scholarly journals New Putative Long Non-Coding RNAs (lncRNA) Revealed by Pan-Transcriptome of the Emerging Human Pathogenic Fungus Talaromyces Marneffei

2021 ◽  
Author(s):  
David Aciole Barbosa ◽  
Alexandre Santos Simeone ◽  
Ana Carolina Humberto ◽  
Yara Natercia Lima Faustino de Maria ◽  
Regina Costa de Oliveira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptome Assembly ◽  
Pathogenic Fungus ◽  
The Novel ◽  
Talaromyces Marneffei ◽  
Expression Control ◽  
Gene Expression Control ◽  
Human Pathogenic Fungus ◽  
Non Coding Rnas

Abstract Previous genomic/transcriptomic analyses of Talaromyces marneffei (TM) unravelled relevant pathogenicity-related elements, as well as chromosomal regions potentially involved with the production of non-coding RNAs (ncRNAs), which have been parsimoniously reported in fungi. This manuscript describes a comprehensive pan-transcriptome assembly for TM that identifies a series of previously undetected genetic elements in this emerging pathogenic fungus. Our results confirm that ~58.28% of the 9,480 genes currently annotated in the TM genome are, in fact, transcribed in vivo and that ~23.6% of them may display alternative isomorphs. Moreover, we identified 585 transcripts that do not match any gene currently mapped in the genome, represented by 90 coding transcripts and 140 ncRNAs, including 48 long non-coding RNAs (lncRNAs). Overall, we expect that the novel elements described herein may contribute to improve the currently available Talaromyces databases and foster studies aiming at characterizing lncRNA-mediated gene expression control in fungi.

Thioridazine inhibits gene expression control of the cell wall signaling pathway (CWI) in the human pathogenic fungus Paracoccidioides brasiliensis

2016 ◽  
Vol 291 (3) ◽  
pp. 1347-1362 ◽  
Author(s):  
Daniela Leite Jabes ◽  
Ana Claudia de Freitas Oliveira ◽  
Valquíria Campos Alencar ◽  
Fabiano Bezerra Menegidio ◽  
Débora Liliane Souza Reno ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Signaling Pathway ◽  
Paracoccidioides Brasiliensis ◽  
Pathogenic Fungus ◽  
Expression Control ◽  
Gene Expression Control ◽  
Human Pathogenic Fungus

scholarly journals Synthetic gene regulatory networks in the opportunistic human pathogen Streptococcus pneumoniae

2019 ◽  
Author(s):  
Robin A. Sorg ◽  
Clement Gallay ◽  
Jan-Willem Veening
Keyword(s):  
Gene Expression ◽  
Streptococcus Pneumoniae ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Combinatorial Libraries ◽  
Regulatory Elements ◽  
Expression Control ◽  
Gene Expression Control

AbstractStreptococcus pneumoniae can cause disease in various human tissues and organs, including the ear, the brain, the blood and the lung, and thus in highly diverse and dynamic environments. It is challenging to study how pneumococci control virulence factor expression, because cues of natural environments and the presence of an immune system are difficult to simulate in vitro. Here, we apply synthetic biology methods to reverse-engineer gene expression control in S. pneumoniae. A selection platform is described that allows for straightforward identification of transcriptional regulatory elements out of combinatorial libraries. We present TetR- and LacI-regulated promoters that show expression ranges of four orders of magnitude. Based on these promoters, regulatory networks of higher complexity are assembled, such as logic AND and IMPLY gates. Finally, we demonstrate single-copy genome-integrated toggle switches that give rise to bimodal population distributions. The tools described here can be used to mimic complex expression patterns, such as the ones found for pneumococcal virulence factors, paving the way for in vivo investigations of the importance of gene expression control on the pathogenicity of S. pneumoniae.

scholarly journals In vivo involvement of mutated initiation factor IF1 in gene expression control at the translational level

FEBS Letters ◽  
2005 ◽  
Vol 579 (5) ◽  
pp. 995-1000 ◽  
Author(s):  
Victor V. Croitoru ◽  
Margarete Bucheli-Witschel ◽  
Leif A. Isaksson
Keyword(s):  
Gene Expression ◽  
Initiation Factor ◽  
Expression Control ◽  
Gene Expression Control ◽  
Translational Level

scholarly journals Epitranscriptomic Signatures in lncRNAs and Their Possible Roles in Cancer

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 52 ◽  
Author(s):  
Sorina Dinescu ◽  
Simona Ignat ◽  
Andreea Lazar ◽  
Carolina Constantin ◽  
Monica Neagu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Modifications ◽  
Chemical Modifications ◽  
Chemically Modified ◽  
Additional Layer ◽  
Expression Control ◽  
Gene Expression Control ◽  
Level Of Knowledge ◽  
Non Coding Rnas ◽  
And Function

