Cellular Adaptations to Cytoplasmic Mg2+ Limitation

2021 ◽  
Vol 75 (1) ◽  
pp. 649-672
Author(s):  
Eduardo A. Groisman ◽  
Carissa Chan
Keyword(s):  
Protein Synthesis ◽  
Bacterial Species ◽  
Transcriptional Regulator ◽  
Living Cells ◽  
Open Reading Frames ◽  
Enzymatic Reactions ◽  
Leader Region ◽  
Coding Regions ◽  
Reading Frames ◽  
Do So

Mg2+ is the most abundant divalent cation in living cells. It is essential for charge neutralization, macromolecule stabilization, and the assembly and activity of ribosomes and as a cofactor for enzymatic reactions. When experiencing low cytoplasmic Mg2+, bacteria adopt two main strategies: They increase the abundance and activity of Mg2+ importers and decrease the abundance of Mg2+-chelating ATP and rRNA. These changes reduce regulated proteolysis by ATP-dependent proteases and protein synthesis in a systemic fashion. In many bacterial species, the transcriptional regulator PhoP controls expression of proteins mediating these changes. The 5′ leader region of some mRNAs responds to low cytoplasmic Mg2+ or to disruptions in translation of open reading frames in the leader regions by furthering expression of the associated coding regions, which specify proteins mediating survival when the cytoplasmic Mg2+ concentration is low. Microbial species often utilize similar adaptation strategies to cope with low cytoplasmic Mg2+ despite relying on different genes to do so.

scholarly journals Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation

2015 ◽  
Author(s):  
David E Weinberg ◽  
Premal Shah ◽  
Stephen W Eichhorn ◽  
Jeffrey A Hussmann ◽  
Joshua B Plotkin ◽  
...  
Keyword(s):  
Translational Control ◽  
Nucleotide Composition ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Coding Regions ◽  
Genome Wide ◽  
Upstream Open Reading Frames ◽  
Improved Methods ◽  
Reading Frames

Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical challenges can confound its analysis. Here, we use improved methods to obtain ribosome-footprint profiles and mRNA abundances that more faithfully reflect gene expression in Saccharomyces cerevisiae. Our results support proposals that both the beginning of coding regions and codons matching rare tRNAs are more slowly translated. They also indicate that emergent polypeptides with as few as three basic residues within a 10-residue window tend to slow translation. With the improved mRNA measurements, the variation attributable to translational control in exponentially growing yeast was less than previously reported, and most of this variation could be predicted with a simple model that considered mRNA abundance, upstream open reading frames, cap-proximal structure and nucleotide composition, and lengths of the coding and 5′- untranslated regions. Collectively, our results reveal key features of translational control in yeast and provide a framework for executing and interpreting ribosome- profiling studies.

scholarly journals Complete Genome Sequence of theBacillus pumilusPhage Leo2

2018 ◽  
Vol 6 (7) ◽  
Author(s):  
Sondos Badran ◽  
Nathanael Morales ◽  
Phillip Schick ◽  
Brandon Jacoby ◽  
William Villella ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bacillus Pumilus ◽  
Open Reading Frames ◽  
Gram Positive ◽  
Coding Regions ◽  
Symbiotic Interactions ◽  
Associated Functions ◽  
Reading Frames

ABSTRACTBacillusspp. are ubiquitous Gram-positive microbes with many ecological and symbiotic interactions and can be pathogens. Phage Leo2 was found to infect aBacillus pumilusstrain isolated from soil. The sequence of phage Leo2 revealed 74 genes; 31% of the genes have associated functions, and 67% of coding regions are unidentified open reading frames.

scholarly journals Identification and Characterization of a Novel Robigovirus Species from Sweet Cherry in Turkey

Pathogens ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 57 ◽  
Author(s):  
Kadriye Çağlayan ◽  
Vahid Roumi ◽  
Mona Gazel ◽  
Eminur Elçi ◽  
Mehtap Acioğlu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Open Reading Frames ◽  
Cherry Tree ◽  
Coding Regions ◽  
Sweet Cherries ◽  
Identification And Characterization ◽  
Reading Frames

