such as Escherichia coli O157:H7 and Salmonella, have been implicated in numerous food poisoning outbreaks associated with the consumption of fresh produce. An understanding of the mechanisms responsible for the establishment of pathogenic bacteria in or on vegetable plants is critical for understanding and ameliorating this problem as well as ensuring the safety of our food supply. While previous studies have described the growth and survival of enteric pathogens in the environment and also the risk factors associated with the contamination of vegetables, the molecular events involved in the colonization of fresh produce by enteric pathogens are just beginning to be elucidated. This review summarizes recent findings on the interactions of several bacterial pathogens with leafy green vegetables. Changes in gene expression linked to the bacterial attachment and colonization of plant structures are discussed in light of their relevance to plant-microbe interactions. We propose a mechanism for the establishment and association of enteric pathogens with plants and discuss potential strategies to address the problem of foodborne illness linked to the consumption of leafy green vegetables.
    Microbes and Environments 05/2014; 29(2). DOI:10.1264/jsme2.ME13139 · 2.42 Impact Factor
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    Betsy Martinez-Vaz
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    ABSTRACT: Biochemistry is probably the most interdisciplinary subject taught in universities and medical schools around the world. The interdisciplinary nature of this field, presents a challenge to effective teaching, curriculum design and implementation of instructional strategies in the classroom. This article examines the educational trends that have influenced the teaching of Biochemistry in the past years. The first part of the paper describes Backward Design, a modern technique used to develop courses with a conceptual approach. The incorporation of inquiry based laboratory exercises and authentic (grant-funded) research into undergraduate Biochemistry courses is also discussed. The second part of this paper analyzes the impact of the genomic revolution, the availability of biological databases and bioinformatics in Biochemistry teaching. The article ends with a description of various activities that use bioinformatics tools to enhance the teaching of fundamental concepts and prepare students for learning Biochemistry with the challenges facing the discipline in the XXI century.
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    ABSTRACT: BACKGROUND: The sinorhizobia are amongst the most well studied members of nitrogen-fixing root nodule bacteria and contribute substantial amounts of fixed nitrogen to the biosphere. While the alfalfa symbiont Sinorhizobium meliloti RM 1021 was one of the first rhizobial strains to be completely sequenced, little information is available about the genomes of this large and diverse species group. RESULTS AND DISCUSSION: Here we report the draft assembly and annotation of 48 strains of Sinorhizobium comprising five genospecies. While S. meliloti and S. medicae are taxonomically related, they displayed different nodulation patterns on diverse Medicago host plants, and have differences in gene content including those involved in conjugation and organic sulfur utilization. Genes involved in Nod-factor and polysaccharide biosynthesis, denitrification and Type III, IV, and VI secretion systems also vary within and between species. Symbiotic phenotyping and mutational analyses indicated that some Type IV secretion genes are symbiosis-related and involved in nitrogen fixation efficiency. Moreover, there is a correlation between the presence of Type IV secretion systems, heme biosynthesis and microaerobic denitrification genes, and symbiotic efficiency. CONCLUSIONS: Our results suggest that each Sinorhizobium strain uses a slightly different strategy to obtain maximum compatibility with a host plant. This large genome data set provides useful information to better understand the functional features of five Sinorhizobium species, especially compatibility in legume-Sinorhizobium interactions. The diversity of genes present in the accessory genomes of members of this genus indicates that each bacterium has adopted slightly different strategies to interact with diverse plant genera and soil environments.
