Decoding the Epitranscriptional Landscape from Native RNA Sequences

AbstractSequencing of native RNA and corresponding cDNA was performed using Oxford Nanopore Technology. The % Error of Specific Bases (%ESB) was higher for native RNA than for cDNA, which enabled detection of ribonucleotide modification sites. Based on %ESB differences of the two templates, a bioinformatic tool ELIGOS was developed and applied to rRNAs of E. coli, yeast and human cells. ELIGOS captured 91%, 95%, ∼75%, respectively, of the known variety of RNA methylation sites in these rRNAs. Yeast transcriptomes from different growth conditions were also compared, which identified an association between metabolic adaptation and inferred RNA modifications. ELIGOS was further applied to human transcriptome datasets, which identified the well-known DRACH motif containing N6-methyadenine being located close to 3’-untranslated regions of mRNA. Moreover, the RNA G-quadruplex motif was uncovered by ELIGOS. In summary, we have developed an experimental method coupled with bioinformatic software to uncover native RNA modifications and secondary-structures within transcripts.

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Accurate detection of m6A RNA modifications in native RNA sequences

10.1101/525741 ◽

2019 ◽

Cited By ~ 6

Author(s):

Huanle Liu ◽

Oguzhan Begik ◽

Morghan C Lucas ◽

Christopher E. Mason ◽

Schraga Schwartz ◽

...

Keyword(s):

Rna Modifications ◽

Rna Sequences ◽

Single Nucleotide ◽

Rna Molecules ◽

Base Calling ◽

Oxford Nanopore ◽

Nucleotide Resolution ◽

The Universe ◽

Oxford Nanopore Technologies ◽

Single Nucleotide Resolution

ABSTRACTThe field of epitranscriptomics has undergone an enormous expansion in the last few years; however, a major limitation is the lack of generic methods to map RNA modifications transcriptome-wide. Here we show that using Oxford Nanopore Technologies, N6-methyladenosine (m6A) RNA modifications can be detected with high accuracy, in the form of systematic errors and decreased base-calling qualities. Our results open new avenues to investigate the universe of RNA modifications with single nucleotide resolution, in individual RNA molecules.

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Exploring prokaryotic transcription, operon structures, rRNA maturation and modifications using Nanopore-based native RNA sequencing

10.1101/2019.12.18.880849 ◽

2019 ◽

Cited By ~ 1

Author(s):

Felix Grünberger ◽

Robert Knüppel ◽

Michael Jüttner ◽

Martin Fenk ◽

Andreas Borst ◽

...

Keyword(s):

Rna Sequencing ◽

Single Molecule ◽

Rrna Processing ◽

Rna Modifications ◽

E Coli ◽

Base Modification ◽

Oxford Nanopore ◽

Processing Pathways ◽

Rrna Maturation ◽

Transcriptional Units

AbstractThe prokaryotic transcriptome is shaped by transcriptional and posttranscriptional events that define the characteristics of an RNA, including transcript boundaries, the base modification status, and processing pathways to yield mature RNAs. Currently, a combination of several specialised short-read sequencing approaches and additional biochemical experiments are required to describe all transcriptomic features. In this study, we present native RNA sequencing of bacterial (E. coli) and archaeal (H. volcanii, P. furiosus) transcriptomes employing the Oxford Nanopore sequencing technology. Based on this approach, we could address multiple transcriptomic characteristics simultaneously with single-molecule resolution. Taking advantage of long RNA reads provided by the Nanopore platform, we could (re-)annotate large transcriptional units and boundaries. Our analysis of transcription termination sites suggests that diverse termination mechanisms are in place in archaea. Moreover, we shed additional light on the poorly understood rRNA processing pathway in Archaea. One of the key features of native RNA sequencing is that RNA modifications are retained. We could confirm this ability by analysing the well-known KsgA-dependent methylation sites and mapping of N4-acetylcytosines modifications in rRNAs. Notably, we were able to follow the relative timely order of the installation of these modifications in the rRNA processing pathway.

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A Rhodobacter sphaeroides Protein Mechanistically Similar to Escherichia coli DksA Regulates Photosynthetic Growth

mBio ◽

10.1128/mbio.01105-14 ◽

2014 ◽

Vol 5 (3) ◽

Cited By ~ 7

Author(s):

Christopher W. Lennon ◽

Kimberly C. Lemmer ◽

Jessica L. Irons ◽

Max I. Sellman ◽

Timothy J. Donohue ◽

...