High throughput sequencing of total RNA isolated from symptomatic leaves of a sweet cherry tree (Prunus avium cv. 0900 Ziraat) from Turkey identified a new member of the genus Robigovirus designated cherry virus Turkey (CVTR). The presence of the virus was confirmed by electron microscopy and overlapping RT-PCR for sequencing its whole-genome. The virus has a ssRNA genome of 8464 nucleotides which encodes five open reading frames (ORFs) and comprises two non-coding regions, 5′ UTR and 3′ UTR of 97 and 296 nt, respectively. Compared to the five most closely related robigoviruses, RdRp, TGB1, TGB2, TGB3 and CP share amino acid identities ranging from 43–53%, 44–60%, 39–43%, 38–44% and 45–50%, respectively. Unlike the four cherry robigoviruses, CVTR lacks ORFs 2a and 5a. Its genome organization is therefore more similar to African oil palm ringspot virus (AOPRV). Using specific primers, the presence of CVTR was confirmed in 15 sweet cherries and two sour cherries out of 156 tested samples collected from three regions in Turkey. Among them, five samples were showing slight chlorotic symptoms on the leaves. It seems that CVTR infects cherry trees with or without eliciting obvious symptoms, but these data should be confirmed by bioassays in woody and possible herbaceous hosts in future studies.

scholarly journals A novel essential RNA-binding protein complex in Trypanosoma brucei

2020 ◽  
Author(s):  
Kathrin Bajak ◽  
Kevin Leiss ◽  
Christine Clayton ◽  
Esteban Erben
Keyword(s):  
Ribosomal Proteins ◽  
Rna Binding ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Gtpase Domain ◽  
Gtp Hydrolysis ◽  
Coding Regions ◽  
Rna Immunoprecipitation ◽  
Reading Frames

AbstractZC3H5 is an essential cytoplasmic trypanosome protein with a single Cx7Cx5Cx3H zinc finger domain. We here show that ZC3H5 forms a complex with three other proteins, encoded by genes Tb927.11.4900, Tb927.8.1500 and Tb927.7.3040. ZC3H5 interacts directly with Tb927.11.4900, which in turn interacts with Tb927.7.3040. Tb927.11.4900 has a circularly permuted GTPase domain, which is required for the Tb927.7.3040 interaction. RNA immunoprecipitation revealed that ZC3H5 is preferentially associated with poorly translated, low-stability mRNAs, the 5’-untranslated regions and coding regions of which are enriched in the motif (U/A)UAG(U/A). Tethering of ZC3H5, or other complex components, to a reporter repressed its expression. However, depletion of ZC3H5 in vivo did not increase the abundance of ZC3H5-bound mRNAs: instead, counter-intuitively, there were very minor decreases in a few targets, and marked increases in the abundances of very stable mRNAs encoding ribosomal proteins. Depletion also resulted in an increase in monosomes at the expense of large polysomes, and appearance of “halfmer” disomes containing two 80S subunits and one 40S subunit. We speculate that the ZC3H5 complex might be implicated in quality control during the translation of sub-optimal open reading frames; complex assembly might be regulated by GTP hydrolysis and GTP-GDP exchange.

scholarly journals Distribution of cp32 Prophages among Lyme Disease-Causing Spirochetes and Natural Diversity of Their Lipoprotein-EncodingerpLoci

2013 ◽  
Vol 79 (13) ◽  
pp. 4115-4128 ◽  
Author(s):  
Dustin Brisson ◽  
Wei Zhou ◽  
Brandon L. Jutras ◽  
Sherwood Casjens ◽  
Brian Stevenson
Keyword(s):  
Lyme Disease ◽  
Surface Proteins ◽  
Open Reading Frames ◽  
Protein Coding ◽  
Content Type ◽  
Coding Regions ◽  
Natural Diversity ◽  
Different Strains ◽  
Main Chromosome ◽  
Reading Frames