    Genome biology 02/2013; 14(2):R17. DOI:10.1186/gb-2013-14-2-r17 · 10.47 Impact Factor
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    Kathryn M Burleson, Betsy M Martinez-Vaz
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    ABSTRACT: In this laboratory exercise, students were taught concepts of microbiology and scientific process through an everyday activity - cosmetic use. The students' goals for the lab were to develop a hypothesis regarding microbial contamination in cosmetics, learn techniques to culture and differentiate microorganisms from cosmetics, and propose best practices in cosmetics use based on their findings. Prior to the lab, students took a pretest to assess their knowledge of scientific hypotheses, microbiology, and cosmetic safety. In the first week, students were introduced to microbiological concepts and methodologies, and cosmetic terminology and safety. Students completed a hypothesis-writing exercise before formulating and testing their own hypotheses regarding cosmetic contamination. Students provided a cosmetic of their own and, in consultation with their lab group, chose one product for testing. Samples were serially diluted and plated on a variety of selective media. In the second week, students analyzed their plates to determine the presence and diversity of microbes and if their hypotheses were supported. Students completed a worksheet of their results and were given a posttest to assess their knowledge. Average test scores improved from 5.2 (pretest) to 7.8 (posttest), with p-values < 0.0001. Seventy-nine percent (79%) of students correctly identified hypotheses that were not falsifiable or lacked variables, and 89% of students improved their scores on questions concerning safe cosmetic use. Ninety-one percent (91%) of students demonstrated increased knowledge of microbial concepts and methods. Based on our results, this lab is an easy, yet effective, way to enhance knowledge of scientific concepts for nonmajors, while maintaining relevance to everyday life.
    12/2011; 12(2):166-75. DOI:10.1128/jmbe.v12i2.320
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    Betsy M. Martinez- Vaz, Makarevitch Irina, Stensland Shane
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    ABSTRACT: A laboratory project was designed to illustrate how to search biological databases and utilize the information provided by these resources to investigate transcriptional regulation in Escherichia coli. The students searched several databases (NCBI Genomes, RegulonDB and EcoCyc) to learn about gene function, regulation, and the organization of transcriptional units. A fluorometer and GFP promoter fusions were used to obtain fluorescence data and measure changes in transcriptional activity. The class designed and performed experiments to investigate the regulation of genes necessary for biosynthesis of amino acids and how expression is affected by environmental signals and transcriptional regulators. Assessment data showed that this activity enhanced students’ knowledge of databases, reporter genes and transcriptional regulation.
    05/2010; DOI:10.1128/jmbe.v11.i1.101
  • Plant-Animal Genome Conference; 01/2010
  • Poonam Srivastava, Betsy Martinez Vaz, Arkady B. Khodursky
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    ABSTRACT: In Escherichia coli K-12 the leucine-responsive regulatory protein (Lrp) affects expression of ~400 genes. Lrp is highly conserved at the amino acid level among many gram negative bacteria. Our study checks the hypothesis that species with highly conserved Lrp orthologs show a conserved pattern of Lrp dependent regulation. E. coli O157:H7 (EHEC) causes hemolytic-uremic syndrome and has Lrp ortholog which is 100% conserved. It differs from E. coli K-12 in having an extra ~25% of genes that are scattered over the entire chromosome. Therefore the work was also aimed to reveal the extent to which new members have joined the regulon. To compare Lrp regulon structures in two organisms, transcript profiles under the same growth conditions were obtained using WT and lrp knock-out strains. To map direct Lrp targets in the chromosomes of both species chromatin immunoprecipitation of LRP bound DNA sequences followed by hybridization on microarray was carried out. The Lrp regulon was operationally defined as a collection of genes whose expression is affected in an lrp mutant and whose regulatory sequences are bound by the Lrp protein, both defined with at least 95% confidence. The regulons were compared between the two species. It was observed that the EHEC regulon fully encompasses the K-12 one. In EHEC, 29 “new” species-specific genes, including some in the LEE locus, could be assigned to the Lrp regulon. Given the proportion of direct Lrp targets in E. coli genome (0.03) and the number of EHEC accrued genes, one would expect at least 49 new Lrp targets in EHEC. The discrepancy (p-value <10-3) could be attributed to multiple instrumental and/or biological factors. Thus we conclude that the structure of the Lrp regulon is highly conserved among the two bacterial species and the Lrp regulon in EHEC has maintained the basic membership and regulatory patterns of the K-12 version.
