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Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 grown with or without manganese

ABSTRACT: The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. In several systems intracellular levels of the redox-active manganous (Mn2+) and ferrous (Fe2+) ions are interrelated and have tight corresponding regulation with respect to one another. We show that limiting manganese concentrations elicit similar growth and biofilm phenotypes to those seen under iron-limiting conditions. Microarray analysis comparing gene expression in manganese-replete versus manganese-limiting conditions identified a small number of differentially regulated transcripts. These results indicate that the redox-active manganous and ferrous ions are required for wild-type levels of growth and biofilm formation, and that the manganese-dependent response is primarily post-transcriptional and complementary to, but not redundant with, the iron-dependent response.

ORGANISM(S): Agrobacterium tumefaciens

PROVIDER: GSE71266 | GEO | 2015/07/24

SECONDARY ACCESSION(S): PRJNA290725

REPOSITORIES: GEO

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Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 grown with or without manganese

Project description:The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. In several systems intracellular levels of the redox-active manganous (Mn2+) and ferrous (Fe2+) ions are interrelated and have tight corresponding regulation with respect to one another. We show that limiting manganese concentrations elicit similar growth and biofilm phenotypes to those seen under iron-limiting conditions. Microarray analysis comparing gene expression in manganese-replete versus manganese-limiting conditions identified a small number of differentially regulated transcripts. These results indicate that the redox-active manganous and ferrous ions are required for wild-type levels of growth and biofilm formation, and that the manganese-dependent response is primarily post-transcriptional and complementary to, but not redundant with, the iron-dependent response. Four biological replicates, independent RNA preparations, two dye swaps.

2015-07-24 | E-GEOD-71266 | biostudies-arrayexpress

Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 grown with or without iron.

Project description:The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. We demonstrate that A. tumefaciens biofilm formation is reduced under limiting iron conditions. Treatment of A. tumefaciens cultures with EDDHA, an iron-specific extracellular chelator, inhibited both planktonic growth rate and adherent biomass. These effects were reversed upon addition of exogenous ferrous iron. This reduced biofilm formation effect is independent of the known iron-responsive regulators Irr and RirA. Transcriptome analysis comparing gene expression under iron-replete versus iron-deficient conditions identified hundreds of genes that are differentially regulated. Downregulated genes suggest an iron sparing response.

2015-07-22 | GSE71138 | GEO

Comparison of expression profiles for Agrobacterium tumefaciens wild-type strain C58 grown with or without iron.

Project description:The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. We demonstrate that A. tumefaciens biofilm formation is reduced under limiting iron conditions. Treatment of A. tumefaciens cultures with EDDHA, an iron-specific extracellular chelator, inhibited both planktonic growth rate and adherent biomass. These effects were reversed upon addition of exogenous ferrous iron. This reduced biofilm formation effect is independent of the known iron-responsive regulators Irr and RirA. Transcriptome analysis comparing gene expression under iron-replete versus iron-deficient conditions identified hundreds of genes that are differentially regulated. Downregulated genes suggest an iron sparing response. Four biological replicates, independent RNA preparations, one dye swap.

2015-07-22 | E-GEOD-71138 | biostudies-arrayexpress

Proteomic Analysis on the Mechanism of Iron-Compensation Substitute for Manganese Deficiency of Streptococcus pneumoniae

Project description:Iron (Fe) and Manganese (Mn) are essential for bacterial survival and virulence as they are involved in catalysis, infection and biofilm formation. The basal metabolism of pathogenic bacteria would be disturbed by the deficiency of metal ions in the host environment. In this study, we found that Streptococcus pneumoniae (S. pneumoniae) can still grow slowly in the medium without manganese ions. Further ICP-MS determination showed that the iron concentration in the bacterium was increased when the manganese content was decreased. The supplement of iron in the manganese deficient culture medium (MDCM) can recovery the bacterial growth. The quantitative proteome using stable-isotope dimethyl labeling was performed to investigate the adaptive growth mechanism of S. pneumoniae in Mn-deficiency condition. Compared with the bacteria cultured in the normal medium, 25 proteins were down-regulated and 54 proteins were up-expressed with more than 1.2-fold alteration (P < 0.05) in S. pneumoniae cultured with MDCM. A large number of depressed proteins are participated in cell energy metabolism, amino acid synthesis process and oxidation products reduction process. The subsequent detection indicated that both intracellar and extracellular hydrogen peroxide levels of in cells were significantly elevated, and the intracellular ATP levels of were evidently decreased in cells cultured in the absence of manganese, meaning that Mn-deficiency can cause multiple metabolic disorders. More importantly, several iron ABC transporters, such as PiuA/PiaA/PitA/SPD_1609, etc, were over-expressed to uptake more iron from the medium. These results suggest that lacking of manganese only disturbed multiple metabolic processes of S. pneumoniae, but also caused the compensatory effect of iron for manganese Mn which is beneficial to the survival of bacteria in extreme environments.

2023-09-30 | PXD008652 | Pride

The innate immune protein calprotectin promotes Pseudomonas aeruginosa and Staphylococcus aureus interaction

Project description:Microorganisms form biofilms containing differentiated cell populations. To determine factors driving differentiation, we study protein distributions in bacterial biofilms using shotgun proteomics. Notably, zinc- and manganese-depleted portions of the biofilm repress the production of anti-staphylococcal molecules. Exposure to calprotectin (a host protein known to sequester metal ions at infectious foci) recapitulates responses occurring within metal-deplete portions of the biofilm and promotes interaction between P. aeruginosa and Staphylococcus aureus. Consistent with these results, the presence of calprotectin promotes co-colonization of the murine lung, and polymicrobial communities are found to co-exist in calprotectin-enriched airspaces of a cystic fibrosis lung explant. These findings, which demonstrate that metal fluctuations are a driving force of microbial community structure, have clinical implications because of the frequent occurrence of P. aeruginosa and S. aureus co-infections.

