Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation.

The cDNAs and genes encoding the intron lariat-debranching enzyme were isolated from the nematode Caenorhabditis elegans and the fission yeast Schizosaccharomyces pombe based on their homology with the Saccharomyces cerevisiae gene. The cDNAs were shown to be functional in an interspecific complementation experiment; they can complement an S. cerevisiae dbr1 null mutant. About 2.5% of budding yeast S. cerevisiae genes have introns, and the accumulation of excised introns in a dbr1 null mutant has little effect on cell growth. In contrast, many S. pombe genes contain introns, and often multiple introns per gene, so that S. pombe is estimated to contain approximately 40 times as many introns as S. cerevisiae. The S. pombe dbr1 gene was disrupted and shown to be nonessential. Like the S. cerevisiae mutant, the S. pombe null mutant accumulated introns to high levels, indicating that intron lariat debranching represents a rate-limiting step in intron degradation in both species. Unlike the S. cerevisiae mutant, the S. pombe dbr1::leu1+ mutant had a severe growth defect and exhibited an aberrant elongated cell shape in addition to an intron accumulation phenotype. The growth defect of the S. pombe dbr1::leu1+ strain suggests that debranching activity is critical for efficient intron RNA degradation and that blocking this pathway interferes with cell growth.

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Escherichia coli Peptidase A, B, or N Can Process Translation Inhibitor Microcin C

Journal of Bacteriology ◽

10.1128/jb.01956-07 ◽

2008 ◽

Vol 190 (7) ◽

pp. 2607-2610 ◽

Cited By ~ 51

Author(s):

Teymur Kazakov ◽

Gaston H. Vondenhoff ◽

Kirill A. Datsenko ◽

Maria Novikova ◽

Anastasia Metlitskaya ◽

...

Keyword(s):

Escherichia Coli ◽

Cell Growth ◽

Trna Synthetase ◽

Methionine Residue ◽

Rate Limiting Step ◽

Limiting Step ◽

Translation Inhibitor ◽

Rate Limiting ◽

Broad Specificity

ABSTRACT The heptapeptide-nucleotide microcin C (McC) targets aspartyl-tRNA synthetase. Upon its entry into a susceptible cell, McC is processed to release a nonhydrolyzable aspartyl-adenylate that inhibits aspartyl-tRNA synthetase, leading to the cessation of translation and cell growth. Here, we surveyed Escherichia coli cells with singly, doubly, and triply disrupted broad-specificity peptidase genes to show that any of three nonspecific oligopeptidases (PepA, PepB, or PepN) can effectively process McC. We also show that the rate-limiting step of McC processing in vitro is deformylation of the first methionine residue of McC.

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Trm11p and Trm112p Are both Required for the Formation of 2-Methylguanosine at Position 10 in Yeast tRNA

Molecular and Cellular Biology ◽

10.1128/mcb.25.11.4359-4370.2005 ◽

2005 ◽

Vol 25 (11) ◽

pp. 4359-4370 ◽

Cited By ~ 73

Author(s):

Suresh K. Purushothaman ◽

Janusz M. Bujnicki ◽

Henri Grosjean ◽

Bruno Lapeyre

Keyword(s):