    American Society for Microbiology, Boston, MA; 05/2008
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    ABSTRACT: Bacterial genome sequences are being determined rapidly, but few species are physiologically well characterized. Predicting regulation from genome sequences usually involves extrapolation from better-studied bacteria, using the hypothesis that a conserved regulator, conserved target gene, and predicted regulator-binding site in the target promoter imply conserved regulation between the two species. However many compared organisms are ecologically and physiologically diverse, and the limits of extrapolation have not been well tested. In E. coli K-12 the leucine-responsive regulatory protein (Lrp) affects expression of approximately 400 genes. Proteus mirabilis and Vibrio cholerae have highly-conserved lrp orthologs (98% and 92% identity to E. coli lrp). The functional equivalence of Lrp from these related species was assessed. Heterologous Lrp regulated gltB, livK and lrp transcriptional fusions in an E. coli background in the same general way as the native Lrp, though with significant differences in extent. Microarray analysis of these strains revealed that the heterologous Lrp proteins significantly influence only about half of the genes affected by native Lrp. In P. mirabilis, heterologous Lrp restored swarming, though with some pattern differences. P. mirabilis produced substantially more Lrp than E. coli or V. cholerae under some conditions. Lrp regulation of target gene orthologs differed among the three native hosts. Strikingly, while Lrp negatively regulates its own gene in E. coli, and was shown to do so even more strongly in P. mirabilis, Lrp appears to activate its own gene in V. cholerae. The overall similarity of regulatory effects of the Lrp orthologs supports the use of extrapolation between related strains for general purposes. However this study also revealed intrinsic differences even between orthologous regulators sharing >90% overall identity, and 100% identity for the DNA-binding helix-turn-helix motif, as well as differences in the amounts of those regulators. These results suggest that predicting regulation of specific target genes based on genome sequence comparisons alone should be done on a conservative basis.
    BMC Microbiology 02/2008; 8:60. DOI:10.1186/1471-2180-8-60 · 2.98 Impact Factor
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    Guanghua Xiao, Betsy Martinez-Vaz, Wei Pan, Arkady B Khodursky
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    ABSTRACT: In prokaryotic genomes, genes are organized in operons, and the genes within an operon tend to have similar levels of expression. Because of co-transcription of genes within an operon, borrowing information from other genes within the same operon can improve the estimation of relative transcript levels; the estimation of relative levels of transcript abundances is one of the most challenging tasks in experimental genomics due to the high noise level in microarray data. Therefore, techniques that can improve such estimations, and moreover are based on sound biological premises, are expected to benefit the field of microarray data analysis In this paper, we propose a hierarchical Bayesian model, which relies on borrowing information from other genes within the same operon, to improve the estimation of gene expression levels and, hence, the detection of differentially expressed genes. The simulation studies and the analysis of experiential data demonstrated that the proposed method outperformed other techniques that are routinely used to estimate transcript levels and detect differentially expressed genes, including the sample mean and SAM t statistics. The improvement became more significant as the noise level in microarray data increases. By borrowing information about transcriptional activity of genes within classified operons, we improved the estimation of gene expression levels and the detection of differentially expressed genes.
    BMC Genomics 02/2006; 7:87. DOI:10.1186/1471-2164-7-87 · 4.04 Impact Factor
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    Betsy M Martinez-Vaz, Yang Xie, Wei Pan, Arkady B Khodursky
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    ABSTRACT: The distribution and location of insertion elements in a genome is an excellent tool to track the evolution of bacterial strains and a useful molecular marker to distinguish between closely related bacterial isolates. The information about the genomic locations of IS elements is available in public sequence databases. However, the locations of mobile elements may vary from strain to strain and within the population of an individual strain. Tools that allow de novo localization of IS elements and are independent of existing sequence information are essential to map insertion elements and advance our knowledge of the role that such elements play in gene regulation and genome plasticity in bacteria. In this study, we present an efficient and reliable method for linear mapping of mobile elements using whole-genome DNA microarrays. In addition, we describe an algorithm for analysis of microarray data that can be applied to find DNA sequences physically juxtaposed with a target sequence of interest. This approach was used to map the locations of the IS5 elements in the genome of Escherichia coli K12. All IS5 elements present in the E. coli genome known from GenBank sequence data were identified. Furthermore, previously unknown insertion sites were predicted with high sensitivity and specificity. Two variants of E. coli K-12 MG1655 within a population of this strain were predicted by our analysis. The only significant difference between these two isolates was the presence of an IS5 element upstream of the main flagella regulator, flhDC. Additional experiments confirmed this prediction and showed that these isolates were phenotypically distinct. The effect of IS5 on the transcriptional activity of motility and chemotaxis genes in the genome of E. coli strain MG1655 was examined. Comparative analysis of expression profiles revealed that the presence of IS5 results in a mild enhancement of transcription of the flagellar genes that translates into a slight increase in motility. In summary, this work presents a case study of an experimental and analytical application of DNA microarrays to map insertion elements in bacteria and gains an insight into biological processes that might otherwise be overlooked by relying solely on the available genome sequence data.
