Proteome analysis of Corynebacterium glutamicum ATCC13032 Δefp
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Corynebacterium Glutamicum Atcc 13032
SUBMITTER: 
Ignasi Forne
LAB HEAD: Prof. Dr. Kirsten Jung
PROVIDER: PXD014742 | Pride | 2020-04-06
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Ref1327_BP_Defp1_20171002.raw | Raw | |||
| Ref1327_BP_Defp2_20171002.raw | Raw | |||
| Ref1327_BP_Defp3_20171002.raw | Raw | |||
| Ref1327_BP_Defp4_20171002.raw | Raw | |||
| Ref1327_BP_WT1_20171002.raw | Raw |
Items per page: 5 1 - 5 of 10 |
Publications
Structure and Function of an Elongation Factor P Subfamily in Actinobacteria.
Pinheiro Bruno B Scheidler Christopher M CM Kielkowski Pavel P Schmid Marina M Forné Ignasi I Ye Suhui S Reiling Norbert N Takano Eriko E Imhof Axel A Sieber Stephan A SA Schneider Sabine S Jung Kirsten K
Cell reports 20200301 13
Translation of consecutive proline motifs causes ribosome stalling and requires rescue via the action of a specific translation elongation factor, EF-P in bacteria and archaeal/eukaryotic a/eIF5A. In Eukarya, Archaea, and all bacteria investigated so far, the functionality of this translation elongation factor depends on specific and rather unusual post-translational modifications. The phylum Actinobacteria, which includes the genera Corynebacterium, Mycobacterium, and Streptomyces, is of both m ...[more]
Similar Datasets
Project description:Protein synthesis is performed by the ribosome and a host of highly conserved elongation factors. Elongation factor P (EF-P) prevents ribosome stalling at difficult-to-translate sequences, particularly polyproline tracts. In bacteria, phenotypes associated with efp deletion range from modest to lethal, suggesting that some species encode an additional translation factor that has similar function to EF-P. Here we identify YfmR as a translation factor that is essential in the absence of EF-P in B. subtilis. YfmR is an ABCF ATPase that is closely related to both Uup and EttA, ABCFs that bind the ribosomal E-site and are conserved in more than 50% of bacterial genomes. We show that YfmR associates with actively translating ribosomes, and that depleting YfmR from ∆efp cells causes severe ribosome stalling at a polyproline tract in vivo. YfmR depletion from ∆efp cells was lethal, and caused reduced levels of actively translating ribosomes. Our results therefore identify YfmR as an important translation factor that is essential in B. subtilis in the absence of EF-P.
2024-03-06 | GSE249203 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2020-03-24 | GSE138829 | GEO
Project description:Monoterpenes are commonly known for their role in the flavors and fragrances industry and are also gaining attention for other uses like insect repellant and as potential renewable fuels for aviation. Corynebacterium glutamicum, a Generally Recognized as Safe microbe, has been a choice organism in industry for the annual million ton-scale bioproduction of amino acids for more than 50 years; however, efforts to produce monoterpenes in C. glutamicum have remained relatively limited. In this study, we report a further expansion of the C. glutamicum biosynthetic repertoire through the development and optimization of a mevalonate-based monoterpene platform. In the course of our initial plasmid design iterations, we demonstrated an increased flux through the mevalonate-based bypass pathway to increase isoprenol production to the highest reported titers to date at nearly 1.5 g/L. These designs also evaluated the effects of backbone, promoter, and GPP synthase homolog source on product titers. Monoterpene production was further improved by disrupting competing pathways for isoprenoid precursor supply and by implementing a biphasic production system to prevent volatilization. With this platform, we achieved 486.3 mg/L (± 54.6 mg/L) of geranoids, 557.3 mg/L of 1,8-cineole (± 12.3 mg/L), and 209.7 mg/L of linalool (±23.9 mg/L). Furthermore, we determined that C. glutamicum oxidizes geraniol through an aldehyde intermediate before asymmetrically reducing geraniol to citronellol.
2024-02-28 | PXD044193 | Pride
Project description:Previous studies with Corynebacterium diphtheriae and Mycobacterium species revealed that the transcriptional regulator DtxR and its ortholog IdeR play a central role in the control of iron metabolism. In the present work, we used genome-based approaches to determine the DtxR regulon of Corynebacterium glutamicum, a nonpathogenic relative of C. diphtheriae. First, global gene expression of a dtxR deletion mutant was compared with that of the wild type using DNA microarrays. Second, we used a computer-based approach to identify 117 putative DtxR binding sites in the C. glutamicum genome. In the third step, 74 of the corresponding genome regions were amplified by PCR, 51 of which were shifted by the DtxR protein. Finally, we analyzed which of the genes preceded by a functional DtxR binding site showed altered mRNA levels in the transcriptome comparison. Fifty-one genes organized in 27 putative operons displayed an increased mRNA level in the DeltadtxR mutant and thus are presumably repressed by DtxR. The majority of these genes are obviously involved in iron acquisition, three encode transcriptional regulators, e.g., the recently identified repressor of iron proteins RipA, and the others encode proteins of diverse or unknown functions. Thirteen genes showed a decreased mRNA level in the DeltadtxR mutant and thus might be activated by DtxR. This group included the suf operon, whose products are involved in the formation and repair of iron-sulfur clusters, and several genes for transcriptional regulators. Our results clearly establish DtxR as the master regulator of iron-dependent gene expression in C. glutamicum.
