scholarly journals DNA Microarray Analysis of Nitrogen Fixation and Fe(III) Reduction in Geobacter sulfurreducens

2005 ◽  
Vol 71 (5) ◽  
pp. 2530-2538 ◽  
Author(s):  
Barbara A. Methé ◽  
Jennifer Webster ◽  
Kelly Nevin ◽  
Jessica Butler ◽  
Derek R. Lovley
Keyword(s):  
Nitrogen Fixation ◽  
Dna Microarray ◽  
Electron Acceptor ◽  
Global Gene Expression ◽  
Geobacter Sulfurreducens ◽  
Unexpected Result ◽  
Transcript Levels ◽  
Gene Coding ◽  
Global Gene Expression Profiling ◽  
Microarray Analyses

ABSTRACT A DNA microarray representing the genome of Geobacter sulfurreducens was constructed for use in global gene expression profiling of cells under steady-state conditions with acetate as the electron donor and Fe(III) or fumarate as the electron acceptor. Reproducible differences in transcript levels were also observed in comparisons between cells grown with ammonia and those fixing atmospheric nitrogen. There was a high correlation between changes in transcript levels determined with microarray analyses and an evaluation of a subset of the genome with quantitative PCR. As expected, cells required to fix nitrogen had higher levels of transcripts of genes associated with nitrogen fixation, further demonstrating that the microarray approach could reliably detect important physiological changes. Cells grown with Fe(III) as the electron acceptor had higher levels of transcripts for omcB, a gene coding for an outer membrane c-type cytochrome that is essential for Fe(III) reduction. Several other c-type cytochrome genes also appeared to be up-regulated. An unexpected result was significantly higher levels of transcripts for genes which have a role in metal efflux, potentially suggesting the importance of maintaining metal homeostasis during release of soluble metals when reducing Fe(III). A substantial proportion (30%) of significantly expressed genes during Fe(III) reduction were genes of unknown function or hypothetical proteins, suggesting differences in Fe(III) reduction physiology among microorganisms which perform this metabolic process.

scholarly journals DNA Microarray and Proteomic Analyses of the RpoS Regulon in Geobacter sulfurreducens

2006 ◽  
Vol 188 (8) ◽  
pp. 2792-2800 ◽  
Author(s):  
Cinthia Núñez ◽  
Abraham Esteve-Núñez ◽  
Carol Giometti ◽  
Sandra Tollaksen ◽  
Tripti Khare ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Electron Acceptor ◽  
Protein Identification ◽  
Tricarboxylic Acid Cycle ◽  
Expression Profiles ◽  
Transcriptional Profiling ◽  
Geobacter Sulfurreducens ◽  
Negative Regulator ◽  
Major Protein ◽  
Subsurface Environments

ABSTRACT The regulon of the sigma factor RpoS was defined in Geobacter sulfurreducens by using a combination of DNA microarray expression profiles and proteomics. An rpoS mutant was examined under steady-state conditions with acetate as an electron donor and fumarate as an electron acceptor and with additional transcriptional profiling using Fe(III) as an electron acceptor. Expression analysis revealed that RpoS acts as both a positive and negative regulator. Many of the RpoS-dependent genes determined play roles in energy metabolism, including the tricarboxylic acid cycle, signal transduction, transport, protein synthesis and degradation, and amino acid metabolism and transport. As expected, RpoS activated genes involved in oxidative stress resistance and adaptation to nutrient limitation. Transcription of the cytochrome c oxidase operon, necessary for G. sulfurreducens growth using oxygen as an electron acceptor, and expression of at least 13 c-type cytochromes, including one previously shown to participate in Fe(III) reduction (MacA), were RpoS dependent. Analysis of a subset of the rpoS mutant proteome indicated that 15 major protein species showed reproducible differences in abundance relative to those of the wild-type strain. Protein identification using mass spectrometry indicated that the expression of seven of these proteins correlated with the microarray data. Collectively, these results indicate that RpoS exerts global effects on G. sulfurreducens physiology and that RpoS is vital to G. sulfurreducens survival under conditions typically encountered in its native subsurface environments.

Global gene expression profiling of porcine endometria on Days 12 and 16 of the estrous cycle and pregnancy

2014 ◽  
Vol 82 (6) ◽  
pp. 897-909 ◽  
Author(s):  
Jolanta Kiewisz ◽  
Kamil Krawczynski ◽  
Pawel Lisowski ◽  
Agnieszka Blitek ◽  
Lech Zwierzchowski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Estrous Cycle ◽  
Expression Profiling ◽  
Global Gene Expression ◽  
Global Gene Expression Profiling

Transcriptome profiling the gills of amoebic gill disease (AGD)-affected Atlantic salmon (Salmo salarL.): a role for tumor suppressor p53 in AGD pathogenesis?

