Daniel Arp

Summary

Affiliation: Oregon State University
Country: USA

Publications

  1. ncbi request reprint The impact of genome analyses on our understanding of ammonia-oxidizing bacteria
    Daniel J Arp
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
    Annu Rev Microbiol 61:503-28. 2007
  2. ncbi request reprint Metabolism of inorganic N compounds by ammonia-oxidizing bacteria
    Daniel J Arp
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Crit Rev Biochem Mol Biol 38:471-95. 2003
  3. pmc Role of a Fur homolog in iron metabolism in Nitrosomonas europaea
    Neeraja Vajrala
    Department of Botany and Plant Pathology, 2082 Cordley, Oregon State University, Corvallis, OR 97331, USA
    BMC Microbiol 11:37. 2011
  4. ncbi request reprint Product and product-independent induction of butane oxidation in Pseudomonas butanovora
    Luis A Sayavedra-Soto
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    FEMS Microbiol Lett 250:111-6. 2005
  5. ncbi request reprint Trichloroethylene degradation by butane-oxidizing bacteria causes a spectrum of toxic effects
    Kimberly H Halsey
    Molecular and Cellular Biology Program, Oregon State University, ALS 3021, Corvallis, OR 97331 2902, USA
    Appl Microbiol Biotechnol 68:794-801. 2005
  6. doi request reprint Nitrification and degradation of halogenated hydrocarbons--a tenuous balance for ammonia-oxidizing bacteria
    Luis A Sayavedra-Soto
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Appl Microbiol Biotechnol 86:435-44. 2010
  7. doi request reprint Extending the alkene substrate range of vinyl chloride utilizing Nocardioides sp. strain JS614 with ethene oxide
    Anne E Taylor
    Oregon State University, Corvallis, 97331, USA
    Appl Microbiol Biotechnol 87:2293-302. 2010
  8. doi request reprint Involvement of BmoR and BmoG in n-alkane metabolism in 'Pseudomonas butanovora'
    Elizabeth G Kurth
    Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, OR 97331, USA
    Microbiology 154:139-47. 2008
  9. ncbi request reprint Butane monooxygenase of 'Pseudomonas butanovora': purification and biochemical characterization of a terminal-alkane hydroxylating diiron monooxygenase
    Bradley L Dubbels
    Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, OR 97331 2902, USA
    Microbiology 153:1808-16. 2007
  10. ncbi request reprint The roles of the three gene copies encoding hydroxylamine oxidoreductase in Nitrosomonas europaea
    Norman G Hommes
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Arch Microbiol 178:471-6. 2002

