Weiwen Zhang

Summary

Affiliation: Pacific Northwest National Laboratory
Country: USA

Publications

  1. ncbi Molecular and biochemical characterization of a novel two-component signal transduction system, amrA- amkA, involved in rifamycin SV production in Amycolatopsis mediterranei U32
    Weiwu Wang
    Laboratory of Molecular Microbiology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, P R China
    Arch Microbiol 178:376-86. 2002
  2. ncbi Oxidative stress and heat-shock responses in Desulfovibrio vulgaris by genome-wide transcriptomic analysis
    Weiwen Zhang
    Microbiology Department, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P O Box 999, Richland, WA 99352, USA
    Antonie Van Leeuwenhoek 90:41-55. 2006
  3. ncbi DNA microarray analysis of anaerobic Methanosarcina barkeri reveals responses to heat shock and air exposure
    Weiwen Zhang
    Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    J Ind Microbiol Biotechnol 33:784-90. 2006
  4. ncbi Global transcriptomic analysis of Desulfovibrio vulgaris on different electron donors
    Weiwen Zhang
    Department of Microbiology, Pacific Northwest National Laboratory, 902 Battelle Boulevard, 999, Richland, WA 99352, USA
    Antonie Van Leeuwenhoek 89:221-37. 2006
  5. ncbi Two-component signal transduction systems of Desulfovibrio vulgaris: structural and phylogenetic analysis and deduction of putative cognate pairs
    Weiwen Zhang
    Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    J Mol Evol 62:473-87. 2006
  6. ncbi A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry
    Weiwen Zhang
    Microbiology Group, Pacific Northwest National Laboratory, Richland, WA, USA
    Proteomics 6:4286-99. 2006
  7. ncbi LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris
    Weiwen Zhang
    Microbiology Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P O Box 999, Richland, WA 99352, USA
    Biochem Biophys Res Commun 349:1412-9. 2006
  8. ncbi Distribution and evolution of multiple-step phosphorelay in prokaryotes: lateral domain recruitment involved in the formation of hybrid-type histidine kinases
    Weiwen Zhang
    Microbiology Department, Pacific Northwest National Laboratory, 902 Battelle Blvd, PO Box 999, Mail Stop P7 50, Richland, WA 99352, USA
    Microbiology 151:2159-73. 2005
  9. ncbi Evolution of the PPM-family protein phosphatases in Streptomyces: duplication of catalytic domain and lateral recruitment of additional sensory domains
    Weiwen Zhang
    Microbiology Department, Pacific Northwest National Laboratory, 902 Battelle Blvd, PO Box 999, Mail Stop P7 50, Richland, WA 99352, USA
    Microbiology 150:4189-97. 2004
  10. ncbi Microarray analyses of the metabolic responses of Saccharomyces cerevisiae to organic solvent dimethyl sulfoxide
    Weiwen Zhang
    Paradigm Genetics Inc, Microbial research group, 108 Alexander Drive, 27709, Research Triangle Park, North Carolina 27709, USA
    J Ind Microbiol Biotechnol 30:57-69. 2003

