scholarly journals Gene expression models based on a reference laboratory strain are bad predictors of Mycobacterium tuberculosis complex transcriptional diversity

2016 ◽  
Author(s):  
Alvaro Chiner-Oms ◽  
Fernando González-Candelas ◽  
Iñaki Comas

ABSTRACTSpecies of the Mycobacterium tuberculosis complex (MTBC) kill more people every year than any other infectious disease. As a consequence of its global distribution and parallel evolution with the human host the bacteria is not genetically homogeneous. The observed genetic heterogeneity has relevance at different phenotypic levels, from gene expression to epidemiological dynamics. However current systems biology datasets have focused in the laboratory reference strain H37Rv. By using large expression datasets testing the role of almost two hundred transcription factors, we have constructed computational models to grab the expression dynamics of Mycobacterium tuberculosis H37Rv genes. However, we have found that many of those transcription factors are deleted or likely dysfunctional across strains of the MTBC. In accordance, we failed to predict expression changes in strains with a different genetic background when compared with experimental data. The results highlight the importance of designing systems biology approaches that take into account the tubercle bacilli, or any other pathogen, genetic diversity if we want to identify universal targets for vaccines, diagnostics and treatments.

2005 ◽  
pp. 168-191
Author(s):  
Fulvio Della Ragione ◽  
Valeria Cucciolla ◽  
Adriana Borriello ◽  
Vincenzo Zappia

2020 ◽  
Author(s):  
Joanna Houghton ◽  
Angela Rodgers ◽  
Graham Rose ◽  
Kristine B. Arnvig

ABSTRACTAlmost 140 years after the identification of Mycobacterium tuberculosis as the etiological agent of tuberculosis, important aspects of its biology remain poorly described. Little is known about the role of post-transcriptional control of gene expression and RNA biology, including the role of most of the small RNAs (sRNAs) identified to date. We have carried out a detailed investigation of the M. tuberculosis sRNA, F6, and show it to be dependent on SigF for expression and significantly induced during in vitro starvation and in a mouse model of infection. However, we found no evidence of attenuation of a ΔF6 strain within the first 20 weeks of infection. A further exploration of F6 using in vitro models of infection suggests a role for F6 as a highly specific regulator of the heat shock repressor, HrcA. Our results point towards a role for F6 during periods of low metabolic activity similar to cold shock and associated with nutrient starvation such as that found in human granulomas in later stages of infection.


2020 ◽  
Author(s):  
Amir Banaei-Esfahani ◽  
Andrej Trauner ◽  
Sonia Borrell ◽  
Sebastian M. Gygli ◽  
Tige R. Rustad ◽  
...  

SummaryThe Mycobacterium tuberculosis (Mtb) complex comprises seven phylogenetically distinct human-adapted lineages exhibiting different geographical distribution and degrees of pathogenicity. Among these, Lineage 1 (L1) has been associated with low virulence whereas Lineage 2 (L2) has been linked to hyper-virulence, enhanced transmission and drug resistance. Here, we conducted multi-layer comparative analyses using whole genome sequencing data combined with quantitative transcriptomic and proteomic profiling of a set of L1 and L2 clinical strains, each grown under two different conditions in vitro. Our data revealed different degrees of correlation between transcript and protein abundances across clinical strains and functional gene categories, indicating variable levels of post-transcriptional regulation in the tested lineages. Contrasting genomic and gene expression data showed that the magnitude of the transcriptional and translational changes was proportional to the phylogenetic distance between strains, with one out of three single nucleotide polymorphisms leading to a transcriptional and/or translational change on average. We devised a new genome-scale transcriptional regulatory model and identified several master transcription factors, strongly linked to the sigma factor network, whose targets were differentially regulated between the two lineages. These differences resulted in a higher basal expression of DosR proteins and a stronger response to nitric oxide (NO) exposure in L2 compared to L1. These patterns are most likely responsible for the shorter NO-induced growth arrest in L2 observed. Given the limited genetic variation between strains, it appears that phenotypic differences in Mtb are substantially driven by differences in the regulation of biochemical networks through master transcriptional regulators.HighlightsProteomic and transcriptomic characterization of fully sequenced diverse L1 and L2 clinical isolates of Mtb.Post-transcriptional control mechanisms for regulatory and virulence genes are mitigated in Mtb L2.By applying a genome-scale transcriptional framework, DosR, Rv1985c, Lsr2 and Rv0691c are identified as master transcription factors responsible for differential target gene expression in L2 strains compared to L1.L1 and L2 DosR proteins respond differently to nitric oxide stress, thus determining a relevant phenotype.