Research Grants

Collaborators

Detail Information

Publications40

  1. ncbi request reprint The impact of genome analyses on our understanding of ammonia-oxidizing bacteria
    Daniel J Arp
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
    Annu Rev Microbiol 61:503-28. 2007
    ..The extension by ammonia monooxygenase provides a mechanism to feed this module using ammonia and O(2)...
  2. ncbi request reprint Metabolism of inorganic N compounds by ammonia-oxidizing bacteria
    Daniel J Arp
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Crit Rev Biochem Mol Biol 38:471-95. 2003
    ..Nonetheless, many questions remain regarding the enzymes and genes involved in these processes and the role of these pathways in ammonia oxidizers...
  3. pmc Role of a Fur homolog in iron metabolism in Nitrosomonas europaea
    Neeraja Vajrala
    Department of Botany and Plant Pathology, 2082 Cordley, Oregon State University, Corvallis, OR 97331, USA
    BMC Microbiol 11:37. 2011
    ..The genome of Nitrosomonas europaea, an ammonia-oxidizing bacterium, carries three genes (NE0616, NE0730 and NE1722) encoding proteins belonging to Fur family...
  4. ncbi request reprint Product and product-independent induction of butane oxidation in Pseudomonas butanovora
    Luis A Sayavedra-Soto
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    FEMS Microbiol Lett 250:111-6. 2005
    ..P. butanovora expressed sBMO product-independent activity at 3.0+/-1 nmol ethylene oxide min(-1) mg protein(-1) in stationary phase. The sBMO product-independent activity likely primes the expression of sBMO by butane...
  5. ncbi request reprint Trichloroethylene degradation by butane-oxidizing bacteria causes a spectrum of toxic effects
    Kimberly H Halsey
    Molecular and Cellular Biology Program, Oregon State University, ALS 3021, Corvallis, OR 97331 2902, USA
    Appl Microbiol Biotechnol 68:794-801. 2005
    ..butanovora cells to lose viability. Together, these results contrast with those previously reported for other bacteria carrying out TCE cometabolism and demonstrate the range of cellular toxicities associated with TCE cometabolism...
  6. doi request reprint Nitrification and degradation of halogenated hydrocarbons--a tenuous balance for ammonia-oxidizing bacteria
    Luis A Sayavedra-Soto
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Appl Microbiol Biotechnol 86:435-44. 2010
    ..These and other biosensors may help to preserve the tenuous balance that exists when nitrification occurs in waste streams containing alternative AOB substrates such as halogenated hydrocarbons...
  7. doi request reprint Extending the alkene substrate range of vinyl chloride utilizing Nocardioides sp. strain JS614 with ethene oxide
    Anne E Taylor
    Oregon State University, Corvallis, 97331, USA
    Appl Microbiol Biotechnol 87:2293-302. 2010
    ..However, higher EtO concentrations (300-400 microM) overcame the negative effects of PrO on Eth-dependent growth...
  8. doi request reprint Involvement of BmoR and BmoG in n-alkane metabolism in 'Pseudomonas butanovora'
    Elizabeth G Kurth
    Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, OR 97331, USA
    Microbiology 154:139-47. 2008
    ..e. </=C(6)). The bmoG-deficient mutant did not grow on C(2)-C(8) n-alkanes; however, it was capable of transcribing bmoX and bmoC of the BMO operon. BmoG may act as a chaperonin to assemble competent BMO...
  9. ncbi request reprint Butane monooxygenase of 'Pseudomonas butanovora': purification and biochemical characterization of a terminal-alkane hydroxylating diiron monooxygenase
    Bradley L Dubbels
    Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, OR 97331 2902, USA
    Microbiology 153:1808-16. 2007
    ..Regiospecificity of sBMO was strongly biased towards primary hydroxylation, with > or = 80 % of the hydroxylations occurring at the terminal carbon atom...
  10. ncbi request reprint The roles of the three gene copies encoding hydroxylamine oxidoreductase in Nitrosomonas europaea
    Norman G Hommes
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Arch Microbiol 178:471-6. 2002
    ..Comparison with the arrangement of hao genes in the closely related strain, Nitrosomonas sp. strain ENI-11, showed a similar organization...
  11. pmc Site-directed amino acid substitutions in the hydroxylase alpha subunit of butane monooxygenase from Pseudomonas butanovora: Implications for substrates knocking at the gate
    Kimberly H Halsey
    Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
    J Bacteriol 188:4962-9. 2006
    ..The structural significance of the results obtained in this study is discussed using a three-dimensional model of BMOH-alpha...
  12. pmc Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255
    Shawn R Starkenburg
    Oregon State University, Corvallis 97331, USA
    Appl Environ Microbiol 72:2050-63. 2006
    ..The genome will serve as a model to study the cellular and molecular processes that control nitrite oxidation and its interaction with other nitrogen-cycling processes...
  13. pmc Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter
    Shawn R Starkenburg
    Department of Microbiology, Oregon State University, 220 Nash Hall, Corvallis, OR 97331, USA
    Appl Environ Microbiol 74:2852-63. 2008
    ..Many of the subcore genes have diverged significantly from, or have origins outside, the alphaproteobacterial lineage and may indicate some of the unique genetic requirements for nitrite oxidation in Nitrobacter...
  14. doi request reprint Expression of a putative nitrite reductase and the reversible inhibition of nitrite-dependent respiration by nitric oxide in Nitrobacter winogradskyi Nb-255
    Shawn R Starkenburg
    Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
    Environ Microbiol 10:3036-42. 2008
    ..In light of this new information, a modified model is proposed to explain how NirK and NO manage electron flux in Nitrobacter...
  15. doi request reprint Construction of recombinant Nitrosomonas europaea expressing green fluorescent protein in response to co-oxidation of chloroform
    Barbara O Gvakharia
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Appl Microbiol Biotechnol 82:1179-85. 2009
    ..The fabricated biosensors had a consistent concentration-dependent response to chloroform; however, these did not respond to other chlorinated compounds that cause similar cellular stress...
  16. pmc Thauera butanivorans sp. nov., a C2-C9 alkane-oxidizing bacterium previously referred to as 'Pseudomonas butanovora'
    Bradley L Dubbels
    Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, OR 97331 2902, USA
    Int J Syst Evol Microbiol 59:1576-8. 2009
    ..nov. is proposed. The type strain is Bu-B1211(T) (=IAM 12574(T)=ATCC 43655(T)=DSM 2080(T))...
  17. ncbi request reprint Molecular analysis of the soluble butane monooxygenase from 'Pseudomonas butanovora'
    Miriam K Sluis
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Microbiology 148:3617-29. 2002
    ..The structural and mechanistic implications of the high sequence identity (up to 64%) between the peptides of butane monooxygenase and methane monooxygenases are discussed...
  18. ncbi request reprint Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea
    Daniel J Arp
    Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, OR 97331 2902, USA
    Arch Microbiol 178:250-5. 2002
    ..N. europaea was selected by the United States Department of Energy for a whole-genome sequencing project. In this article, we review recent research on the molecular biology and biochemistry of NH(3) oxidation in nitrifiers...
  19. pmc Roles for the two 1-butanol dehydrogenases of Pseudomonas butanovora in butane and 1-butanol metabolism
    Alisa S Vangnai
    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331 2902, USA
    J Bacteriol 184:4343-50. 2002
    ..The former pathway may function primarily in energy generation, while the latter may be more important in the detoxification of 1-butanol...
  20. doi request reprint Role of Nitrosomonas europaea NitABC iron transporter in the uptake of Fe3+-siderophore complexes
    Neeraja Vajrala
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Arch Microbiol 192:899-908. 2010
    ..The mechanisms to transport iron in either the Fe(3+) or Fe(2+) forms or Fe(3+) associated with enterobactin or aerobactin siderophores into the cell across the cytoplasmic membrane are as yet undetermined...
  21. pmc Evidence for modified mechanisms of chloroethene oxidation in Pseudomonas butanovora mutants containing single amino acid substitutions in the hydroxylase alpha-subunit of butane monooxygenase
    Kimberly H Halsey
    Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
    J Bacteriol 189:5068-74. 2007
    ..The use of CEs as substrates in combination with P. butanovora BMOH-alpha mutants might allow insights into the catalytic mechanism of BMO to be obtained...
  22. pmc Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly 'Pseudomonas butanovora'
    Richard B Cooley
    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
    Microbiology 155:2086-96. 2009
    ..These results represent, to the best of our knowledge, the first kinetic in vitro characterization of the closest known homologue of sMMO...
  23. pmc Global transcriptional response of Nitrosomonas europaea to chloroform and chloromethane
    Barbara O Gvakharia
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Appl Environ Microbiol 73:3440-5. 2007
    ..N. europaea has higher levels of transcripts for a variety of defense genes when exposed to chloroform or chloromethane...
  24. ncbi request reprint A combined method for determining inhibition type, kinetic parameters, and inhibition coefficients for aerobic cometabolism of 1,1,1-trichloroethane by a butane-grown mixed culture
    Young Kim
    Department of Civil, Construction, and Environmental Engineering, Oregon State University, Corvallis, Oregon 97331 2302, USA
    Biotechnol Bioeng 77:564-76. 2002
    ..Detailed studies with pure cultures and purified enzymes are needed to further demonstrate the utility of this method...
  25. pmc Two distinct alcohol dehydrogenases participate in butane metabolism by Pseudomonas butanovora
    Alisa S Vangnai
    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331 2902, USA
    J Bacteriol 184:1916-24. 2002
    ..The results support the involvement of two distinct NAD(+)-independent, PQQ-containing alcohol dehydrogenases, BOH (a quinoprotein) and BDH (a quinohemoprotein), in the butane oxidation pathway of P. butanovora...
  26. ncbi request reprint Transcript profiles of Nitrosomonas europaea during growth and upon deprivation of ammonia and carbonate
    Xueming Wei
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    FEMS Microbiol Lett 257:76-83. 2006
    ..Compared to heterotrophic bacteria, N. europaea downregulates a greater proportion of its genes and fewer genes appear to be associated with the adaptation to starvation...
  27. ncbi request reprint Trichloroethylene degradation by toluene-oxidizing bacteria grown on non-aromatic substrates
    Chris M Yeager
    Molecular and Cellular Biology Program, Corvallis, OR 97331 2902, USA
    Biodegradation 15:19-28. 2004
    ..These traits include oxygenase induction, effective TCE turnover, and some level of resistance to TCE mediated toxicity...