Saccharomyces Cerevisiae ◽

Enzymatic Activity ◽

Zinc Binding ◽

Growth Defect ◽

Putative Protein ◽

Yeast Trna ◽

Protein Methyltransferase ◽

Severe Growth Defect ◽

Severe Growth

ABSTRACT N 2 -Monomethylguanosine-10 (m2G10) and N 2 ,N 2 -dimethylguanosine-26 (m2 2G26) are the only two guanosine modifications that have been detected in tRNA from nearly all archaea and eukaryotes but not in bacteria. In Saccharomyces cerevisiae, formation of m2 2G26 is catalyzed by Trm1p, and we report here the identification of the enzymatic activity that catalyzes the formation of m2G10 in yeast tRNA. It is composed of at least two subunits that are associated in vivo: Trm11p (Yol124c), which is the catalytic subunit, and Trm112p (Ynr046w), a putative zinc-binding protein. While deletion of TRM11 has no detectable phenotype under laboratory conditions, deletion of TRM112 leads to a severe growth defect, suggesting that it has additional functions in the cell. Indeed, Trm112p is associated with at least four proteins: two tRNA methyltransferases (Trm9p and Trm11p), one putative protein methyltransferase (Mtc6p/Ydr140w), and one protein with a Rossmann fold dehydrogenase domain (Lys9p/Ynr050c). In addition, TRM11 interacts genetically with TRM1, thus suggesting that the absence of m2G10 and m2 2G26 affects tRNA metabolism or functioning.

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bioA mutant of Mycobacterium tuberculosis shows severe growth defect and imparts protection against tuberculosis in guinea pigs

PLoS ONE ◽

10.1371/journal.pone.0179513 ◽

2017 ◽

Vol 12 (6) ◽

pp. e0179513 ◽

Cited By ~ 8

Author(s):

Ritika Kar ◽

Prachi Nangpal ◽

Shubhita Mathur ◽

Swati Singh ◽

Anil K. Tyagi

Keyword(s):

Mycobacterium Tuberculosis ◽

Guinea Pigs ◽

Growth Defect ◽

Severe Growth Defect ◽

Severe Growth

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Transcriptome maps of general eukaryotic RNA degradation factors

eLife ◽

10.7554/elife.47040 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 8

Author(s):

Salma Sohrabi-Jahromi ◽

Katharina B Hofmann ◽

Andrea Boltendahl ◽

Christian Roth ◽

Saskia Gressel ◽

...

Keyword(s):

Rna Processing ◽

Rna Binding ◽

Global Analysis ◽

Rna Degradation ◽

Degradation Pathway ◽

Yeast Saccharomyces Cerevisiae ◽

Rate Limiting Step ◽

Optimal Codons ◽

Rate Limiting ◽

Functional Rnas

RNA degradation pathways enable RNA processing, the regulation of RNA levels, and the surveillance of aberrant or poorly functional RNAs in cells. Here we provide transcriptome-wide RNA-binding profiles of 30 general RNA degradation factors in the yeast Saccharomyces cerevisiae. The profiles reveal the distribution of degradation factors between different RNA classes. They are consistent with the canonical degradation pathway for closed-loop forming mRNAs after deadenylation. Modeling based on mRNA half-lives suggests that most degradation factors bind intact mRNAs, whereas decapping factors are recruited only for mRNA degradation, consistent with decapping being a rate-limiting step. Decapping factors preferentially bind mRNAs with non-optimal codons, consistent with rapid degradation of inefficiently translated mRNAs. Global analysis suggests that the nuclear surveillance machinery, including the complexes Nrd1/Nab3 and TRAMP4, targets aberrant nuclear RNAs and processes snoRNAs.

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Dynamical localization of a thylakoid membrane binding protein is required for acquisition of photosynthetic competency

10.1101/199943 ◽

2017 ◽

Author(s):

Andrian Gutu ◽

Frederick Chang ◽

Erin K. O‘Shea

Keyword(s):

Spatial Distribution ◽

Thylakoid Membrane ◽

Growth Conditions ◽

Dynamical Localization ◽

Growth Defect ◽

Cell Periphery ◽

Diffuse Fraction ◽

Photosynthetic Complexes ◽

Severe Growth Defect ◽

Severe Growth

SUMMARYVipp1 is highly conserved and essential for photosynthesis, but its function is unclear as it does not participate directly in light-dependent reactions. We analyzed Vipp1 localization in live cyanobacterial cells and show that Vipp1 is highly dynamic, continuously exchanging between a diffuse fraction that is uniformly distributed throughout the cell and a punctate fraction that is concentrated at high curvature regions of the thylakoid located at the cell periphery. Experimentally perturbing the spatial distribution of Vipp1 by relocalizing it to the nucleoid causes a severe growth defect during the transition from non-photosynthetic (dark) to photosynthetic (light) growth. However, the same perturbation of Vipp1 in dark alone or light alone growth conditions causes no growth or thylakoid morphology defects. We propose that the punctuated dynamics of Vipp1 at the cell periphery in regions of high thylakoid curvature enable acquisition of photosynthetic competency, perhaps by facilitating biogenesis of photosynthetic complexes involved in light-dependent reactions of photosynthesis.