1980 ◽  
Vol 61 (5) ◽  
pp. 58
Author(s):  
O. A. Irtuganova

The aim of the work was to select variants of mycobacterium tuberculosis with altered drug resistance under the influence of anti-tuberculosis drugs. The laboratory strain H37RV was selected by 15 passages of one colony on solid Lowenstein-Jensen medium. In the obtained genetically homogeneous variant of mycobacteria for 1012 individuals, there was not a single one resistant to rifampicin, isoniazid, streptomycin, ethionamide and ethambutol.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2385-2385
Author(s):  
Ananya Sengupta ◽  
Ghanshyam Upadhyay ◽  
Sayani Sen ◽  
Shireen Saleque

Abstract Introduction: Appropriate diversification of hematopoietic lineages from multi-potent progenitors is essential for normal development and health. The molecular programs that govern the divergence of erythroid and megakaryocytic lineages remain incompletely defined. Gene targeting experiments have shown the transcriptional repressor Gfi1b (Growth factor independence 1b) to be essential for erythro-megakaryocyte lineage development. Transcriptional repression of Gfi1b target genes is mediated by the cofactors LSD (lysine demethylase) 1 and Rcor (CoREST) 1. To understand the mechanism of Gfi1b action, its target genes were identified by chromatin immunoprecipitation (ChIP on Chip) screens. Three members of the Rgs (Regulator of G protein signaling) family were prominently represented in this target gene pool. In this study we present the role of Rgs18, a GTPase activating protein (GAP), in modulating erythro-megakaryocytic lineage divergence in hematopoietic progenitors. The results presented below demonstrate Rgs18 as a key arbitrator of this process in murine and human contexts. Approach: Following identification of Rgs18 as a potential Gfi1b and LSD1 target, its regulation by these factors was ascertained in erythro-megakaryocytic cells. Subsequently, to interrogate the role of Rgs18 in erythro-megakaryocyte differentiation, cDNA and shRNA mediated manipulations were performed in primary hematopoietic progenitors and cell lines, and the resulting phenotypes were analyzed. Finally, to trace the underlying mechanistic alterations responsible for these phenotypes the status of two branches of the MAPK (mitogen activated protein kinase) pathway and gene expression patterns of the mutually antagonistic transcription factors Fli1 (Friend leukemia integration [site] 1/Klf1 (Krupple like factor 1) were determined in Rgs18 manipulated cells. Result: Rgs18 expression was found to be low in immature megakaryoblasts in keeping with strong Gfi1b and LSD1 expression, but was reciprocally upregulated in mature megakaryocytes following declining Gfi1b and LSD1 levels in cells and on the rgs18 promoter. In contrast, expression of Gfi1b was strong in immature erythroid cells and increased further in mature cells, while Rgs18 expression which was modest in immature erythroid cells exhibited a reciprocal decline during maturation. Manipulation of Rgs18 expression in murine hematopoietic progenitors and a bipotential human cell line produced divergent outcomes, with expression augmenting megakaryocytic, and potently suppressing erythroid differentiation and vice versa. These phenotypes resulted from differential impact of Rgs18 expression on the P38 and ERK branches of MAPK signaling in the erythroid and megakaryocytic lineages. Repercussions of these signaling changes impacted relative expression of the mutually antagonistic transcription factors Fli1 and Klf1 and were compensated by ectopic Fli1 expression demonstrating activity of this transcription factor downstream of Rgs18. Conclusion: These results identify Rgs18 as a critical downstream effector of Gfi1b and an upstream regulator of MAPK signaling and Klf1/Fli1 gene expression. Sustained Gfi1b expression during erythroid differentiation represses Rgs18 and limits megakaryocytic gene expression. However during progression of megakaryocytic differentiation, declining Gfi1b levels results in robust expression of Rgs18 and lineage progression. Overall, this study provides new perspectives on lineage determination by highlighting multi-tier interactions between transcriptional and signaling networks in orchestrating hematopoietic lineage divergence. These insights could exemplify generic mechanisms exhibited by this large family of signal modulators in mediating lineage diversification in various contexts. Disclosures No relevant conflicts of interest to declare.


2007 ◽  
Vol 23 (4) ◽  
pp. 317-323 ◽  
Author(s):  
Koichi Asaba ◽  
Yasumasa Iwasaki ◽  
Masato Asai ◽  
Masanori Yoshida ◽  
Takeshi Nigawara ◽  
...  

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