Degradation of RNA in bacteria: comparison of mRNA and stable RNA

Deutscher, Murray P.

doi:10.1093/nar/gkj472

Cited by 383 publications

(369 citation statements)

References 56 publications

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“…Third, the influence on total cell numbers or 16S rRNA abundances was tested, revealing that the different sampling procedures did not cause significant differences between the treatments (Mann-Whitney test; Supplementary Figure 4). This result was expected because these parameters are considered to be more stable and do not change as quickly in time as, for example, mRNA levels (Deutscher, 2006). The median total cell numbers of 8.8 Â 10 5 cells ml À1 ( ± 1.8 Â 10 5 cells ml À1 ) for all the different treatments were also consistent with the values determined in other studies, even those going 20 years back, of the central Baltic Sea (Brettar and Rheinheimer, 1991), indicating an overall comparability of the environmental samples investigated.…”

Section: Resultsmentioning

confidence: 97%

Measuring unbiased metatranscriptomics in suboxic waters of the central Baltic Sea using a new in situ fixation system

et al. 2011

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An analysis of the microbial metabolism is fundamental to understanding globally important element transformations. One culture-independent approach to deduce those prokaryotic metabolic functions is to analyze metatranscriptomes. Unfortunately, since mRNA is extremely labile, it is unclear whether the abundance patterns detected in nature are vulnerable to considerable modification in situ simply due to sampling procedures. Exemplified on comparisons of metatranscriptomes retrieved from pelagic suboxic zones of the central Baltic Sea (70-120 m depth), earlier identified as areas of high aerobic ammonium oxidation activity, and quantification of specific transcripts in them, we show that different sampling techniques significantly influence the relative abundance of transcripts presumably diagnostic of the habitat. In situ fixation using our newly developed automatic flow injection sampler resulted in an abundance of thaumarchaeal ammonia monooxygenase transcripts that was up to 30-fold higher than that detected in samples obtained using standard oceanographic sampling systems. By contrast, the abundance of transcripts indicative of cellular stress was significantly greater in non-fixed samples. Thus, the importance of in situ fixation in the reliable evaluation of distinct microbial activities in the ecosystem based on metatranscriptomics is obvious. In consequence, our data indicate that the significance of thaumarchaeota to aerobic ammonium oxidation could yet have been considerably underestimated. Taken these results, this could in general also be the case in attempts aimed at an unbiased gene expression analysis of areas below the epipelagic zone, which cover 90% of the world's oceans. The ISME Journal (2012) 6, 461-470; doi:10.1038/ismej.2011.94; published online 21 July 2011 Subject Category: microbial ecology and functional diversity of natural habitats

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Section: Resultsmentioning

confidence: 97%

Measuring unbiased metatranscriptomics in suboxic waters of the central Baltic Sea using a new in situ fixation system

et al. 2011

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“…Additional technical precautions are needed in metatranscriptomics studies. For example, when sequencing messenger RNA (mRNA), all efforts are needed in order to ‘freeze’ the gene expression at sampling and protect mRNA from degradation by using stabilizing solutions, since microbial mRNA has extremely short half‐life (Rauhut and Klug, 1999; Deutscher, 2006). In addition, mRNA is only a small percentage of the total RNA extracted from the sample, which is mainly rRNA.…”

Section: Exploring Microbial Functions Directly In Foodmentioning

confidence: 99%

Metagenomics insights into food fermentations

Filippis

Parente

2016

Microbial Biotechnology

191

117

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SummaryThis review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High‐throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety.

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“…Importantly, we remark that it may not be possible to substantially impair tRNA degradation with a single mutation, since many of the RNases in E. coli possess overlapping activities. 33,57 …”

Section: Ribonuclease Ementioning

confidence: 99%

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

2018

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Production of the translation apparatus of E. coli is carefully matched to the demand for protein synthesis posed by a given growth condition. For example, the fraction of RNA polymerases that transcribe rRNA and tRNA drops from 80% during rapid growth to 24% within minutes of a sudden amino acid starvation. We recently reported in Nucleic Acids Research that the tRNA pool is more dynamically regulated than previously thought. In addition to the regulation at the level of synthesis, we found that tRNAs are subject to demand-based regulation at the level of their degradation. In this point-of-view article we address the question of why this phenomenon has not previously been described. We also present data that expands on the mechanism of tRNA degradation, and we discuss the possible implications of tRNA instability for the ability of E. coli to cope with stresses that affect the translation process.

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Degradation of RNA in bacteria: comparison of mRNA and stable RNA

Cited by 383 publications

References 56 publications

Measuring unbiased metatranscriptomics in suboxic waters of the central Baltic Sea using a new in situ fixation system

Measuring unbiased metatranscriptomics in suboxic waters of the central Baltic Sea using a new in situ fixation system

Metagenomics insights into food fermentations

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

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