2006 ◽  
Vol 26 (1) ◽  
pp. 15-34 ◽  
Author(s):  
Richard N. Morrison ◽  
Glenn A. Cooper ◽  
Ben F. Koop ◽  
Matthew L. Rise ◽  
Andrew R. Bridle ◽  
...  
Keyword(s):  
Tumor Suppressor ◽  
Atlantic Salmon ◽  
Gill Tissue ◽  
Transcriptome Profiling ◽  
Global Gene Expression ◽  
Nuclear Antigen ◽  
Independent Experiment ◽  
Gill Disease ◽  
P53 Tumor Suppressor Protein ◽  
Microarray Analyses

Neoparamoeba spp. are amphizoic amoebae with the capacity to colonize the gills of some marine fish, causing AGD. Here, the gill tissue transcriptome response of Atlantic salmon ( Salmo salar L.) to AGD is described. Tanks housing Atlantic salmon were inoculated with Neoparamoeba spp. and fish sampled at time points up to 8 days postinoculation (pi.). Gill tissues were taken from AGD-affected fish, and a DNA microarray was used to compare global gene expression against tissues from AGD-unaffected fish. A total of 206 genes, representing 190 unique transcripts, were reproducibly identified as up- or downregulated in response to Neoparamoeba spp. infection. Informative transcripts having GO biological process identifiers were grouped according to function. Although a number of genes were placed into each category, no distinct patterns were observed. One Atlantic salmon cDNA that was upregulated in infected gill relative to noninfected gill at 114 and 189 h pi. showed significant identity with the Xenopus, mouse, and human anterior gradient-2 (AG-2) homologs. Two Atlantic salmon AG-2 mRNA transcripts, designated asAG-2/1 and asAG-2/2, were cloned, sequenced, and shown to be predominantly expressed in the gill, intestine, and brain of a healthy fish. In AGD-affected fish, differential asAG-2 expression was confirmed in samples used for microarray analyses as well as in AGD-affected gill tissue taken from fish in an independent experiment. The asAG-2 upregulation was restricted to AGD lesions relative to unaffected tissue from the same gill arch, while p53 tumor suppressor protein mRNA was concurrently downregulated in AGD lesions. Differential expression of p53-regulated transcripts, proliferating cell nuclear antigen and growth arrest and DNA damage-inducible gene-45β (GADD45β) in AGD lesions, suggests a role for p53 in AGD pathogenesis. Thus AGD may represent a novel model for comparative analysis of p53 and p53-regulated pathways.

scholarly journals Lactose-over-Glucose Preference in Bifidobacterium longum NCC2705: glcP, Encoding a Glucose Transporter, Is Subject to Lactose Repression

2006 ◽  
Vol 188 (4) ◽  
pp. 1260-1265 ◽  
Author(s):  
Stephan Parche ◽  
Manfred Beleut ◽  
Enea Rezzonico ◽  
Doris Jacobs ◽  
Fabrizio Arigoni ◽  
...  
Keyword(s):  
Glucose Transport ◽  
Culture Medium ◽  
Glucose Transporter ◽  
Glucose Utilization ◽  
Bifidobacterium Longum ◽  
Global Gene Expression ◽  
Dna Arrays ◽  
Transporter Gene ◽  
Global Gene Expression Profiling ◽  
Culture Supernatants

ABSTRACT Analysis of culture supernatants obtained from Bifidobacterium longum NCC2705 grown on glucose and lactose revealed that glucose utilization is impaired until depletion of lactose. Thus, unlike many other bacteria, B. longum preferentially uses lactose rather than glucose as the primary carbon source. Glucose uptake experiments with B. longum cells showed that glucose transport was repressed in the presence of lactose. A comparative analysis of global gene expression profiling using DNA arrays led to the identification of only one gene repressed by lactose, the putative glucose transporter gene glcP. The functionality of GlcP as glucose transporter was demonstrated by heterologous complementation of a glucose transport-deficient Escherichia coli strain. Additionally, GlcP exhibited the highest substrate specificity for glucose. Primer extension and real-time PCR analyses confirmed that expression of glcP was mediated by lactose. Hence, our data demonstrate that the presence of lactose in culture medium leads to the repression of glucose transport and transcriptional down-regulation of the glucose transporter gene glcP. This may reflect the highly adapted life-style of B. longum in the gastrointestinal tract of mammals.

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