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Title: Final Report Construction of Whole Genome Microarrays, and Expression Analysis of Desulfovibrio vulgaris cells in Metal-Reducing Conditions

Abstract

We continue to utilize the oligonucleotide microarrays that were constructed through funding with this project to characterize growth responses of Desulfovibrio vulgaris relevant to metal-reducing conditions. To effectively immobilize heavy metals and radionuclides via sulfate-reduction, it is important to understand the cellular responses to adverse factors observed at contaminated subsurface environments (e.g., nutrients, pH, contaminants, growth requirements and products). One of the major goals of the project is to construct whole-genome microarrays for Desulfovibrio vulgaris. First, in order to experimentally establish the criteria for designing gene-specific oligonucleotide probes, an oligonucleotide array was constructed that contained perfect match (PM) and mismatch (MM) probes (50mers and 70mers) based upon 4 genes. The effects of probe-target identity, continuous stretch, mismatch position, and hybridization free energy on specificity were examined. Little hybridization was observed at a probe-target identity of <85% for both 50mer and 70mer probes. 33 to 48% of the PM signal intensities were detected at a probe-target identity of 94% for 50mer oligonucleotides, and 43 to 55% for 70mer probes at a probe-target identity of 96%. When the effects of sequence identity and continuous stretch were considered independently, a stretch probe (>15 bases) contributed an additional 9% of the PM signal intensitymore » compared to a non-stretch probe (< 15 bases) at the same identity level. Cross-hybridization increased as the length of continuous stretch increased. A 35-base stretch for 50mer probes or a 50-base stretch for 70mer probes had approximately 55% of the PM signal. Mismatches should be as close to the middle position of an oligonucleotide probe as possible to minimize cross-hybridization. Little cross-hybridization was observed for probes with a minimal binding free energy greater than -30 kcal/mol for 50mer probes or -40 kcal/mol for 70mer probes. Based on the experimental results, a set of criteria were suggested for the design of gene-specific and group-specific oligonucleotide probes, and these criteria should provide valuable information for the development of new software and algorithms for microarray-based studies. Secondly, in order to empirically determine the effect of probe length on signal intensities, microarrays with oligonucleotides of different lengths were used to monitor gene expression at a whole genome level. To determine what length of oligonucleotide is a better alternative to PCR-generated probes, the performance of oligonucleotide probes was systematically compared to that of their PCR-generated counterparts for 96 genes from Shewanella oneidensis MR-1 in terms of overall signal intensity, numbers of detected genes, specificity, sensitivity and differential gene expression under experimental conditions. Hybridizations conducted at 42 C, 45 C, 50 C, and 60 C indicated that good sensitivities were obtained at 45 C for oligonucleotide probes in the presence of 50% formamide, under which conditions specific signals were detected by both PCR and oligonucleotide probes. Signal intensities increased as the length of oligonucleotide probes increased, and the 70mer oligonucleotide probes produced similar signal intensities and detected a similar number of ORFs compared to the PCR probes. cDNA, 70mer, 60mer and 50mer arrays had detection sensitivities at 5.0, 25, 100 and 100 ng of genomic DNA, or an approximately equivalent of 1.9 x 10{sup 6}, 9.2 x 10{sup 6}, 3.7 x 10{sup 7} and 3.7 x 10{sup 7} copies, respectively when the array was hybridized with genomic DNA. To evaluate differential gene expression under experimental conditions, S. oneidensis MR-1 cells were exposed to low or high pH conditions for 30 and 60 min, and the transcriptional profiling detected by oligonucleotide probes (50mer, 60mer, and 70mer) was closely correlated with that detected by the PCR probes. The results demonstrated that 70mer oligonucleotides can achieve the most comparable performance with PCR-generated probes. We have analyzed expression data as D. vulgaris transitioned during electron donor depletion. As the cells transitioned from exponential to stationary-phase a majority of the down-expressed genes were involved in translation and transcription, and this trend continued in the remaining time points. Interestingly, most phage-related genes were up-expressed at the onset of stationary-phase. This result suggested that nutrient depletion may impact community dynamics and DNA transfer mechanisms of sulfate-reducing bacteria via phage cycle. The putative feoAB system (in addition to other presumptive iron metabolism genes) was significantly up-expressed, and suggested the possible importance of Fe{sup 2+} acquisition under metal-reducing conditions. Namely, that iron availability should be considered when sulfate-reducing conditions are stimulated in the subsurface for heavy metal reduction.« less

Authors:
; ; ;
Publication Date:
Research Org.:
Miami Univ., Oxford, OH (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
929541
Report Number(s):
DOE/ER/63765-1
TRN: US201011%%57
DOE Contract Number:  
FG02-04ER63765
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; BACTERIA; BINDING ENERGY; BIOLOGICAL FUNCTIONS; BIOREMEDIATION; CONSTRUCTION; DESULFOVIBRIO; DNA; ENERGY CONVERSION; FREE ENERGY; GENES; HEAVY METALS; HYBRIDIZATION; IRON; OLIGONUCLEOTIDES; PROBES; RADIOISOTOPES; SULFATE-REDUCING BACTERIA; TRANSCRIPTION; VALENCE