    BMC Genomics 02/2005; 6(1):81. DOI:10.1186/1471-2164-6-81 · 4.04 Impact Factor
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    ABSTRACT: s-Triazine ring compounds are common indus-trial chemicals: pesticides, resin intermediates, dyes, and explosives. The fate of these compounds in the environ-ment is directly correlated with the ability of microbes to metabolize them. Microbes metabolize melamine and the triazine herbicides such as atrazine via enzyme-catalyzed hydrolysis reactions. Hydrolytic removal of substituents on the s-triazine ring is catalyzed by enzymes from the amidohydrolase superfamily and yields cyanuric acid as an intermediate. Cyanuric acid is hydrolytically pro-cessed to yield 3 mol each of ammonia and carbon diox-ide. In those cases studied, the genes underlying the hy-drolytic reactions are localized to large catabolic plasm-ids. One such plasmid, pADP-1 from Pseudomonas sp. ADP, has been completely sequenced and contains the genes for atrazine catabolism. Insertion sequence ele-ments play a role in constructing different atrazine cata-bolic plasmids in different bacteria. Atrazine chlorohy-drolase has been purified to homogeneity from two sourc-es. Recombinant Escherichia coli strains expressing at-razine chlorohydrolase have been constructed and chemi-cally cross-linked to generate catalytic particles used for atrazine remediation in soil. The method was used for cleaning up a spill of 1,000 pounds of atrazine to attain a level of herbicide acceptable to regulatory agencies.
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    L.P.Wackett, M.J. Sadowsky, Betsy Martinez-Vaz, N. Shapir
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    ABSTRACT: s-Triazine ring compounds are common indus-trial chemicals: pesticides, resin intermediates, dyes, and explosives. The fate of these compounds in the environ-ment is directly correlated with the ability of microbes to metabolize them. Microbes metabolize melamine and the triazine herbicides such as atrazine via enzyme-catalyzed hydrolysis reactions. Hydrolytic removal of substituents on the s-triazine ring is catalyzed by enzymes from the amidohydrolase superfamily and yields cyanuric acid as an intermediate. Cyanuric acid is hydrolytically pro-cessed to yield 3 mol each of ammonia and carbon diox-ide. In those cases studied, the genes underlying the hy-drolytic reactions are localized to large catabolic plasm-ids. One such plasmid, pADP-1 from Pseudomonas sp. ADP, has been completely sequenced and contains the genes for atrazine catabolism. Insertion sequence ele-ments play a role in constructing different atrazine cata-bolic plasmids in different bacteria. Atrazine chlorohy-drolase has been purified to homogeneity from two sourc-es. Recombinant Escherichia coli strains expressing at-razine chlorohydrolase have been constructed and chemi-cally cross-linked to generate catalytic particles used for atrazine remediation in soil. The method was used for cleaning up a spill of 1,000 pounds of atrazine to attain a level of herbicide acceptable to regulatory agencies.
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    L.P.Wackett, M.J.Sadowsky, Betsy Martinez-Vaz, N. Shapir
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    ABSTRACT: s-Triazine ring compounds are common indus-trial chemicals: pesticides, resin intermediates, dyes, and explosives. The fate of these compounds in the environ-ment is directly correlated with the ability of microbes to metabolize them. Microbes metabolize melamine and the triazine herbicides such as atrazine via enzyme-catalyzed hydrolysis reactions. Hydrolytic removal of substituents on the s-triazine ring is catalyzed by enzymes from the amidohydrolase superfamily and yields cyanuric acid as an intermediate. Cyanuric acid is hydrolytically pro-cessed to yield 3 mol each of ammonia and carbon diox-ide. In those cases studied, the genes underlying the hy-drolytic reactions are localized to large catabolic plasm-ids. One such plasmid, pADP-1 from Pseudomonas sp. ADP, has been completely sequenced and contains the genes for atrazine catabolism. Insertion sequence ele-ments play a role in constructing different atrazine cata-bolic plasmids in different bacteria. Atrazine chlorohy-drolase has been purified to homogeneity from two sourc-es. Recombinant Escherichia coli strains expressing at-razine chlorohydrolase have been constructed and chemi-cally cross-linked to generate catalytic particles used for atrazine remediation in soil. The method was used for cleaning up a spill of 1,000 pounds of atrazine to attain a level of herbicide acceptable to regulatory agencies.