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Insufficient levels of thenrdAB-encoded ribonucleotide reductase underlie the severe growth defect of the Δhda E. colistrain

Molecular Microbiology ◽

10.1111/mmi.13632 ◽

2017 ◽

Vol 104 (3) ◽

pp. 377-399 ◽

Cited By ~ 7

Author(s):

Vignesh M. P. Babu ◽

Mark Itsko ◽

Jamie C. Baxter ◽

Roel M. Schaaper ◽

Mark D. Sutton

Keyword(s):

Ribonucleotide Reductase ◽

Growth Defect ◽

Severe Growth Defect ◽

Severe Growth

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RelA/p65 Regulation of IκBβ

Molecular and Cellular Biology ◽

10.1128/mcb.25.12.4956-4968.2005 ◽

2005 ◽

Vol 25 (12) ◽

pp. 4956-4968 ◽

Cited By ~ 23

Author(s):

Erin Hertlein ◽

Jingxin Wang ◽

Katherine J. Ladner ◽

Nadine Bakkar ◽

Denis C. Guttridge

Keyword(s):

Postnatal Development ◽

26S Proteasome ◽

Carboxyl Terminus ◽

Growth Defect ◽

Tight Control ◽

Resistant Form ◽

Specific Manner ◽

Severe Growth Defect ◽

Severe Growth ◽

Hyperphosphorylated Form

ABSTRACT IκB inhibitor proteins are the primary regulators of NF-κB. In contrast to the defined regulatory interplay between NF-κB and IκBα, much less is known regarding the regulation of IκBβ by NF-κB. Here, we describe in detail the regulation of IκBβ by RelA/p65. Using p65 −/− fibroblasts, we show that IκBβ is profoundly reduced in these cells, but not in other NF-κB subunit knockouts. This regulation prevails during embryonic and postnatal development in a tissue-specific manner. Significantly, in both p65 −/− cells and tissues, IκBα is also reduced, but not nearly to the same extent as IκBβ, thus highlighting the degree to which IκBβ is dependent on p65. This dependence is based on the ability of p65 to stabilize IκBβ protein from the 26S proteasome, a process mediated in large part through the p65 carboxyl terminus. Furthermore, IκBβ was found to exist in both a basally phosphorylated and a hyperphosphorylated form. While the hyperphosphorylated form is less abundant, it is also more stable and less dependent on p65 and its carboxyl domain. Finally, we show that in p65 −/− fibroblasts, expression of a proteolysis-resistant form of IκBβ, but not IκBα, causes a severe growth defect associated with apoptosis. Based on these findings, we propose that tight control of IκBβ protein by p65 is necessary for the maintenance of cellular homeostasis.

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Human mutation D157G in ferroportin leads to hepcidin-independent binding of Jak2 and ferroportin down-regulation

Blood ◽

10.1182/blood-2009-10-251306 ◽

2010 ◽

Vol 115 (14) ◽

pp. 2956-2959 ◽

Cited By ~ 10

Author(s):

Ivana De Domenico ◽

Eric Lo ◽

Diane M. Ward ◽

Jerry Kaplan

Keyword(s):

