Hydrogen peroxide‐induced oxidative stress responses in <i>Desulfovibrio vulgaris</i> Hildenborough

Zhou, Aifen; He, Zhili; Redding-Johanson, Alyssa M.; Mukhopadhyay, Aindrila; Hemme, Christopher L.; Joachimiak, Marcin P.; Luo, Feng; Deng, Ye; Bender, Kelly S.; He, Qiang; Keasling, Jay D.; Stahl, David A.; Fields, Matthew W.; Hazen, Terry C.; Arkin, Adam P.; Wall, Judy D.; Zhou, Jizhong

doi:10.1111/j.1462-2920.2010.02234.x

Cited by 43 publications

(51 citation statements)

References 47 publications

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“…The RMT identifies the threshold by observing a transition point of nearest-neighbor spacing distribution of eigenvalues from Gaussian to Poisson distribution, which are two universal extreme distributions (36). The RMT-based approach is a reliable and robust tool for network construction and has been successfully applied to construct various networks, including gene regulatory networks (49)(50)(51)(52)(53), functional molecular ecological networks (36), and phylogenetic molecular ecological networks (37). Second, the same cutoff of 0.78 was applied to construct co-occurrence networks for fungal communities at aCO 2 and eCO 2 , with the purpose of comparing between different networks.…”

Section: Methodsmentioning

confidence: 99%

Fungal Communities Respond to Long-Term CO ₂ Elevation by Community Reassembly

Yuan

et al. 2015

Appl Environ Microbiol

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Fungal communities play a major role as decomposers in the Earth's ecosystems. Their community-level responses to elevated CO 2 (eCO 2 ), one of the major global change factors impacting ecosystems, are not well understood. Using 28S rRNA gene amplicon sequencing and co-occurrence ecological network approaches, we analyzed the response of soil fungal communities in the BioCON (biodiversity, CO 2 , and N deposition) experimental site in Minnesota, USA, in which a grassland ecosystem has been exposed to eCO 2 for 12 years. Long-term eCO 2 did not significantly change the overall fungal community structure and species richness, but significantly increased community evenness and diversity. The relative abundances of 119 operational taxonomic units (OTU; ϳ27% of the total captured sequences) were changed significantly. Significantly changed OTU under eCO 2 were associated with decreased overall relative abundance of Ascomycota, but increased relative abundance of Basidiomycota. Cooccurrence ecological network analysis indicated that eCO 2 increased fungal community network complexity, as evidenced by higher intermodular and intramodular connectivity and shorter geodesic distance. In contrast, decreased connections for dominant fungal species were observed in the eCO 2 network. Community reassembly of unrelated fungal species into highly connected dense modules was observed. Such changes in the co-occurrence network topology were significantly associated with altered soil and plant properties under eCO 2 , especially with increased plant biomass and NH 4 ؉ availability. This study provided novel insights into how eCO 2 shapes soil fungal communities in grassland ecosystems.

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Section: Methodsmentioning

confidence: 99%

Fungal Communities Respond to Long-Term CO ₂ Elevation by Community Reassembly

Yuan

et al. 2015

Appl Environ Microbiol

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“…Each array was hybridized with Cy3-labeled gDNA (as a control for normalization) and Cy5-labeled cDNA on a Tecan HS4800 hybridization station (Tecan Group, Durham, NC). Hybridization conditions as well as washing conditions and performance of image scanning were as described previously (7,16,36,51). The microarray raw data processing was performed as described previously (36).…”