Keyword(s):

Escherichia Coli ◽

Structure Function ◽

Rhodobacter Sphaeroides ◽

Fatty Acid Content ◽

Regulatory Protein ◽

Growth Conditions ◽

Globular Domain ◽

Content Type ◽

E Coli

ABSTRACTDksA is a global regulatory protein that, together with the alarmone ppGpp, is required for the “stringent response” to nutrient starvation in the gammaproteobacteriumEscherichia coliand for more moderate shifts between growth conditions. DksA modulates the expression of hundreds of genes, directly or indirectly. Mutants lacking a DksA homolog exhibit pleiotropic phenotypes in other gammaproteobacteria as well. Here we analyzed the DksA homolog RSP2654 in the more distantly relatedRhodobacter sphaeroides, an alphaproteobacterium. RSP2654 is 42% identical and similar in length toE. coliDksA but lacks the Zn finger motif of theE. coliDksA globular domain. Deletion of the RSP2654 gene results in defects in photosynthetic growth, impaired utilization of amino acids, and an increase in fatty acid content. RSP2654 complements the growth and regulatory defects of anE. colistrain lacking thedksAgene and modulates transcriptionin vitrowithE. coliRNA polymerase (RNAP) similarly toE. coliDksA. RSP2654 reduces RNAP-promoter complex stabilityin vitrowith RNAPs fromE. coliorR. sphaeroides, alone and synergistically with ppGpp, suggesting that even though it has limited sequence identity toE. coliDksA (DksAEc), it functions in a mechanistically similar manner. We therefore designate the RSP2654 protein DksARsp. Our work suggests that DksARsphas distinct and important physiological roles in alphaproteobacteria and will be useful for understanding structure-function relationships in DksA and the mechanism of synergy between DksA and ppGpp.IMPORTANCEThe role of DksA has been analyzed primarily in the gammaproteobacteria, in which it is best understood for its role in control of the synthesis of the translation apparatus and amino acid biosynthesis. Our work suggests that DksA plays distinct and important physiological roles in alphaproteobacteria, including the control of photosynthesis inRhodobacter sphaeroides. The study of DksARsp, should be useful for understanding structure-function relationships in the protein, including those that play a role in the little-understood synergy between DksA and ppGpp.

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The Escherichia coli cysG promoter belongs to the ‘extended −10’ class of bacterial promoters

Biochemical Journal ◽

10.1042/bj2960851 ◽

1993 ◽

Vol 296 (3) ◽

pp. 851-857 ◽

Cited By ~ 23

Author(s):

T Belyaeva ◽

L Griffiths ◽

S Minchin ◽

J Cole ◽

S Busby

Keyword(s):

Escherichia Coli ◽

Point Mutations ◽

Growth Conditions ◽

Upstream Region ◽

E Coli ◽

Run Off ◽

A Site ◽

Specific Sequences

The Escherichia coli cysG promoter has been subcloned and shown to function constitutively in a range of different growth conditions. Point mutations identify the -10 hexamer and an important 5′-TGN-3′ motif immediately upstream. The effects of different deletions suggest that specific sequences in the -35 region are not essential for the activity of this promoter in vivo. This conclusion was confirmed by in vitro run-off transcription assays. The DNAase I footprint of RNA polymerase at the cysG promoter reveals extended protection upstream of the transcript start, and studies with potassium permanganate as a probe suggest that the upstream region is distorted in open complexes. Taken together, the results show that the cysG promoter belongs to the ‘extended -10’ class of promoters, and the base sequence is similar to that of the P1 promoter of the E. coli galactose operon, another promoter in this class. In vivo, messenger initiated at the cysG promoter appears to be processed by cleavage at a site 41 bases downstream from the transcript start point.