Collaborators

Detail Information

Publications27

  1. ncbi Molecular and biochemical characterization of a novel two-component signal transduction system, amrA- amkA, involved in rifamycin SV production in Amycolatopsis mediterranei U32
    Weiwu Wang
    Laboratory of Molecular Microbiology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, P R China
    Arch Microbiol 178:376-86. 2002
    ..Although the detailed regulatory mechanism is still unknown, this is the first report regarding the involvement of two-component signal systems in rifamycin biosynthesis in the genus Amycolatopsis...
  2. ncbi Oxidative stress and heat-shock responses in Desulfovibrio vulgaris by genome-wide transcriptomic analysis
    Weiwen Zhang
    Microbiology Department, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P O Box 999, Richland, WA 99352, USA
    Antonie Van Leeuwenhoek 90:41-55. 2006
    ..vulgaris. This hypothesis was further supported by the identification of a conserved motif upstream of these stress-responsive genes...
  3. ncbi DNA microarray analysis of anaerobic Methanosarcina barkeri reveals responses to heat shock and air exposure
    Weiwen Zhang
    Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    J Ind Microbiol Biotechnol 33:784-90. 2006
    ..In response to heat shock, both Hsp70 (DnaK-DnaJ-GrpE chaperone system) the Hsp60 (GroEL) systems were up-regulated, suggesting that they may play an important role in protein biogenesis in M. barkeri during heat stress...
  4. ncbi Global transcriptomic analysis of Desulfovibrio vulgaris on different electron donors
    Weiwen Zhang
    Department of Microbiology, Pacific Northwest National Laboratory, 902 Battelle Boulevard, 999, Richland, WA 99352, USA
    Antonie Van Leeuwenhoek 89:221-37. 2006
    ..The study provides the first global description and functional interpretation of transcriptomic response to growth phase and electron donor in D. vulgaris...
  5. ncbi Two-component signal transduction systems of Desulfovibrio vulgaris: structural and phylogenetic analysis and deduction of putative cognate pairs
    Weiwen Zhang
    Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    J Mol Evol 62:473-87. 2006
    ..vulgaris. The results provided a preliminary list of possible cognate HK-RR pairs and constitute a basis for further exploration of interaction and physiological function of TCSTSs in D. vulgaris...
  6. ncbi A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry
    Weiwen Zhang
    Microbiology Group, Pacific Northwest National Laboratory, Richland, WA, USA
    Proteomics 6:4286-99. 2006
    ..This study provides the first proteomic overview of the cellular metabolism of D. vulgaris. The complete list of proteins identified in this study and their abundances (peptide hits) is provided in Supplementary Table 1...
  7. ncbi LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris
    Weiwen Zhang
    Microbiology Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P O Box 999, Richland, WA 99352, USA
    Biochem Biophys Res Commun 349:1412-9. 2006
    ..This study demonstrated that a combination of proteomics and bioinformatics methodologies can provide verification of the expression of hypothetical proteins and improve genome annotation...
  8. ncbi Distribution and evolution of multiple-step phosphorelay in prokaryotes: lateral domain recruitment involved in the formation of hybrid-type histidine kinases
    Weiwen Zhang
    Microbiology Department, Pacific Northwest National Laboratory, 902 Battelle Blvd, PO Box 999, Mail Stop P7 50, Richland, WA 99352, USA
    Microbiology 151:2159-73. 2005
    ..In addition, fewer HPTs than hybrid-type HKs were identified in all prokaryotic genomes...
  9. ncbi Evolution of the PPM-family protein phosphatases in Streptomyces: duplication of catalytic domain and lateral recruitment of additional sensory domains
    Weiwen Zhang
    Microbiology Department, Pacific Northwest National Laboratory, 902 Battelle Blvd, PO Box 999, Mail Stop P7 50, Richland, WA 99352, USA
    Microbiology 150:4189-97. 2004
    ..This study provides an insight into how Streptomyces spp. may have expanded their PPM-based signal transduction networks to enable them to respond to a greater range of environmental changes...
  10. ncbi Microarray analyses of the metabolic responses of Saccharomyces cerevisiae to organic solvent dimethyl sulfoxide
    Weiwen Zhang
    Paradigm Genetics Inc, Microbial research group, 108 Alexander Drive, 27709, Research Triangle Park, North Carolina 27709, USA
    J Ind Microbiol Biotechnol 30:57-69. 2003
    ....
  11. ncbi Development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and its responses to oxidative stress
    Johannes C M Scholten
    Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Biochem Biophys Res Commun 358:571-7. 2007
    ....
  12. ncbi Comparative transcriptome analysis of Desulfovibrio vulgaris grown in planktonic culture and mature biofilm on a steel surface
    Weiwen Zhang
    Microbiology Department, Pacific Northwest National Laboratory, 902 Battelle Blvd, Mail Stop P7 50, PO Box 999, Richland, WA 99352, USA
    Appl Microbiol Biotechnol 76:447-57. 2007
    ..The study provided insights into the metabolic networks associated with the formation and maintenance of a D. vulgaris biofilm on a steel surface...
  13. doi Microbial dynamics in upflow anaerobic sludge blanket (UASB) bioreactor granules in response to short-term changes in substrate feed
    William P Kovacik
    Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99354, USA
    Microbiology 156:2418-27. 2010
    ..Our results demonstrated that microbial communities, even highly structured ones such as in UASB biogranules, are very capable of responding to rapid and major changes in their environment...
  14. ncbi Comparative analysis of eukaryotic-type protein phosphatases in two streptomycete genomes