Section: Methodsmentioning

confidence: 99%

Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough

Zhou

Chen

Zane

et al. 2012

Appl Environ Microbiol

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Crp/Fnr-type global transcriptional regulators regulate various metabolic pathways in bacteria and typically function in response to environmental changes. However, little is known about the function of four annotated Crp/Fnr homologs (DVU0379, DVU2097, DVU2547, and DVU3111) in Desulfovibrio vulgaris Hildenborough. A systematic study using bioinformatic, transcriptomic, genetic, and physiological approaches was conducted to characterize their roles in stress responses. Similar growth phenotypes were observed for the crp/fnr deletion mutants under multiple stress conditions. Nevertheless, the idea of distinct functions of Crp/Fnr-type regulators in stress responses was supported by phylogeny, gene transcription changes, fitness changes, and physiological differences. The four D. vulgaris Crp/Fnr homologs are localized in three subfamilies (HcpR, CooA, and cc). The crp/fnr knockout mutants were well separated by transcriptional profiling using detrended correspondence analysis (DCA), and more genes significantly changed in expression in a ⌬DVU3111 mutant (JW9013) than in the other three paralogs. In fitness studies, strain JW9013 showed the lowest fitness under standard growth conditions (i.e., sulfate reduction) and the highest fitness under NaCl or chromate stress conditions; better fitness was observed for a ⌬DVU2547 mutant (JW9011) under nitrite stress conditions and a ⌬DVU2097 mutant (JW9009) under air stress conditions. A higher Cr(VI) reduction rate was observed for strain JW9013 in experiments with washed cells. These results suggested that the four Crp/Fnr-type global regulators play distinct roles in stress responses of D. vulgaris. DVU3111 is implicated in responses to NaCl and chromate stresses, DVU2547 in nitrite stress responses, and DVU2097 in air stress responses.T ranscription factors, promoter sequences, and regulatory circuit architecture are often referred as "the regulatory genome" (27, 33), and transcription factors are central to the function of regulatory networks (5). Organisms rely on regulatory networks to orchestrate the transcription of genes in response to internal or external environmental changes in order to optimize metabolism and enhance survival. Crp/Fnr regulators are global transcriptional regulators widely distributed in bacteria. The characteristic structure of Crp/Fnr is a C-terminal helix-turn-helix (HTH) motif that fits the DNA major groove and an N-terminal nucleotide binding domain (34). This class of transcriptional factors is named after the first two representatives discovered in Escherichia coli, i.e., the Crp (cyclic AMP [cAMP] receptor protein) and Fnr (fumarate and nitrate reductase regulator protein) (4, 21, 24, 27). Crp/Fnr regulators are generally classified into different subfamilies (e.g., CooA, Crp, Dnr, FixK, Fnr, HbaR, NnrR, etc.) according to phylogenetic affiliations (50). The increasing number of sequenced whole genomes has added to a growing list of Crp/Fnr family regulators identified in bacteria (9, 26); however, functions for most are not well defin...

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“…Array hybridizations were carried out with TECAN hybridization station (TECAN HS4800, TECAN Group Ltd, Durham, NC, USA). Array hybridization and data analysis were performed as described previously (Mukhopadhyay et al, 2006;Zhou et al, 2010). Microarray data have been deposited in the NCBI GEO database under accession number GSE39675.…”

Section: Microarray Hybridization and Data Analysismentioning

confidence: 99%

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution

Zhou

Baidoo

et al. 2013

The ISME Journal

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Desulfovibrio vulgaris Hildenborough strains with significantly increased tolerance to NaCl were obtained via experimental evolution. A NaCl-evolved strain, ES9-11, isolated from a population cultured for 1200 generations in medium amended with 100 mM NaCl, showed better tolerance to NaCl than a control strain, EC3-10, cultured for 1200 generations in parallel but without NaCl amendment in medium. To understand the NaCl adaptation mechanism in ES9-11, we analyzed the transcriptional, metabolite and phospholipid fatty acid (PLFA) profiles of strain ES9-11 with 0, 100-or 250 mM-added NaCl in medium compared with the ancestral strain and EC3-10 as controls. In all the culture conditions, increased expressions of genes involved in amino-acid synthesis and transport, energy production, cation efflux and decreased expression of flagellar assembly genes were detected in ES9-11. Consistently, increased abundances of organic solutes and decreased cell motility were observed in ES9-11. Glutamate appears to be the most important osmoprotectant in D. vulgaris under NaCl stress, whereas, other organic solutes such as glutamine, glycine and glycine betaine might contribute to NaCl tolerance under low NaCl concentration only. Unsaturation indices of PLFA significantly increased in ES9-11. Branched unsaturated PLFAs i17:1 x9c, a17:1 x9c and branched saturated i15:0 might have important roles in maintaining proper membrane fluidity under NaCl stress. Taken together, these data suggest that the accumulation of osmolytes, increased membrane fluidity, decreased cell motility and possibly an increased exclusion of Na þ contribute to increased NaCl tolerance in NaCl-evolved D. vulgaris.

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Hydrogen peroxide‐induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough

Cited by 43 publications

References 47 publications

Fungal Communities Respond to Long-Term CO ₂ Elevation by Community Reassembly

Fungal Communities Respond to Long-Term CO ₂ Elevation by Community Reassembly

Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution

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Hydrogen peroxide‐induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough

Cited by 43 publications

References 47 publications

Fungal Communities Respond to Long-Term CO 2 Elevation by Community Reassembly

Fungal Communities Respond to Long-Term CO 2 Elevation by Community Reassembly

Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution

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Fungal Communities Respond to Long-Term CO ₂ Elevation by Community Reassembly

Fungal Communities Respond to Long-Term CO ₂ Elevation by Community Reassembly