| S-EPMC1446976 | biostudies-literature
Project description:We have reported a transcription profile of an adapted Corynebacterium glutamicum that showed enhanced oxidative stress resistance. To construct an artificial oxidative stress-resistant strain, gene clusters in the β-ketoadipate pathway, which were up-regulated in the adapted strain, were artificially expressed in the wild-type C. glutamicum. The wild-type strain was unable to grow under 2 mM H2O2 containing minimal medium, while the strains expressing pca gene clusters restored growth under the same medium, and the pcaHGBC expression showed the most significant effect among the gene clusters. The expressions of pca gene clusters also enabled the wild-type to increase its resistance against oxidative stressors, such as diamide and cumene hydroperoxide, as well as H2O2. The oxidative stress tolerance of the strain was correlated to the reactive oxygen species (ROS)-scavenging activity of the cell extract. The reason for the enhanced oxidative stress-resistance of C. glutamicum and its applications on the synthetic strain development are discussed.
| S-EPMC4052852 | biostudies-literature
Project description:Not available
2007-11-09 | PRD000026 | Pride
Project description:Stalling of ribosomes due to consecutive proline motifs during polypeptide synthesis is a challenge faced by organisms across all kingdoms. To overcome this, bacteria employ translation elongation factor P (EF-P), while archaea and eukaryotes rely on a/eIF5A. Typically, these elongation factors become active only after undergoing post-translational modifications (PTMs) such as ß-lysinylation, (deoxy-)hypusinylation, rhamnosylation, or 5-aminopentanolyation. An exception to this rule is found in EF-P members of the PGKGP-subfamily, which remain unmodified. However, the mechanism behind the ability of certain bacteria to bypass metabolically and energetically costly PTMs, thus retaining active EF-P, remains unclear. In this study, we investigated the design principles governing the full functionality of unmodified EF-Ps in Escherichia coli. We first screened for naturally unmodified EF-Ps that are active in an E. coli reporter strain. We identified EF-P from Rhodomicrobium vannielii capable of rescuing the growth deficiencies and changes in the proteome of E. coli ΔepmA mutant lacking the gene for the modifying EF-P-(R)-ß-lysine ligase. We then identified specific amino acids in domain I of the unmodified EF-P variant that affected its activity. Ultimately, we transferred these functional properties to other marginally active members of the PGKGP EF-P subfamily, resulting in fully functional unmodified variants in E. coli. These results have not only implications for the improved heterologous expression of polyproline-containing proteins in E. coli but offer applications for other bacterial hosts. Understanding the mechanisms that underlie the functionality of unmodified EF-P provides insights into cellular adaptations to optimize protein synthesis.
2024-04-08 | PXD044929 | Pride
Project description:Corynebacterium glutamicum is a well-studied bacterium which naturally overproduces glutamate when induced by an elicitor. Glutamate production is accompanied by decreased 2-oxoglutatate dehydrogenase activity. Elicitors of glutamate production by C. glutamicum analyzed to molecular detail target the cell envelope.Ciprofloxacin, an inhibitor of bacterial DNA gyrase and topoisomerase IV, was shown to inhibit growth of C. glutamicum wild type with concomitant excretion of glutamate. Enzyme assays showed that 2-oxoglutarate dehydrogenase activity was decreased due to ciprofloxacin addition. Transcriptome analysis revealed that this inhibitor of DNA gyrase increased RNA levels of genes involved in DNA synthesis, repair and modification. Glutamate production triggered by ciprofloxacin led to glutamate titers of up to 37?±?1 mM and a substrate specific glutamate yield of 0.13 g/g. Even in the absence of the putative glutamate exporter gene yggB, ciprofloxacin effectively triggered glutamate production. When C. glutamicum wild type was cultivated under nitrogen-limiting conditions, 2-oxoglutarate rather than glutamate was produced as consequence of exposure to ciprofloxacin. Recombinant C. glutamicum strains overproducing lysine, arginine, ornithine, and putrescine, respectively, secreted glutamate instead of the desired amino acid when exposed to ciprofloxacin.Ciprofloxacin induced DNA synthesis and repair genes, reduced 2-oxoglutarate dehydrogenase activity and elicited glutamate production by C. glutamicum. Production of 2-oxoglutarate could be triggered by ciprofloxacin under nitrogen-limiting conditions.