ABSTRACTLyme disease spirochetes possess complex genomes, consisting of a main chromosome and 20 or more smaller replicons. Among those small DNAs are the cp32 elements, a family of prophages that replicate as circular episomes. All complete cp32s contain anerplocus, which encodes surface-exposed proteins. Sequences were compared for all 193erpalleles carried by 22 different strains of Lyme disease-causing spirochete to investigate their natural diversity and evolutionary histories. These included multiple isolates from a focus where Lyme disease is endemic in the northeastern United States and isolates from across North America and Europe. Bacteria were derived from diseased humans and from vector ticks and included members of 5 differentBorreliagenospecies. Allerpoperon 5′-noncoding regions were found to be highly conserved, as were the initial 70 to 80 bp of allerpopen reading frames, traits indicative of a common evolutionary origin. However, the majority of the protein-coding regions are highly diverse, due to numerous intra- and intergenic recombination events. Mosterpalleles are chimeras derived from sequences of closely related and distantly relatederpsequences and from unknown origins. Since known functions of Erp surface proteins involve interactions with various host tissue components, this diversity may reflect both their multiple functions and the abilities of Lyme disease-causing spirochetes to successfully infect a wide variety of vertebrate host species.

scholarly journals New Small, Acid-Soluble Proteins Unique to Spores ofBacillus subtilis: Identification of the Coding Genes and Regulation and Function of Two of These Genes

1998 ◽  
Vol 180 (24) ◽  
pp. 6704-6712 ◽  
Author(s):  
Irina Bagyan ◽  
Barbara Setlow ◽  
Peter Setlow
Keyword(s):  
Rna Polymerase ◽  
Mother Cell ◽  
Genomic Sequence ◽  
Complete Sequence ◽  
Soluble Proteins ◽  
Open Reading Frames ◽  
Coding Regions ◽  
Spore Outgrowth ◽  
And Function ◽  
Reading Frames

ABSTRACT Eleven small, acid-soluble proteins (SASP) which are present in spores but not in growing cells of Bacillus subtilis were identified by sequence analysis of proteins separated by acrylamide gel electrophoresis of acid extracts from spores which lack the three major SASP (α, β, and γ). Six of these proteins are encoded by open reading frames identified previously or by analysis of the complete sequence of the B. subtilis genome, including two minor α/β-type SASP (SspC and SspD) and a putative spore coat protein (CotK). Five proteins are encoded by short open reading frames that were not identified as coding regions in the analysis of the completeB. subtilis genomic sequence. Studies of the regulation of two of the latter genes, termed sspG and sspJ, showed that both are expressed only in sporulation. ThesspG gene is transcribed in the mother cell compartment by RNA polymerase with the mother cell-specific sigma factor for RNA polymerase, ςK, and is cotranscribed with a downstream gene, yurS; sspG transcription also requires the DNA binding protein GerE. In contrast, sspJ is transcribed in the forespore compartment by RNA polymerase with the forespore-specific ςG and appears to give a monocistronic transcript. A mutation eliminating SspG had no effect on sporulation or spore properties, while loss of SspJ caused a slight decrease in the rate of spore outgrowth in an otherwise wild-type background.

scholarly journals Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

2020 ◽  
Author(s):  
Tamara Ouspenskaia ◽  
Travis Law ◽  
Karl R. Clauser ◽  
Susan Klaeger ◽  
Siranush Sarkizova ◽  
...  
Keyword(s):  
Somatic Mutations ◽  
Tumor Antigens ◽  
Ribosome Profiling ◽  
Lymphocytic Leukemia ◽  
Open Reading Frames ◽  
Specific Expression ◽  
Protein Coding ◽  
Mhc I ◽  
Coding Regions ◽  
Reading Frames

AbstractTumor epitopes – peptides that are presented on surface-bound MHC I proteins - provide targets for cancer immunotherapy and have been identified extensively in the annotated protein-coding regions of the genome. Motivated by the recent discovery of translated novel unannotated open reading frames (nuORFs) using ribosome profiling (Ribo-seq), we hypothesized that cancer-associated processes could generate nuORFs that can serve as a new source of tumor antigens that harbor somatic mutations or show tumor-specific expression. To identify cancer-specific nuORFs, we generated Ribo-seq profiles for 29 malignant and healthy samples, developed a sensitive analytic approach for hierarchical ORF prediction, and constructed a high-confidence database of translated nuORFs across tissues. Peptides from 3,555 unique translated nuORFs were presented on MHC I, based on analysis of an extensive dataset of MHC I-bound peptides detected by mass spectrometry, with >20-fold more nuORF peptides detected in the MHC I immunopeptidomes compared to whole proteomes. We further detected somatic mutations in nuORFs of cancer samples and identified nuORFs with tumor-specific translation in melanoma, chronic lymphocytic leukemia and glioblastoma. NuORFs thus expand the pool of MHC I-presented, tumor-specific peptides, targetable by immunotherapies.

