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

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

Molecular and Cellular Biology ◽

10.1128/mcb.17.2.809 ◽

1997 ◽

Vol 17 (2) ◽

pp. 809-818 ◽

Cited By ~ 41

Author(s):

K Nam ◽

G Lee ◽

J Trambley ◽

S E Devine ◽

J D Boeke

Keyword(s):

Cell Growth ◽

Schizosaccharomyces Pombe ◽

Rna Degradation ◽

Growth Defect ◽

Null Mutant ◽

Rate Limiting Step ◽

Genes Encoding ◽

Severe Growth Defect ◽

Rate Limiting ◽

Severe Growth

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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The Nucleolar DExD/H Protein Hel66 is Involved in Ribosome Biogenesis in Trypanosoma Brucei

10.21203/rs.3.rs-612898/v1 ◽

2021 ◽

Author(s):

Majeed Bakari-Soale ◽

Nonso Josephat Ikenga ◽

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

Abstract 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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Iron-Dependent Remodeling of Fungal Metabolic Pathways Associated with Ferrichrome Biosynthesis

Applied and Environmental Microbiology ◽

10.1128/aem.00659-10 ◽

2010 ◽

Vol 76 (12) ◽

pp. 3806-3817 ◽

Cited By ~ 20

Author(s):

Alexandre Mercier ◽

Simon Labbé

Keyword(s):

Metabolic Pathways ◽

Present Report ◽

Glutamate Synthase ◽

Growth Defect ◽

Dependent Manner ◽

Iron Deprivation ◽

Severe Growth Defect ◽

Coupled Enzymes ◽

Hydrolysis Of ◽

Severe Growth

ABSTRACT The fission yeast Schizosaccharomyces pombe excretes and accumulates the hydroxamate-type siderophore ferrichrome. The sib1 + and sib2 + genes encode, respectively, a siderophore synthetase and an l-ornithine N5-oxygenase that participate in ferrichrome biosynthesis. In the present report, we demonstrate that sib1 + and sib2 + are repressed by the GATA-type transcriptional repressor Fep1 in response to high levels of iron. We further found that the loss of Fep1 results in increased ferrichrome production. We showed that a sib1Δ sib2Δ mutant strain exhibits a severe growth defect on iron-poor media. We determined that two metabolic pathways are involved in biosynthesis of ornithine, an obligatory precursor of ferrichrome. Ornithine is produced by hydrolysis of arginine by the Car1 and Car3 proteins. Although car3 + was constitutively expressed, car1 + transcription levels were repressed upon exposure to iron, with a concomitant decrease of Car1 arginase activity. Ornithine is also generated by transformation of glutamate, which itself is produced by two separate biosynthetic pathways which are transcriptionally regulated by iron in an opposite fashion. In one pathway, the glutamate dehydrogenase Gdh1, which produces glutamate from 2-ketoglutarate, was repressed under iron-replete conditions in a Fep1-dependent manner. The other pathway involves two coupled enzymes, glutamine synthetase Gln1 and Fe-S cluster-containing glutamate synthase Glt1, which were both repressed under iron-limiting conditions but were expressed under iron-replete conditions. Collectively, these results indicate that under conditions of iron deprivation, yeast remodels metabolic pathways linked to ferrichrome synthesis in order to limit iron utilization without compromising siderophore production and its ability to sequester iron from the environment.

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Species Specificity in Ribosome Biogenesis: a Nonconserved Phosphoprotein Is Required for Formation of the Large Ribosomal Subunit in Trypanosoma brucei

Eukaryotic Cell ◽

10.1128/ec.4.1.30-35.2005 ◽

2005 ◽

Vol 4 (1) ◽

pp. 30-35 ◽

Cited By ~ 27

Author(s):

Bryan C. Jensen ◽

Deirdre L. Brekken ◽

Amber C. Randall ◽

Charles T. Kifer ◽

Marilyn Parsons

Keyword(s):

Trypanosoma Brucei ◽

Small Rnas ◽

Ribosome Biogenesis ◽

Large Subunit ◽

Ribosomal Subunit ◽

Protozoan Parasite ◽

Growth Defect ◽

Large Ribosomal Subunit ◽

Severe Growth Defect ◽

Severe Growth

ABSTRACT In the protozoan parasite Trypanosoma brucei, the large rRNA, which is a single 3.4- to 5-kb species in most organisms, is further processed to form six distinct RNAs, two larger than 1 kb (LSU1 and LSU2) and four smaller than 220 bp. The small rRNA SR1 separates the two large RNAs, while the remaining small RNAs are clustered at the 3′ end of the precursor rRNA. One would predict that T. brucei possesses specific components to carry out these added processing events. We show here that the trypanosomatid-specific nucleolar phosphoprotein NOPP44/46 is involved in this further processing. Cells depleted of NOPP44/46 by RNA interference had a severe growth defect and demonstrated a defect in large-ribosomal-subunit biogenesis. Concurrent with this defect, a significant decrease in processing intermediates, particularly for SR1, was seen. In addition, we saw an accumulation of aberrant processing intermediates caused by cleavage within either LSU1 or LSU2. Though it is required for large-subunit biogenesis, we show that NOPP44/46 is not incorporated into the nascent particle. Thus, NOPP44/46 is an unusual protein in that it is both nonconserved and required for ribosome biogenesis.

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