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Bacterial growth laws reflect the evolutionary importance of energy efficiency

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1421138111 ◽

2014 ◽

Vol 112 (2) ◽

pp. 406-411 ◽

Cited By ~ 87

Author(s):

Arijit Maitra ◽

Ken A. Dill

Keyword(s):

Energy Efficiency ◽

Bacterial Growth ◽

Growth Conditions ◽

High Energy ◽

Fast Growth ◽

Growth Speed ◽

Energy Costs ◽

Extensive Literature ◽

E Coli ◽

Growth Laws

We are interested in the balance of energy and protein synthesis in bacterial growth. How has evolution optimized this balance? We describe an analytical model that leverages extensive literature data on growth laws to infer the underlying fitness landscape and to draw inferences about what evolution has optimized inEscherichia coli. IsE. colioptimized for growth speed, energy efficiency, or some other property? Experimental data show that at its replication speed limit,E. coliproduces about four mass equivalents of nonribosomal proteins for every mass equivalent of ribosomes. This ratio can be explained if the cell’s fitness function is the the energy efficiency of cells under fast growth conditions, indicating a tradeoff between the high energy costs of ribosomes under fast growth and the high energy costs of turning over nonribosomal proteins under slow growth. This model gives insight into some of the complex nonlinear relationships between energy utilization and ribosomal and nonribosomal production as a function of cell growth conditions.

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Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex–Duplex Hybrid Formation

Biomolecules ◽

10.3390/biom11081236 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1236

Author(s):

Dorota Gudanis ◽

Karolina Zielińska ◽

Daniel Baranowski ◽

Ryszard Kierzek ◽

Piotr Kozłowski ◽

...

Keyword(s):

Target Sequence ◽

Rich Region ◽

Rna Sequences ◽

Single Nucleotide ◽

Alternative Structures ◽

Single Nucleotide Change ◽

G Quadruplex ◽

Quadruplex Formation ◽

Target Rna ◽

Insight Into

In this paper, a method to discriminate between two target RNA sequences that differ by one nucleotide only is presented. The method relies on the formation of alternative structures, i.e., quadruplex–duplex hybrid (QDH) and duplex with dangling ends (Dss), after hybridization of DNA or RNA G-rich oligonucleotides with target sequences containing 5′–GGGCUGG–3′ or 5′–GGGCGGG–3′ fragments. Using biophysical methods, we studied the effect of oligonucleotide types (DNA, RNA), non-nucleotide modifications (aliphatic linkers or abasic), and covalently attached G4 ligand on the ability of G-rich oligonucleotides to assemble a G-quadruplex motif. We demonstrated that all examined non-nucleotide modifications could mimic the external loops in the G-quadruplex domain of QDH structures without affecting their stability. Additionally, some modifications, in particular the presence of two abasic residues in the G-rich oligonucleotide, can induce the formation of non-canonical QDH instead of the Dss structure upon hybridization to a target sequence containing the GGGCUGG motif. Our results offer new insight into the sequential requirements for the formation of G-quadruplexes and provide important data on the effects of non-nucleotide modifications on G-quadruplex formation.

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Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

10.1101/2020.03.23.003236 ◽

2020 ◽

Cited By ~ 1

Author(s):

Colton J. Lloyd ◽

Jonathan Monk ◽

Laurence Yang ◽

Ali Ebrahim ◽

Bernhard O. Palsson

Keyword(s):

Amino Acids ◽

Growth Conditions ◽

Anaerobic Growth ◽

Metabolic Phenotype ◽

E Coli ◽

Scale Models ◽

Protein Components ◽

K 12 ◽

Genome Scale ◽

Prosthetic Groups

AbstractSustaining a robust metabolic network requires a balanced and fully functioning proteome. In addition to amino acids, many enzymes require cofactors (coenzymes and engrafted prosthetic groups) to function properly. Extensively validated genome-scale models of metabolism and gene expression (ME-models) have the unique ability to compute an optimal proteome composition underlying a metabolic phenotype, including the provision of all required cofactors. Here we use the ME-model for Escherichia coli K-12 MG1655 to computationally examine how environmental conditions change the proteome and its accompanying cofactor usage. We found that: (1) The cofactor requirements computed by the ME model mostly agree with the standard biomass objective function used in models of metabolism alone (M models); (2) ME-model computations reveal non-intuitive variability in cofactor use under different growth conditions; (3) An analysis of ME-model predicted protein use in aerobic and anaerobic conditions suggests an enrichment in the use of prebiotic amino acids in the proteins used to sustain anaerobic growth (4) The ME-model could describe how limitation in key protein components affect the metabolic state of E. coli. Genome-scale models have thus reached a level of sophistication where they reveal intricate properties of functional proteomes and how they support different E. coli lifestyles.