In contrast to the amazing exponential growth in knowledge related to long non-coding RNAs (lncRNAs) involved in cell homeostasis or dysregulated pathological states, little is known so far about the links between the chemical modifications occurring in lncRNAs and their function. Generally, ncRNAs are post-transcriptional regulators of gene expression, but RNA modifications occurring in lncRNAs generate an additional layer of gene expression control. Chemical modifications that have been reported in correlation with lncRNAs include m6A, m5C and pseudouridylation. Up to date, several chemically modified long non-coding transcripts have been identified and associated with different pathologies, including cancers. This review presents the current level of knowledge on the most studied cancer-related lncRNAs, such as the metastasis associated lung adenocarcinoma transcript 1 (MALAT1), the Hox transcript antisense intergenic RNA (HOTAIR), or the X-inactive specific transcript (XIST), as well as more recently discovered forms, and their potential roles in different types of cancer. Understanding how these RNA modifications occur, and the correlation between lncRNA changes in structure and function, may open up new therapeutic possibilities in cancer.

scholarly journals Small Molecule-Inducible RNA-Targeting Systems for Temporal Control of RNA Regulation in Vivo

2020 ◽  
Author(s):  
Simone Rauch ◽  
Krysten A. Jones ◽  
Bryan Dickinson
Keyword(s):  
Gene Expression ◽  
Small Molecule ◽  
Rna Regulation ◽  
Base Editing ◽  
Expression Control ◽  
Gene Expression Control ◽  
Rna Targeting ◽  
Dynamics And Control ◽  
And Control

RNA regulation is critical for gene expression control, but tools to temporally manipulate RNA regulatory mechanisms are lacking. Here, we present small molecule-inducible RNA-targeting effectors based on our previously developed CRISPR/Cas-inspired RNA targeting system (CIRTS), which can trigger RNA editing, degradation, or translation on target transcripts. We go on to show the inducible CIRTS editor can be deployed for RNA base editing in vivo, providing a new set of tools to probe RNA regulatory dynamics and control gene expression.

scholarly journals Small Molecule-Inducible RNA-Targeting Systems for Temporal Control of RNA Regulation in Vivo

2020 ◽  
Author(s):  
Simone Rauch ◽  
Krysten A. Jones ◽  
Bryan Dickinson
Keyword(s):  
Gene Expression ◽  
Small Molecule ◽  
Rna Regulation ◽  
Base Editing ◽  
Expression Control ◽  
Gene Expression Control ◽  
Rna Targeting ◽  
Dynamics And Control ◽  
And Control

RNA regulation is critical for gene expression control, but tools to temporally manipulate RNA regulatory mechanisms are lacking. Here, we present small molecule-inducible RNA-targeting effectors based on our previously developed CRISPR/Cas-inspired RNA targeting system (CIRTS), which can trigger RNA editing, degradation, or translation on target transcripts. We go on to show the inducible CIRTS editor can be deployed for RNA base editing in vivo, providing a new set of tools to probe RNA regulatory dynamics and control gene expression.

scholarly journals Expression Patterns in Reductive Iron Assimilation and Functional Consequences during Phagocytosis of Lichtheimia corymbifera, an Emerging Cause of Mucormycosis

2021 ◽  
Vol 7 (4) ◽  
pp. 272
Author(s):  
Felicia Adelina Stanford ◽  
Nina Matthias ◽  
Zoltán Cseresnyés ◽  
Marc Thilo Figge ◽  
Mohamed I. Abdelwahab Hassan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Iron Uptake ◽  
Intracellular Transport ◽  
Pathogenic Fungus ◽  
Expression Patterns ◽  
Iron Depletion ◽  
Iron Assimilation ◽  
Human Pathogenic Fungus ◽  
Hyphal Formation ◽  
Yeast Mutants

Iron is an essential micronutrient for most organisms and fungi are no exception. Iron uptake by fungi is facilitated by receptor-mediated internalization of siderophores, heme and reductive iron assimilation (RIA). The RIA employs three protein groups: (i) the ferric reductases (Fre5 proteins), (ii) the multicopper ferroxidases (Fet3) and (iii) the high-affinity iron permeases (Ftr1). Phenotyping under different iron concentrations revealed detrimental effects on spore swelling and hyphal formation under iron depletion, but yeast-like morphology under iron excess. Since access to iron is limited during pathogenesis, pathogens are placed under stress due to nutrient limitations. To combat this, gene duplication and differential gene expression of key iron uptake genes are utilized to acquire iron against the deleterious effects of iron depletion. In the genome of the human pathogenic fungus L. corymbifera, three, four and three copies were identified for FRE5, FTR1 and FET3 genes, respectively. As in other fungi, FET3 and FTR1 are syntenic and co-expressed in L. corymbifera. Expression of FRE5, FTR1 and FET3 genes is highly up-regulated during iron limitation (Fe-), but lower during iron excess (Fe+). Fe- dependent upregulation of gene expression takes place in LcFRE5 II and III, LcFTR1 I and II, as well as LcFET3 I and II suggesting a functional role in pathogenesis. The syntenic LcFTR1 I–LcFET3 I gene pair is co-expressed during germination, whereas LcFTR1 II- LcFET3 II is co-expressed during hyphal proliferation. LcFTR1 I, II and IV were overexpressed in Saccharomyces cerevisiae to represent high and moderate expression of intracellular transport of Fe3+, respectively. Challenge of macrophages with the yeast mutants revealed no obvious role for LcFTR1 I, but possible functions of LcFTR1 II and IVs in recognition by macrophages. RIA expression pattern was used for a new model of interaction between L. corymbifera and macrophages.

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