| S-EPMC5055667 | biostudies-literature
Project description:Besides metabolic pathways and regulatory networks, transport systems are also pivotal for cellular metabolism and hyperproduction of biochemicals using microbial cell factories. The identification and characterization of transporters are therefore of great significance for the understanding and engineering of transport reactions. Herein, a novel l-glutamate exporter, MscCG2, which exists extensively in Corynebacterium glutamicum strains but is distinct from the only known l-glutamate exporter, MscCG, was discovered in an industrial l-glutamate-producing C. glutamicum strain. MscCG2 was predicted to possess three transmembrane helices in the N-terminal region and located in the cytoplasmic membrane, which are typical structural characteristics of the mechanosensitive channel of small conductance. MscCG2 has a low amino acid sequence identity (23%) to MscCG and evolved separately from MscCG with four transmembrane helices. Despite the considerable differences between MscCG2 and MscCG in sequence and structure, gene deletion and complementation confirmed that MscCG2 also functioned as an l-glutamate exporter and an osmotic safety valve in C. glutamicum Besides, transcriptional analysis showed that MscCG2 and MscCG genes were transcribed in similar patterns and not induced by l-glutamate-producing conditions. It was also demonstrated that MscCG2-mediated l-glutamate excretion was activated by biotin limitation or penicillin treatment and that constitutive l-glutamate excretion was triggered by a gain-of-function mutation of MscCG2 (A151V). Discovery of MscCG2 will enrich the understanding of bacterial amino acid transport and provide additional targets for exporter engineering.IMPORTANCE The exchange of matter, energy, and information with surroundings is fundamental for cellular metabolism. Therefore, studying transport systems that are essential for these processes is of great significance. Besides, transport systems of bacterial cells are usually related to product excretion as well as product reuptake, making transporter engineering a useful strategy for strain improvement. The significance of our research is in identifying and characterizing a novel l-glutamate exporter from the industrial workhorse Corynebacterium glutamicum, which will enrich the understanding of l-glutamate excretion and provide a new target for studying bacterial amino acid transport and engineering transport reactions.
| S-EPMC5835739 | biostudies-literature
Project description:BackgroundCorynebacterium glutamicum contains the glycosylated C50 carotenoid decaprenoxanthin as yellow pigment. Starting from isopentenyl pyrophosphate, which is generated in the non-mevalonate pathway, decaprenoxanthin is synthesized via the intermediates farnesyl pyrophosphate, geranylgeranyl pyrophosphate, lycopene and flavuxanthin.ResultsHere, we showed that the genes of the carotenoid gene cluster crtE-cg0722-crtBIYeYfEb are co-transcribed and characterized defined gene deletion mutants. Gene deletion analysis revealed that crtI, crtEb, and crtYeYf, respectively, code for the only phytoene desaturase, lycopene elongase, and carotenoid C45/C50 ε-cyclase, respectively. However, the genome of C. glutamicum also encodes a second carotenoid gene cluster comprising crtB2I2-1/2 shown to be co-transcribed, as well. Ectopic expression of crtB2 could compensate for the lack of phytoene synthase CrtB in C. glutamicum ΔcrtB, thus, C. glutamicum possesses two functional phytoene synthases, namely CrtB and CrtB2. Genetic evidence for a crtI2-1/2 encoded phytoene desaturase could not be obtained since plasmid-borne expression of crtI2-1/2 did not compensate for the lack of phytoene desaturase CrtI in C. glutamicum ΔcrtI. The potential of C. glutamicum to overproduce carotenoids was estimated with lycopene as example. Deletion of the gene crtEb prevented conversion of lycopene to decaprenoxanthin and entailed accumulation of lycopene to 0.03 ± 0.01 mg/g cell dry weight (CDW). When the genes crtE, crtB and crtI for conversion of geranylgeranyl pyrophosphate to lycopene were overexpressed in C. glutamicum ΔcrtEb intensely red-pigmented cells and an 80 fold increased lycopene content of 2.4 ± 0.3 mg/g CDW were obtained.ConclusionC. glutamicum possesses a certain degree of redundancy in the biosynthesis of the C50 carotenoid decaprenoxanthin as it possesses two functional phytoene synthase genes. Already metabolic engineering of only the terminal reactions leading to lycopene resulted in considerable lycopene production indicating that C. glutamicum may serve as a potential host for carotenoid production.
| S-EPMC3598387 | biostudies-literature