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Aerobic Fermentation of d-Glucose by an Evolved Cytochrome Oxidase-Deficient Escherichia coli Strain

Applied and Environmental Microbiology ◽

10.1128/aem.00880-08 ◽

2008 ◽

Vol 74 (24) ◽

pp. 7561-7569 ◽

Cited By ~ 41

Author(s):

Vasiliy A. Portnoy ◽

Markus J. Herrgård ◽

Bernhard Ø. Palsson

Keyword(s):

Escherichia Coli ◽

Oxygen Uptake ◽

Growth Conditions ◽

Aerobic Growth ◽

Acid Fermentation ◽

Mixed Acid Fermentation ◽

E Coli ◽

Knockout Strain ◽

Mixed Acid ◽

Cytochrome Oxidases

ABSTRACT Fermentation of glucose to d-lactic acid under aerobic growth conditions by an evolved Escherichia coli mutant deficient in three terminal oxidases is reported in this work. Cytochrome oxidases (cydAB, cyoABCD, and cbdAB) were removed from the E. coli K12 MG1655 genome, resulting in the ECOM3 (E. coli cytochrome oxidase mutant) strain. Removal of cytochrome oxidases reduced the oxygen uptake rate of the knockout strain by nearly 85%. Moreover, the knockout strain was initially incapable of growing on M9 minimal medium. After the ECOM3 strain was subjected to adaptive evolution on glucose M9 medium for 60 days, a growth rate equivalent to that of anaerobic wild-type E. coli was achieved. Our findings demonstrate that three independently adaptively evolved ECOM3 populations acquired different phenotypes: one produced lactate as a sole fermentation product, while the other two strains exhibited a mixed-acid fermentation under oxic growth conditions with lactate remaining as the major product. The homofermenting strain showed a d-lactate yield of 0.8 g/g from glucose. Gene expression and in silico model-based analyses were employed to identify perturbed pathways and explain phenotypic behavior. Significant upregulation of ygiN and sodAB explains the remaining oxygen uptake that was observed in evolved ECOM3 strains. E. coli strains produced in this study showed the ability to produce lactate as a fermentation product from glucose and to undergo mixed-acid fermentation during aerobic growth.

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Relationship of growth conditions to desiccation tolerance of Salmonella enterica, Escherichia coli, and Listeria monocytogenes

Journal of Food Protection ◽

10.4315/jfp-21-077 ◽

2021 ◽

Author(s):

Rachel K Streufert ◽

Susanne E Keller ◽

Joelle K Salazar

Keyword(s):

Escherichia Coli ◽

Listeria Monocytogenes ◽

Desiccation Tolerance ◽

Salmonella Enterica ◽

Growth Conditions ◽

Initial Population ◽

Desiccation Resistance ◽

E Coli ◽

Solid Media ◽

Agar Media

Growth on solid media as sessile cells is believed to increase the desiccation tolerance of Salmonella enterica . However, the reasons behind increased resistance have not been well explored. In addition, the same effect has not been examined for other foodborne pathogens such as pathogenic Escherichia coli or Listeria monocytogenes . The purpose of this research was two-fold: first, to determine the role of oxygenation during growth on the desiccation resistance of S. enterica , E. coli , and L. monocytogenes , and second, to determine the effect of sessile versus planktonic growth on the desiccation resistance of these pathogens. Three different serotypes each of Salmonella , E. coli , and L. monocytogenes were cultured in trypticase soy broth with 0.6% yeast extract (TSBYE), with (aerobic) shaking or on TSBYE with agar (TSAYE) under either aerobic or anaerobic conditions and harvested in stationary phase. After adding cell suspensions to cellulose filter disks, pathogen survival was determined by enumeration at 0 and after drying for 24 h. Results showed statistical differences in harvested initial populations prior to drying (0 h). For Salmonella , a correlation was found between high initial population and greater survival on desiccation (p = 0.05). In addition, statistical differences (p ≤ 0.05) between survival based on growth type were identified. However, differences found were not the same for the three pathogens, or between their serotypes. In general, Salmonella and E. coli desiccation resistance followed the pattern of aerobic agar media ≥ liquid media ≥ anaerobic agar media. For L. monocytogenes serotypes, resistance to desiccation was not statistically different based on mode of growth. These results indicate growth on solid media under aerobic conditions is not always necessary for optimal desiccation survival but may be beneficial when the desiccation resistance of the test serotype is unknown.

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