Citation Formats

Fields, M W, Wall, J D, Keasling, J, and Zhou, J. Final Report Construction of Whole Genome Microarrays, and Expression Analysis of Desulfovibrio vulgaris cells in Metal-Reducing Conditions. United States: N. p., 2008. Web. doi:10.2172/929541.
Fields, M W, Wall, J D, Keasling, J, & Zhou, J. Final Report Construction of Whole Genome Microarrays, and Expression Analysis of Desulfovibrio vulgaris cells in Metal-Reducing Conditions. United States. doi:10.2172/929541.
Fields, M W, Wall, J D, Keasling, J, and Zhou, J. Thu . "Final Report Construction of Whole Genome Microarrays, and Expression Analysis of Desulfovibrio vulgaris cells in Metal-Reducing Conditions". United States. doi:10.2172/929541. https://www.osti.gov/servlets/purl/929541.
@article{osti_929541,
title = {Final Report Construction of Whole Genome Microarrays, and Expression Analysis of Desulfovibrio vulgaris cells in Metal-Reducing Conditions},
author = {Fields, M W and Wall, J D and Keasling, J and Zhou, J},
abstractNote = {We continue to utilize the oligonucleotide microarrays that were constructed through funding with this project to characterize growth responses of Desulfovibrio vulgaris relevant to metal-reducing conditions. To effectively immobilize heavy metals and radionuclides via sulfate-reduction, it is important to understand the cellular responses to adverse factors observed at contaminated subsurface environments (e.g., nutrients, pH, contaminants, growth requirements and products). One of the major goals of the project is to construct whole-genome microarrays for Desulfovibrio vulgaris. First, in order to experimentally establish the criteria for designing gene-specific oligonucleotide probes, an oligonucleotide array was constructed that contained perfect match (PM) and mismatch (MM) probes (50mers and 70mers) based upon 4 genes. The effects of probe-target identity, continuous stretch, mismatch position, and hybridization free energy on specificity were examined. Little hybridization was observed at a probe-target identity of <85% for both 50mer and 70mer probes. 33 to 48% of the PM signal intensities were detected at a probe-target identity of 94% for 50mer oligonucleotides, and 43 to 55% for 70mer probes at a probe-target identity of 96%. When the effects of sequence identity and continuous stretch were considered independently, a stretch probe (>15 bases) contributed an additional 9% of the PM signal intensity compared to a non-stretch probe (< 15 bases) at the same identity level. Cross-hybridization increased as the length of continuous stretch increased. A 35-base stretch for 50mer probes or a 50-base stretch for 70mer probes had approximately 55% of the PM signal. Mismatches should be as close to the middle position of an oligonucleotide probe as possible to minimize cross-hybridization. Little cross-hybridization was observed for probes with a minimal binding free energy greater than -30 kcal/mol for 50mer probes or -40 kcal/mol for 70mer probes. Based on the experimental results, a set of criteria were suggested for the design of gene-specific and group-specific oligonucleotide probes, and these criteria should provide valuable information for the development of new software and algorithms for microarray-based studies. Secondly, in order to empirically determine the effect of probe length on signal intensities, microarrays with oligonucleotides of different lengths were used to monitor gene expression at a whole genome level. To determine what length of oligonucleotide is a better alternative to PCR-generated probes, the performance of oligonucleotide probes was systematically compared to that of their PCR-generated counterparts for 96 genes from Shewanella oneidensis MR-1 in terms of overall signal intensity, numbers of detected genes, specificity, sensitivity and differential gene expression under experimental conditions. Hybridizations conducted at 42 C, 45 C, 50 C, and 60 C indicated that good sensitivities were obtained at 45 C for oligonucleotide probes in the presence of 50% formamide, under which conditions specific signals were detected by both PCR and oligonucleotide probes. Signal intensities increased as the length of oligonucleotide probes increased, and the 70mer oligonucleotide probes produced similar signal intensities and detected a similar number of ORFs compared to the PCR probes. cDNA, 70mer, 60mer and 50mer arrays had detection sensitivities at 5.0, 25, 100 and 100 ng of genomic DNA, or an approximately equivalent of 1.9 x 10{sup 6}, 9.2 x 10{sup 6}, 3.7 x 10{sup 7} and 3.7 x 10{sup 7} copies, respectively when the array was hybridized with genomic DNA. To evaluate differential gene expression under experimental conditions, S. oneidensis MR-1 cells were exposed to low or high pH conditions for 30 and 60 min, and the transcriptional profiling detected by oligonucleotide probes (50mer, 60mer, and 70mer) was closely correlated with that detected by the PCR probes. The results demonstrated that 70mer oligonucleotides can achieve the most comparable performance with PCR-generated probes. We have analyzed expression data as D. vulgaris transitioned during electron donor depletion. As the cells transitioned from exponential to stationary-phase a majority of the down-expressed genes were involved in translation and transcription, and this trend continued in the remaining time points. Interestingly, most phage-related genes were up-expressed at the onset of stationary-phase. This result suggested that nutrient depletion may impact community dynamics and DNA transfer mechanisms of sulfate-reducing bacteria via phage cycle. The putative feoAB system (in addition to other presumptive iron metabolism genes) was significantly up-expressed, and suggested the possible importance of Fe{sup 2+} acquisition under metal-reducing conditions. Namely, that iron availability should be considered when sulfate-reducing conditions are stimulated in the subsurface for heavy metal reduction.},
doi = {10.2172/929541},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2008},
month = {5}
}