Iron Homeostasis ◽

Fluorescent Protein ◽

Transferrin Saturation ◽

High Serum ◽

Growth Defect ◽

Down Regulation ◽

Severe Growth Defect ◽

Human Mutation ◽

Green Fluorescent ◽

Severe Growth

Abstract Mutations in the iron exporter ferroportin (Fpn) result in iron overload in macrophages or hepatocytes depending upon the mutation. Patients with Fpn mutation D157G show high serum ferritin and normal to slightly elevated transferrin saturation. Here, we show that Fpn(D157G)–green fluorescent protein (GFP) is down-regulated independent of hepcidin, and that this down-regulation is due to the constitutive binding of Jak2 and Fpn phosphorylation. Expression of Fpn(D157G)-GFP in Danio rerio results in a severe growth defect, which can be rescued by iron supplementation. These results identify a hepcidin-independent regulation of Fpn that can result in alterations in iron homeostasis.

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Phosphorylation-Independent Activity of Atypical Response Regulators of Helicobacter pylori

Journal of Bacteriology ◽

10.1128/jb.187.9.3100-3109.2005 ◽

2005 ◽

Vol 187 (9) ◽

pp. 3100-3109 ◽

Cited By ~ 63

Author(s):

Jennifer Schär ◽

Albert Sickmann ◽

Dagmar Beier

Keyword(s):

Helicobacter Pylori ◽

Cell Growth ◽

Response Regulator ◽

Consensus Sequence ◽

Open Reading Frames ◽

Growth Defect ◽

Response Regulators ◽

Two Component ◽

Severe Growth Defect ◽

Regulator Genes

ABSTRACT The genome of the gastric pathogen Helicobacter pylori harbors a remarkably low number of regulatory genes, including three and five open reading frames encoding two-component histidine kinases and response regulators, respectively, which are putatively involved in transcriptional regulation. Two of the response regulator genes, hp1043 and hp166, proved to be essential for cell growth, and inactivation of the response regulator gene hp1021 resulted in a severe growth defect, as indicated by a small-colony phenotype. The sequences of the receiver domains of response regulators HP1043 and HP1021 differ from the consensus sequence of the acidic pocket of the receiver domain which is involved in the phosphotransfer reaction from the histidine kinase to the response regulator. Using a genetic complementation system, we demonstrated that the function of response regulator HP166, which is essential for cell growth, can be provided by a mutated derivative carrying a D52N substitution at the site of phosphorylation. We found that the atypical receiver sequences of HP1043 and HP1021 are not crucial for the function of these response regulators. Phosphorylation of the receiver domains of HP1043 and HP1021 is not needed for response regulator function and may not occur at all. Thus, the phosphorylation-independent action of these regulators differs from the well-established two-component paradigm.

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The nucleolar DExD/H protein Hel66 is involved in ribosome biogenesis in Trypanosoma brucei

10.1101/2021.06.11.448066 ◽

2021 ◽

Author(s):

Majeed Bakari-Soale ◽

Nonso Josephat Ikenge ◽

Marion Scheibe ◽

Falk Butter ◽

Nicola Gail Jones ◽

...

Keyword(s):

Ribosomal Rna ◽

Ribosomal Proteins ◽

Ribosome Biogenesis ◽

Growth Defect ◽

Rrna Processing ◽

Ribosomal Subunits ◽

Comprehensive Picture ◽

Severe Growth Defect ◽

H Protein ◽

Severe Growth

The biosynthesis of ribosomes is a complex cellular process involving ribosomal RNA, ribosomal proteins and several further trans-acting factors. DExD/H box proteins constitute the largest family of trans-acting protein factors involved in this process. Several members of this protein family have been directly implicated in ribosome biogenesis in yeast. In trypanosomes, ribosome biogenesis differs in several features from the process described in yeast. Here, we have identified the DExD/H box helicase Hel66 as being involved in ribosome biogenesis. The protein is unique to Kinetoplastida, localises to the nucleolus and its depletion via RNAi caused a severe growth defect. Loss of the protein resulted in a decrease of global translation and accumulation of rRNA processing intermediates for both the small and large ribosomal subunits. Only a few factors involved in trypanosome rRNA biogenesis have been described so far and our findings contribute to gaining a more comprehensive picture of this essential process.

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