2016-06-22 | PXD004081 | Pride

Temporal dynamics of gene expression in Campylobacter jejuni biofilm formation

Project description:Campylobacter jejuni, an important pathogen of bacterial gastrointestinal infections, forms biofilms that are crucial for its survival in different environments. We used RNA sequencing to investigate the changes in gene expression at different stages of biofilm formation (16 h, 24 h, 48 h and 72 h). The results showed that early biofilms (16 h and 24 h biofilms) show increased expression of genes involved in cysteine and methionine amino acid metabolism, while mature biofilms (48 h and 72 h biofilms) show decreased expression of capsular polysaccharides and lipooligosaccharides. Both early and mature biofilms are characterized by increased expression of genes involved in flagella formation, leucine amino acid metabolism and oxidative stress response, and decreased expression of genes involved in energy metabolism, iron acquisition and transmembrane transport. Thus, we provide a deeper understanding of the molecular mechanisms of C. jejuni biofilm maturation, environmental resistance and the dynamic nature of gene expression that facilitates adaptation to biofilm-associated lifestyles

2024-12-02 | GSE272440 | GEO

Study physiological and biochemical response of Phaeocystis antarctica to different irradiance and manganese/ iron deficiency

Project description:Iron and light are typically recognized as major limiting factors controlling phytoplankton growth in the Southern Ocean. Recent field-based evidence suggests, however, that manganese concentrations in this region can be low enough to impact phytoplankton physiology and primary productivity. Our study examined the interactive influence of combined iron and manganese deprivation on protein expression and photophysiology in Phaeocystis antarctica, a key Antarctic phytoplankter, and provide taxon-specific proteomic evidence that natural Southern Ocean Phaeocystis populations regularly experience stress due to combined low manganese and iron availability. In culture, combined low iron and manganese induced large scale changes in the Phaeocystis proteome and resulted in reorganization of key components of the photosynthetic apparatus; these differences were largely distinct from those arising from changes in irradiance. These results implicate manganese availability as an important driver of Southern Ocean productivity and demonstrate the utility of peptide mass spectrometry as a tool for mapping of manganese contributions to HNLC conditions in this region.

2019-06-25 | PXD010974 | Pride

Transcriptomic analysis of Streptococcus suis in response to ferrous iron and cobalt toxicity

Project description:We explored the transcriptome change of Streptococcus suis in the presence of ferrous iron and cobalt by RNA sequencing. The data revealed that expression of a lot of genes was altered to respond to ferrous iron and cobalt toxicity. Moreover, most of the genes differentially expressed in response to cobalt are the same as those in response to ferrous iron.

2020-07-04 | GSE153766 | GEO

The hierarchy of transition metal homeostasis: Iron controls manganese accumulation in a unicellular cyanobacterium.

Project description:Iron and manganese are part of a small group of transition metals required for photosynthetic electron transport. Here, we present evidence for a functional link between iron and manganese homeostasis. In the unicellular cyanobacterium, Synechocystis sp. PCC 6803 Fe and Mn deprivation resulted in distinct modifications of the function of the photosynthetic apparatus. For example, iron limitation modifies the rate of QA re-oxidation in photosystem II, a complex that contains more Mn than Fe. The intracellular elemental quotas of Fe and Mn are also linked. Fe limitation reduces the intracellular Mn quota. Mn limitation did not exert a reciprocal effect on Fe quotas. Microarray analysis comparing Mn and Fe limitation revealed a stark difference in the extent of the transcriptional response to the two limiting conditions, reflective of the physiological data. The effects of Fe limitation on the transcriptional network are widespread while the effects on Mn limitation are highly specific. Our analysis also revealed an overlap in the transcriptional response of specific Fe and Mn transporters. This overlap provides a framework for explaining Fe limitation induced changes in Mn quotas. Fe transporters can serve as a low affinity Mn transport system. Under iron limitation the specificity of the Fe transport system changes, making it a less efficient Mn transport system. We monitored the gene expression of Synechocystis PCC6083 at standard conditions and after 2 days of iron limitation (0Fe), manganese limitation (0Mn) and combined iron and manganese limitation (0Fe0Mn). Each timepoint and condition was sampled in triplicates. Due to strong deviations in one of the three repeats for the 0Mn and 0Fe0Mn conditions, the corresponding replicates were excluded from further analysis.

2013-06-29 | E-GEOD-48416 | biostudies-arrayexpress

Psl polysaccharide deficient mutant

Project description:Analysis of Pseudomonas aeruginosa PA01 (ATCC 15692) Psl polysaccharide deficient mutant. Psl polysaccharide deficient mutant is evaluated with microarray to understand the genes affected by this polysaccharide. Our results provide new vision on the roles played by Psl polysaccharide in P. aeruginosa. Exopolysaccharide Psl is a critical biofilm matrix component in Pseudomonas aeruginosa, which forms a fiber-like matrix to enmesh bacteria communities. Iron has been shown to serve as a signal in P. aeruginosa biofilm development, yet how iron controls biofilm formation is not clear. Here we perform a transcriptomic analysis to compare Psl negative strain versus its isogenic wild-type strain PAO1. The results indicate that the expression of genes involved in iron homeostasis and oxidative stress response increased drastically at transcriptional level in Psl negative strain, suggesting Psl deficiency induces iron limitation. Subsequent studies confirm that Psl can efficiently bind iron in vitro and Psl fibers functions as an iron storage channel in P. aeruginosa biofilms.

2016-01-26 | GSE77163 | GEO

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