Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R

Yukawa, Hideaki; Omumasaba, Crispinus A.; Nonaka, Hiroshi; Kós, Péter B.; Okai, Naoko; Suzuki, Nobuaki; Suda, Masako; Tsuge, Yota; Watanabe, Junko; Ikeda, Yoko; Vertès, Alain A.; Inui, Masayuki

doi:10.1099/mic.0.2006/003657-0

Cited by 223 publications

(119 citation statements)

References 95 publications

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“…PCR primers (20-mers) were designed to amplify the full-length coding DNA segments of 3080 predicted ORFs based on the annotation of the complete C. glutamicum R genome sequence (Yukawa et al, 2007). Aminoterminus primers amplified 20 bp downstream from the initiation codon, which was included.…”

Section: Methodsmentioning

confidence: 99%

“…We previously observed that when aerobically grown C. glutamicum R (Yukawa et al, 2007) is packed to a high cell density under oxygen deprivation conditions, despite the cessation of cellular growth, the cells remain able to excrete in significant amounts several metabolites, including lactate and succinate (Inui et al, 2004b). There are two main advantages of using these oxygen deprivation conditions for the production of organic acids in corynebacteria.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptional profiling of Corynebacterium glutamicum metabolism during organic acid production under oxygen deprivation conditions

et al. 2007

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A transcriptional profiling of the metabolism of Corynebacterium glutamicum under oxygen deprivation conditions is reported. It was observed that the glucose consumption rate per cell when C. glutamicum cells were incubated under oxygen deprivation conditions was higher than that achieved by cells incubated under aerobic growth conditions. Furthermore, DNA microarray and quantitative RT-PCR analyses revealed that the genes of several key enzymes of the glycolytic and organic acid production pathways, including gapA, pgk, tpi, ppc, ldhA and mdh, were significantly upregulated under oxygen deprivation conditions. The corresponding enzymic activities consistently correlated with the regulation patterns of the genetic expression observed at the transcriptional level. Studies of lacZ fusions with the gapA, ldhA and mdh genes indicated not only that these genes are strongly induced at the onset of the stationary phase under aerobic growth conditions, but also that high expression levels are maintained under oxygen deprivation conditions. These results indicate that the genetic expression of several key metabolic enzymes in C. glutamicum cells incubated under oxygen deprivation conditions is chiefly regulated at the transcriptional level. The physiological consequence of the observed increased transcription under oxygen deprivation conditions is an increased rate of carbon source consumption, which is accompanied by a concomitant increase in organic acid production.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Transcriptional profiling of Corynebacterium glutamicum metabolism during organic acid production under oxygen deprivation conditions

et al. 2007

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“…Some spacers showed very high similarities with the coding sequences, prophages or un-annotated regions in other C. diphtheriae strains, Corynebacterium jeikeium, Corynebacterium urealyticum and Corynebacterium ulcerans, and other bacterial species (Tables S2-S4), which might indicate the presence of a previously unappreciated diversity of broad host range corynebacteriophages. Interestingly, corynebacteria appear to be devoid of a natural competence system (Yukawa et al, 2007) and have multiple putative restriction-modification systems within their genomes (Sangal et al, 2012a, b) offering further barriers to recombination in these organisms.…”

Section: Source Of Spacer Diversitymentioning

confidence: 99%

Novel configurations of type I and II CRISPR–Cas systems in Corynebacterium diphtheriae

2013

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Clustered regularly interspaced short palindromic repeats (CRISPRs) are major barriers to recombination through recognition of invading nucleic acids, such as phage and plasmids, and promoting their degredation through the action of CRISPR associated (Cas) proteins. The genomic comparison of 17 Corynebacterium diphtheriae strains led to the identification of three novel CRISPR-Cas system variants, based on the Type II (Type II-C) or type I-E systems. The type II-C system was the most common (11/17 isolates) but it lacked the csn2 and cas4 genes that are involved in spacer acquisition. We also identified that this variant type II-C CRISPR-Cas system is present in other bacteria, and the first system was recently characterized in Neisseria meningitidis. In the remaining isolates, the type II-C system was replaced by a variant of type I-E (I-E-a), where the repeat arrays are inserted between the cas3 and cse1 genes. Three isolates with the type II-C system also possess an additional variant of type I-E (I-E-b), elsewhere in the genome, that exhibits a novel divergent gene organization within the cas operon. The nucleotide sequences of the palindromic repeats and the cas1 gene were phylogenetically incongruent to the core genome. The G+C content of the systems is lower (46.0-49.5 mol%) than the overall DNA G+C content (53 mol%), and they are flanked by mobile genetic elements, providing evidence that they were acquired in three independent horizontal gene transfer events. The majority of spacers lack identity with known phage or plasmid sequences, indicating that there is an unexplored reservoir of corynebacteriophages and plasmids. These novel CRISPR-Cas systems may represent a unique mechanism for spacer acquisitions and defence against invading DNA.

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“…Since the complete genome sequence of C. glutamicum became available (7)(8)(9), a number of transcriptional regulators controlling genes involved in central carbon metabolism have been characterized (10,11). Genome-wide studies reveal that a global transcription regulatory system for carbon source-dependent regulation in C. glutamicum is quite different from the well-established systems in Escherichia coli and Bacillus subtilis.…”

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confidence: 99%

Involvement of Regulatory Interactions among Global Regulators GlxR, SugR, and RamA in Expression of ramA in Corynebacterium glutamicum

et al. 2013

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The central carbon metabolism genes in Corynebacterium glutamicum are under the control of a transcriptional regulatory network composed of several global regulators. It is known that the promoter region of ramA, encoding one of these regulators, interacts with its gene product, RamA, as well as with the two other regulators, GlxR and SugR, in vitro and/or in vivo. Although RamA has been confirmed to repress its own expression, the roles of GlxR and SugR in ramA expression have remained unclear. In this study, we examined the effects of GlxR binding site inactivation on expression of the ramA promoter-lacZ fusion in the genetic background of single and double deletion mutants of sugR and ramA. In the wild-type background, the ramA promoter activity was reduced to undetectable levels by the introduction of mutations into the GlxR binding site but increased by sugR deletion, indicating that GlxR and SugR function as the transcriptional activator and repressor, respectively. The marked repression of ramA promoter activity by the GlxR binding site mutations was largely compensated for by deletions of sugR and/or ramA. Furthermore, ramA promoter activity in the ramA-sugR double mutant was comparable to that in the ramA mutant but was significantly higher than that in the sugR mutant. Taken together, it is likely that the level of ramA expression is dynamically balanced by GlxR-dependent activation and repression by RamA along with SugR in response to perturbation of extracellular and/or intracellular conditions. These findings add multiple regulatory loops to the transcriptional regulatory network model in C. glutamicum.

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Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R

Cited by 223 publications

References 95 publications

Transcriptional profiling of Corynebacterium glutamicum metabolism during organic acid production under oxygen deprivation conditions

Transcriptional profiling of Corynebacterium glutamicum metabolism during organic acid production under oxygen deprivation conditions

Novel configurations of type I and II CRISPR–Cas systems in Corynebacterium diphtheriae

Involvement of Regulatory Interactions among Global Regulators GlxR, SugR, and RamA in Expression of ramA in Corynebacterium glutamicum

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