Anthropogenic N deposition, fungal gene expression, and an increasing soil carbon sink in the Northern Hemisphere

Ecology ◽  
2019 ◽  
Vol 100 (10) ◽  
Author(s):  
Donald R. Zak ◽  
William A. Argiroff ◽  
Zachary B. Freedman ◽  
Rima A. Upchurch ◽  
Elizabeth M. Entwistle ◽  
...  
Keyword(s):  
Gene Expression ◽  
Soil Carbon ◽  
Northern Hemisphere ◽  
Carbon Sink ◽  
N Deposition ◽  
Fungal Gene Expression ◽  
Fungal Gene

scholarly journals Differential accumulation of poly(A)+ RNA between virulent and double-stranded RNA-induced hypovirulent strains of Cryphonectria (Endothia) parasitica.

1987 ◽  
Vol 7 (10) ◽  
pp. 3688-3693 ◽  
Author(s):  
W A Powell ◽  
N K Van Alfen
Keyword(s):  
Gene Expression ◽  
Specific Effect ◽  
Rna Sequences ◽  
Double Stranded Rna ◽  
Total Rna ◽  
Rna Sequence ◽  
Differential Hybridization ◽  
Endothia Parasitica ◽  
Fungal Gene Expression ◽  
Fungal Gene

The double-stranded RNA responsible for transmissible hypovirulence in Cryphonectria (Endothia) parasitica was found to affect the accumulation of specific poly(A)+ RNA. Using differential hybridization techniques, two genes were isolated, Vir1 and Vir2, which were specifically expressed as poly(A)+ RNAs in the virulent cells. The highly expressed RNA sequences from these genes were not found in total RNA isolated from either American or European hypovirulent strains, although the genes were present in their genomes. Other virulence- and hypovirulence-specific RNA sequences were also detected. One isolated hypovirulence-specific RNA sequence was expressed in both virulent and hypovirulent cells, but in a two- to fourfold-higher concentration in the hypovirulent cells. The results show that hypovirulence is associated with concurrent changes in a few highly expressed poly(A)+ RNAs, which suggests a specific effect of the double-stranded RNA on fungal gene expression.

FungiExp: A Comprehensive Platform For Exploring Fungal Gene Expression and Alternative Splicing Based On 35,821 RNA-Seq Experiments From 220 Fungi

2021 ◽  
Author(s):  
Jinding Liu ◽  
Fei Yin ◽  
Kun Lang ◽  
Wencai Jie ◽  
Suxu Tan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Sequence Similarity ◽  
Expression Regulation ◽  
Rna Seq ◽  
Specific Expression ◽  
Data Accessibility ◽  
Wide Range ◽  
Fungal Gene Expression ◽  
Fungal Gene

Abstract Background: RNA-seq has become a standard tool in biology and has produced large and diverse transcriptomic datasets for users to explore fungal expression regulation. Fungal alternative splicing, which is attracting increasing attention because of evolutionary adaptations to changing external conditions has not been thoroughly investigated in previous studies, unlike that of animals and plants. However, the analyses of RNA-seq datasets are made difficult by the heterogeneity of study design and complex bioinformatics approaches. Comprehensive analyses of these published datasets should contribute new insights into fungal expression regulation.Results: We have developed a web-based platform called FungiExp hosting fungal gene expression levels and alternative splicing profiles in 35,821 curated RNA-seq experiments from 220 species. It allows users to perform retrieval via diverse terms and sequence similarity. Moreover, users can customize experimental groups to perform differential and specific expression analyses. The wide range of data visualization is an additional important feature that should help users intuitively understand retrieval and analysis results.Conclusions: With its uniform data processing, easy data accessibility, convenient retrieval, and analysis functions, FungiExp is a valuable resource and tool that allows users to (re)use published RNA-seq datasets. It is accessible at http://bioinfo.njau.edu.cn/fungiExp.

scholarly journals Phases of Infection and Gene Expression of Fusarium graminearum During Crown Rot Disease of Wheat

2008 ◽  
Vol 21 (12) ◽  
pp. 1571-1581 ◽  
Author(s):  
Amber E. Stephens ◽  
Donald M. Gardiner ◽  
Rosemary G. White ◽  
Alan L. Munn ◽  
John M. Manners
Keyword(s):  
Gene Expression ◽  
Fusarium Graminearum ◽  
Quantitative Polymerase Chain Reaction ◽  
Crown Rot ◽  
Fungal Colonization ◽  
Published Data ◽  
In Planta ◽  
Head Blight ◽  
Fungal Gene Expression ◽  
Fungal Gene

Fusarium graminearum causes head blight (FHB) and crown rot (CR) diseases in wheat. Compared with FHB, CR symptom development occurs slowly, usually taking 4 to 8 weeks to become visible. To characterize CR development, we used histological and real-time quantitative polymerase chain reaction analyses to assess fungal colonization during a timecourse of infection. Three distinct phases of infection were identified: i) initial spore germination with formation of a superficial hyphal mat at the inoculation point, ii) colonization of the adaxial epidermis of the outer leaf sheath and mycelial growth from the inoculation point to the crown, concomitant with a drop in fungal biomass, and iii) extensive colonization of the internal crown tissue. Fungal gene expression was examined during each phase using Affymetrix GeneChips. In total, 1,839 F. graminearum genes were significantly upregulated, including some known FHB virulence genes (e.g., TRI5 and TRI14), and 2,649 genes were significantly downregulated in planta compared with axenically cultured mycelia. Global comparisons of fungal gene expression with published data for FHB showed significant similarities between early stages of FHB and CR. These results indicate that CR disease development involves distinct phases of colonization, each of which is associated with a different fungal gene expression program.

scholarly journals Regulation of Gene Expression by Ambient pH in Filamentous Fungi and Yeasts

2002 ◽  
Vol 66 (3) ◽  
pp. 426-446 ◽  
Author(s):  
Miguel A. Peñalva ◽  
Herbert N. Arst
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Regulation Of Gene Expression ◽  
Regulatory System ◽  
Gene Products ◽  
Animal Kingdom ◽  
Fungal Pathogenicity ◽  
Fungal Gene Expression ◽  
Fungal Gene ◽  
Secreted Enzymes

SUMMARY Life, as we know it, is water based. Exposure to hydroxonium and hydroxide ions is constant and ubiquitous, and the evolutionary pressure to respond appropriately to these ions is likely to be intense. Fungi respond to their environments by tailoring their output of activities destined for the cell surface or beyond to the ambient pH. We are beginning to glimpse how they sense ambient pH and transmit this information to the transcription factor, whose roles ensure that a suitable collection of gene products will be made. Although relatively little is known about pH signal transduction itself, its consequences for the cognate transcription factor are much clearer. Intriguingly, homologues of components of this system mediating the regulation of fungal gene expression by ambient pH are to be found in the animal kingdom. The potential applied importance of this regulatory system lies in its key role in fungal pathogenicity of animals and plants and in its control of fungal production of toxins, antibiotics, and secreted enzymes.

Sign in / Sign up

Export Citation Format

Share Document