    Applied Microbiology and Biotechnology 12/2001; 59:39-45. DOI:10.1007/s00253-001-0862-y · 3.81 Impact Factor
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    ABSTRACT: The complete 108,845-nucleotide sequence of catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP was determined. Plasmid pADP-1 was previously shown to encode AtzA, AtzB, and AtzC, which catalyze the sequential hydrolytic removal of s-triazine ring substituents from the herbicide atrazine to yield cyanuric acid. Computational analyses indicated that pADP-1 encodes 104 putative open reading frames (ORFs), which are predicted to function in catabolism, transposition, and plasmid maintenance, transfer, and replication. Regions encoding transfer and replication functions of pADP-1 had 80 to 100% amino acid sequence identity to pR751, an IncPbeta plasmid previously isolated from Enterobacter aerogenes. pADP-1 was shown to contain a functional mercury resistance operon with 99% identity to Tn5053. Complete copies of transposases with 99% amino acid sequence identity to TnpA from IS1071 and TnpA from Pseudomonas pseudoalcaligenes were identified and flank each of the atzA, atzB, and atzC genes, forming structures resembling nested catabolic transposons. Functional analyses identified three new catabolic genes, atzD, atzE, and atzF, which participate in atrazine catabolism. Crude extracts from Escherichia coli expressing AtzD hydrolyzed cyanuric acid to biuret. AtzD showed 58% amino acid sequence identity to TrzD, a cyanuric acid amidohydrolase, from Pseudomonas sp. strain NRRLB-12227. Two other genes encoding the further catabolism of cyanuric acid, atzE and atzF, reside in a contiguous cluster adjacent to a potential LysR-type transcriptional regulator. E. coli strains bearing atzE and atzF were shown to encode a biuret hydrolase and allophanate hydrolase, respectively. atzDEF are cotranscribed. AtzE and AtzF are members of a common amidase protein family. These data reveal the complete structure of a catabolic plasmid and show that the atrazine catabolic genes are dispersed on three disparate regions of the plasmid. These results begin to provide insight into how plasmids are structured, and thus evolve, to encode the catabolism of compounds recently added to the biosphere.
    Journal of Bacteriology 11/2001; 183(19):5684-97. DOI:10.1128/JB.183.19.5684-5697.2001 · 2.69 Impact Factor
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    ABSTRACT: The complete 108,845-nucleotide sequence of catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP was determined. Plasmid pADP-1 was previously shown to encode AtzA, AtzB, and AtzC, which catalyze the sequential hydrolytic removal of s-triazine ring substituents from the herbicide atrazine to yield cyanuric acid. Computational analyses indicated that pADP-1 encodes 104 putative open reading frames (ORFs), which are predicted to function in catabolism, transposition, and plasmid maintenance, transfer, and replication. Re-gions encoding transfer and replication functions of pADP-1 had 80 to 100% amino acid sequence identity to pR751, an IncP plasmid previously isolated from Enterobacter aerogenes. pADP-1 was shown to contain a functional mercury resistance operon with 99% identity to Tn5053. Complete copies of transposases with 99% amino acid sequence identity to TnpA from IS1071 and TnpA from Pseudomonas pseudoalcaligenes were iden-tified and flank each of the atzA, atzB, and atzC genes, forming structures resembling nested catabolic trans-posons. Functional analyses identified three new catabolic genes, atzD, atzE, and atzF, which participate in atrazine catabolism. Crude extracts from Escherichia coli expressing AtzD hydrolyzed cyanuric acid to biuret. AtzD showed 58% amino acid sequence identity to TrzD, a cyanuric acid amidohydrolase, from Pseudomonas sp. strain NRRLB-12227. Two other genes encoding the further catabolism of cyanuric acid, atzE and atzF, reside in a contiguous cluster adjacent to a potential LysR-type transcriptional regulator. E. coli strains bearing atzE and atzF were shown to encode a biuret hydrolase and allophanate hydrolase, respectively. atzDEF are cotranscribed. AtzE and AtzF are members of a