  28. pmc Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices that enhance protein functionality
    Richard B Cooley
    Department of Biochemistry and Biophysics, 2011 Ag and Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA
    J Mol Biol 404:232-46. 2010
    ....
  29. ncbi request reprint Kinetic and inhibition studies for the aerobic cometabolism of 1,1,1-trichloroethane, 1,1-dichloroethylene, and 1,1-dichloroethane by a butane-grown mixed culture
    Young Kim
    Department of Civil, Construction, and Environmental Engineering, Oregon State University, Corvallis 97331 2302, USA
    Biotechnol Bioeng 80:498-508. 2002
    ..Thus, determining inhibition type and measuring inhibition coefficients is important in designing CAH treatment systems...
  30. pmc Chemolithoorganotrophic growth of Nitrosomonas europaea on fructose
    Norman G Hommes
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 2902, USA
    J Bacteriol 185:6809-14. 2003
    ..These results show that N. europaea can be grown in CO(2)-free medium by using fructose and pyruvate as carbon sources and may now be considered a facultative chemolithoorganotroph...
  31. ncbi request reprint The transcription of the cbb operon in Nitrosomonas europaea
    Xueming Wei
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331 2902, USA
    Microbiology 150:1869-79. 2004
    ..In actively growing cells, mRNAs from the five genes in the RubisCO operon were present at different levels, probably due to premature termination of transcription, rapid mRNA processing and mRNA degradation...
  32. doi request reprint D-Lactate metabolism and the obligate requirement for CO2 during growth on nitrite by the facultative lithoautotroph Nitrobacter hamburgensis
    Shawn R Starkenburg
    Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
    Microbiology 154:2473-81. 2008
    ..75 mM sodium carbonate was required for mixotrophic growth and for optimum organotrophic growth on D-lactate...
  33. pmc Disruption of sucA, which encodes the E1 subunit of alpha-ketoglutarate dehydrogenase, affects the survival of Nitrosomonas europaea in stationary phase
    Norman G Hommes
    Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley, Corvallis, OR 97331 2902, USA
    J Bacteriol 188:343-7. 2006
    ..In addition, unlike wild-type cells, the mutant strain showed a marked lag in the ability to resume growth in response to pH adjustments in late stationary phase...
  34. ncbi request reprint Characterization of the ferrioxamine uptake system of Nitrosomonas europaea
    Xueming Wei
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331 2902, USA
    Microbiology 153:3963-72. 2007
    ..For efficient acquisition of Fe-loaded ferrioxamine, N. europaea needs both ferrioxamine transporters FoxA(1) and FoxA(2). FoxA(1) probably regulates its own production, and it controls the production of FoxA(2) as well...
  35. ncbi request reprint Iron nutrition and physiological responses to iron stress in Nitrosomonas europaea
    Xueming Wei
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331 2902, USA
    Arch Microbiol 186:107-18. 2006
    ..europaea to Fe-limited conditions...
  36. pmc Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment
    Jeanette M Norton
    Department of Plants, Soils, and Climate, Utah State University, Logan, UT 84322 4820, USA
    Appl Environ Microbiol 74:3559-72. 2008
    ..The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments...
  37. ncbi request reprint Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation
    Lisa Y Stein
    Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
    Environ Microbiol 9:2993-3007. 2007
    ..eutropha C91 and other AOB, even the closely related N. europaea, and several distinctive properties of the N. eutropha genome that are supportive of niche specialization...
  38. pmc Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707
    Martin G Klotz
    Department of Biology, University of Louisville, 139 Life Science Building, Louisville, KY 40292, USA
    Appl Environ Microbiol 72:6299-315. 2006
    ..The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H(+)-dependent F(0)F(1) type, one Na(+)-dependent V type)...
  39. pmc Inhibition of membrane-bound methane monooxygenase and ammonia monooxygenase by diphenyliodonium: implications for electron transfer
    Andrew K Shiemke
    Department of Biochemistry and Molecular Pharmacology, Robert C Byrd Health Sciences Center, West Virginia University School of Medicine, Morgantown, West Virginia 26506 9142, USA
    J Bacteriol 186:928-37. 2004
    ..DPI does not affect hydroxylamine oxidoreductase activity and does not require AMO turnover to exert its inhibitory effect. Implications of these data for the electron transfer pathway from the quinone pool to pMMO and AMO are discussed...
  40. pmc Nitrite reductase of Nitrosomonas europaea is not essential for production of gaseous nitrogen oxides and confers tolerance to nitrite
    Hubertus J E Beaumont
    BioCentrum Amsterdam, Department of Molecular Cell Physiology, Vrije Universiteit, NL 1081 Amsterdam, The Netherlands
    J Bacteriol 184:2557-60. 2002
    ..This demonstrates that NirK is not essential for the production of NO and N(2)O by N. europaea. Inactivation of the putative fnr gene showed that Fnr is not essential for the expression of nirK...

Research Grants8

  1. MOLECULAR DIVERSITY OF BACTERIAL BUTANE MONOOXYGENASES
    Daniel Arp; Fiscal Year: 2000
    ....
  2. Butane metabolism in Pseudomonas butanovora
    Daniel Arp; Fiscal Year: 2006
    ..Studies of parallel pathways will be relevant to other metabolic pathways where toxic metabolites are necessarily produced as part of the metabolism of a growth supporting substrate. ..