scholarly journals Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

2015 ◽  
Author(s):  
Anil Raj ◽  
Sidney H. Wang ◽  
Heejung Shim ◽  
Arbel Harpak ◽  
Yang I. Li ◽  
...  
Keyword(s):  
Significant Negative Correlation ◽  
Selective Constraint ◽  
Open Reading Frames ◽  
Sequence Information ◽  
The Novel ◽  
Protein Coding ◽  
Coding Sequences ◽  
Coding Regions ◽  
Human Lymphoblastoid Cell ◽  
Reading Frames

AbstractAccurate annotation of protein coding regions is essential for understanding how genetic information is translated into biological functions. Here we describe riboHMM, a new method that uses ribosome footprint data along with gene expression and sequence information to accurately infer translated sequences. We applied our method to human lymphoblastoid cell lines and identified 7,273 previously unannotated coding sequences, including 2,442 translated upstream open reading frames. We observed an enrichment of harringtonine-treated ribosome footprints at the inferred initiation sites, validating many of the novel coding sequences. The novel sequences exhibit significant signatures of selective constraint in the reading frames of the inferred proteins, suggesting that many of these are functional. Nearly 40% of bicistronic transcripts showed significant negative correlation in the levels of translation of their two coding sequences, suggesting a key regulatory role for these novel translated sequences. Our work significantly expands the set of known coding regions in humans.

scholarly journals Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Anil Raj ◽  
Sidney H Wang ◽  
Heejung Shim ◽  
Arbel Harpak ◽  
Yang I Li ◽  
...  
Keyword(s):  
Selective Constraint ◽  
Open Reading Frames ◽  
The Novel ◽  
Drug Induced ◽  
Protein Coding ◽  
Coding Sequences ◽  
Coding Regions ◽  
Human Lymphoblastoid Cell ◽  
Validation Rate ◽  
Reading Frames

Accurate annotation of protein coding regions is essential for understanding how genetic information is translated into function. We describe riboHMM, a new method that uses ribosome footprint data to accurately infer translated sequences. Applying riboHMM to human lymphoblastoid cell lines, we identified 7273 novel coding sequences, including 2442 translated upstream open reading frames. We observed an enrichment of footprints at inferred initiation sites after drug-induced arrest of translation initiation, validating many of the novel coding sequences. The novel proteins exhibit significant selective constraint in the inferred reading frames, suggesting that many are functional. Moreover, ~40% of bicistronic transcripts showed negative correlation in the translation levels of their two coding sequences, suggesting a potential regulatory role for these novel regions. Despite known limitations of mass spectrometry to detect protein expressed at low level, we estimated a 14% validation rate. Our work significantly expands the set of known coding regions in humans.

scholarly journals orfipy: a fast and flexible tool for extracting ORFs

2020 ◽  
Author(s):  
Urminder Singh ◽  
Eve Syrkin Wurtele
Keyword(s):  
Open Reading Frames ◽  
Supplementary Information ◽  
Rna Seq ◽  
Flexible Tool ◽  
Coding Regions ◽  
Link Type ◽  
Alternative Reading Frames ◽  
Downstream Analysis ◽  
Fine Tune ◽  
Reading Frames

SummarySearching for ORFs in transcripts is a critical step prior to annotating coding regions in newly-sequenced genomes and to search for alternative reading frames within known genes. With the tremendous increase in RNA-Seq data, faster tools are needed to handle large input datasets. These tools should be versatile enough to fine-tune search criteria and allow efficient downstream analysis. Here we present a new python based tool, orfipy, which allows the user to flexibly search for open reading frames in fasta sequences. The search is rapid and is fully customizable, with a choice of Fasta and BED output formats.Availability and implementationorfipy is implemented in python and is compatible with python v3.6 and higher. Source code: https://github.com/urmi-21/orfipy. Installation: from the source, or via PyPi (https://pypi.org/project/orfipy) or bioconda (https://anaconda.org/bioconda/orfipy)[email protected], [email protected] informationSupplementary data are available at https://github.com/urmi-21/orfipy

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