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| Status |
Public on Sep 25, 2020 |
| Title |
Comparative analysis of global transcriptional profile of Escherichia coli and Schizosaccharomyces pombe in respiratory and fermentative growth: Inferring the evolution of analog circuits of post-transcriptional regulation |
| Organisms |
Escherichia coli; Schizosaccharomyces pombe |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Next Generation sequencing techniques have ushered in a new era in life sciences, especially genomic research. Currently, massive RNA sequencing (RNA-seq) has increased knowledge about the "RNA universe" from the global characterization of transcriptomes, differential gene expression studies and the continued discovery of non-coding regulatory transcripts such as non-coding RNAs (ncRNAs). Post-transcriptional gene regulation is a mechanism for controlling gene expression that is present in both prokaryote and eukaryote organisms and regulates multiple biological processes. Examples of ncRNAs that regulate the levels of transcripts of genes related to central carbon metabolism have been described in bacteria and higher eukaryotes. In order to describe whether analogies exist in regulatory circuits mediated by ncRNAs in two cell patterns, a comparative analysis of the transcriptome of Escherichia coli and Schizosaccharomyces pombe in similar growth conditions was carried out using two carbon source, 2 % glucose and a mix of 2% glycerol and 0.2 % sodium acetate. Twelve RNA-seq libraries were performed. The RNA-seq data contained a number unambiguously mapped readings on the genome of each organism ranged from 1-1.3 million. A total of 739 and 743 genes were detected as differentially expressed for E. coli and S, pombe respectively with a module of log FC > 1 and FDR > 0.05. In aerobic glicolisis GO asciated to cell proliferetionweres detected in both organisms. Among the genes differentially expressed in glycerol/acetate general transcription factors such as fliA, 11 literature validated sRNAs, and assembly flagellum maquinary gene were detected in E. coli, whereas in fission yeast, hexose transporters, switches integral membrane proteins and ncRNAs related to cellular stress are highlighted. In general, our study shows that a conserved "foraging behaviour" response is observed in eukaryotic and procaryotic organism when there is no present glycolityc carbon source.
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| Overall design |
12 Ribosomal depleted Total RNA profiles of mid-log phase of E. coli K-12 MG1655 and S. pombe 972 h- in two growth were generated by deep sequencing, in triplicate, using Illumina Next-seq.
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| Contributor(s) |
Vichi J, Salazar E, Jiménez V, Olvera L, Grande R, Morett E, Dantán E, Hernández A |
| Citation(s) |
33730068 |
| Submission date |
Sep 26, 2019 |
| Last update date |
Apr 07, 2021 |
| Contact name |
Veronica Jimenez-Jacinto |
| E-mail(s) |
vjimenez@ibt.unam.mx
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| Phone |
+52(777) 3291719
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| Organization name |
Universidad Nacional Autonoma de Mexico
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| Department |
Unidad Universitaria de Secuenciación Masiva y Bioinformática
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| Street address |
Av. Universidad 2001. Col. chamilpa
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| City |
Cuernavaca |
| State/province |
Morelos |
| ZIP/Postal code |
62130 |
| Country |
Mexico |
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| Platforms (2) |
| GPL20584 |
Illumina NextSeq 500 (Schizosaccharomyces pombe) |
| GPL21222 |
Illumina NextSeq 500 (Escherichia coli) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA574477 |
| SRA |
SRP223452 |
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