    Liang Shi
    Microbiology Group, Pacific Northwest National Laboratory, 902 Battelle Blvd, PO Box 999, MSIN P7 50, Richland, WA 99352, USA
    Microbiology 150:2247-56. 2004
    ..coelicolor A3(2) and S. avermitilis constitute a basis for further exploration of the signal transduction pathways mediated by these phosphatases in industrially important strains of streptomycetes...
  15. ncbi Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: Involvement of an ancient horizontal gene transfer
    Johannes C Scholten
    Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Biochem Biophys Res Commun 352:48-54. 2007
    ..vulgaris. This report provides novel insights into the origin and evolution of bacterial genes linked to the lifestyle change of D. vulgaris from a syntrophic to a sulfate-reducing lifestyle...
  16. ncbi Optimization of RNA isolation from the archaebacterium Methanosarcina barkeri and validation for oligonucleotide microarray analysis
    David E Culley
    Microbiology Group, Pacific Northwest National Laboratory, P O Box 999, Mail Stop P7 50, Richland, WA 99352, USA
    J Microbiol Methods 67:36-43. 2006
    ..In addition, functional analysis of the microarray results obtained with RNA from the optimized protocol showed that, as expected, the genes involved in methanogenesis were among the most highly expressed genes in M. barkeri...
  17. ncbi Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: zero-inflated Poisson regression models to predict abundance of undetected proteins
    Lei Nie
    Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University Washington DC 20057, USA
    Bioinformatics 22:1641-7. 2006
    ..vulgaris grown on lactate-based versus formate-based media. These models correctly predicted increased expression of Ech hydrogenase and decreased expression of Coo hydrogenase for D.vulgaris grown on formate...
  18. doi Characterization of a negative regulator AveI for avermectin biosynthesis in Streptomyces avermitilis NRRL8165
    Lei Chen
    Laboratory of Molecular Microbiology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, People s Republic of China
    Appl Microbiol Biotechnol 80:277-86. 2008
    ....
  19. doi Integrative analyses of posttranscriptional regulation in the yeast Saccharomyces cerevisiae using transcriptomic and proteomic data
    Gang Wu
    Department of Molecular Micriobiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
    Curr Microbiol 57:18-22. 2008
    ..Taken together, all posttranscriptional biological properties contributed to 33.15% of the total variation of mRNA-protein correlation...
  20. ncbi Characterization of a novel two-component regulatory system involved in the regulation of both actinorhodin and a type I polyketide in Streptomyces coelicolor
    Yinhua Lu
    Laboratory of Molecular Microbiology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, People s Republic of China
    Appl Microbiol Biotechnol 77:625-35. 2007
    ..coelicolor, and the effects exerted by RapA1/A2 were dependent on the pathway-specific regulatory genes...
  21. ncbi Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism
    Gang Wu
    Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
    Microbiology 151:2175-87. 2005
    ..The PHX genes exclusive to each genome, and what they imply regarding cellular metabolism, are also discussed...
  22. pmc Directed evolution and structural analysis of N-carbamoyl-D-amino acid amidohydrolase provide insights into recombinant protein solubility in Escherichia coli
    Shimin Jiang
    Laboratory of Molecular Microbiology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, People s Republic of China
    Biochem J 402:429-37. 2007
    ..The present study provides new insights into recombinant protein solubility in E. coli...
  23. pmc Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: a quantitative analysis
    Lei Nie
    Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University, Washington, DC 20057, USA
    Genetics 174:2229-43. 2006
    ..vulgaris and adds new insights into the relative importance of various sequence features in prokaryotic protein translation...
  24. ncbi Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations
    Lei Nie
    Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, USA
    Biochem Biophys Res Commun 339:603-10. 2006
    ..The study presents the first quantitative analysis of the contributions of various biochemical and physical sources to the correlation of mRNA and protein abundance in D. vulgaris...
  25. ncbi Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence
    Gang Wu
    Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
    Antonie Van Leeuwenhoek 89:135-46. 2006
    ..The results provided the first estimates of global gene expression patterns in N. farcinica, which will be useful in guiding experimental design for further investigations...
  26. ncbi Relation between mRNA expression and sequence information in Desulfovibrio vulgaris: combinatorial contributions of upstream regulatory motifs and coding sequence features to variations in mRNA abundance
    Gang Wu
    Department of Biological Sciences, University of Maryland at Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
    Biochem Biophys Res Commun 344:114-21. 2006
    ..This result demonstrates that upstream regulatory motifs and coding sequence information contribute to the overall mRNA expression in a combinatorial rather than an additive manner...
  27. ncbi Integrative analysis of transcriptomic and proteomic data: challenges, solutions and applications
    Lei Nie
    Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Washington, DC, USA
    Crit Rev Biotechnol 27:63-75. 2007
    ..In addition, some new applications of integrated transcriptomic and proteomic analysis to the investigation of post-transcriptional regulation are also discussed...