common amidase protein family. These data reveal the complete structure of a catabolic plasmid and show that the atrazine catabolic genes are dispersed on three disparate regions of the plasmid. These results begin to provide insight into how plasmids are structured, and thus evolve, to encode the catabolism of compounds recently added to the biosphere. Many bacteria contain plasmids that carry genes functional in antibiotic resistance, virulence for animal or plant hosts, or the catabolism of diverse chemical compounds. While much has been learned since Lederberg's initial discovery of plas-mids in 1952 (36), genomic approaches will further enhance our understanding of plasmid structure and evolution. Re-cently, the complete nucleotide sequences of approximately 90 bacterial and 10 archaeal plasmids have been obtained (5,Genomes/eub_p.html). However, most of the sequenced plas-mids are relatively small, are used as vectors in molecular biology, or are of medical importance. The latter group of plasmids consist predominantly of those known to contain antibiotic resistance genes or encode virulence determinants associated with infectious diseases (5, 29, 52). In contrast, catabolic plasmids, which have been identified in many non-pathogenic soil bacteria (49), have been shown to transfer among bacteria, thus disseminating genes encoding the metab-olism of environmentally relevant compounds (11). For exam-ple, plasmids encoding the catabolism of toluene, camphor, naphthalene, and 2,4-dichlorophenoxyacetate are known (3, 12, 45, 64). Many of the genes involved in their respective catabolic pathways have been cloned and sequenced, but to date only one catabolic plasmid, pNL1, from Sphingomonas aromaticivorans strain F199 has been completely sequenced (46). This plasmid contains genes encoding enzymes for the metabolism of biphenyl, naphthalene, m-xylene, and p-cresol. Metabolism of the herbicide atrazine has also been shown to be linked to catabolic plasmids. Mandelbaum et al. (38) iso-lated Pseudomonas sp. strain ADP, which metabolizes atrazine to carbon dioxide and ammonia. The first three enzymatic steps, encoded by the genes atzA, atzB, and atzC, transform atrazine to cyanuric acid (9, 15, 47). Cyanuric acid has been shown to be a common intermediate in the degradation path-ways for melamine (2,4,6-triamino-s-triazine) and atrazine (21, 22, 47) in Pseudomonas sp. strain NRRLB-12227 and Pseudo-monas sp. strain ADP, respectively (Fig. 1). However, while the hydrolysis of cyanuric acid in Pseudomonas sp. strain NRRLB-12227 proceeds through biuret and urea intermediates, the reactions involved in cyanuric acid degradation in Pseudomo-nas sp. strain ADP were not established. The atzA, atzB, and atzC genes in Pseudomonas sp. strain ADP have been localized to an approximately 100 kb plasmid, pADP-1 (17), and DNA regions with homology to IS1071 have been shown to flank atzA (18). Recently, plasmid-localized
    Journal of bacteriology 10/2001; 19(183):5684-5697. · 2.69 Impact Factor
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    ABSTRACT: Pseudomonas strain ADP metabolizes the herbicide atrazine via three enzymatic steps, encoded by the genes atzABC, to yield cyanuric acid, a nitrogen source for many bacteria. Here, we show that five geographically distinct atrazine-degrading bacteria contain genes homologous to atzA, -B, and -C. The sequence identities of the atz genes from different atrazine-degrading bacteria were greater than 99% in all pairwise comparisons. This differs from bacterial genes involved in the catabolism of other chlorinated compounds, for which the average sequence identity in pairwise comparisons of the known members of a class ranged from 25 to 56%. Our results indicate that globally distributed atrazine-catabolic genes are highly conserved in diverse genera of bacteria.
    Journal of Bacteriology 04/1998; 180(7):1951-4. · 2.69 Impact Factor
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    Betsy Milagros. Martinez-Vaz
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    ABSTRACT: Thesis (Ph. D.)--University of Minnesota, 2001. Includes bibliographical references.

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