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Genetics and Physiology of Corynebacteria

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (28 February 2021) | Viewed by 36183

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Dr. Miroslav Pátek

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Institute of Microbiology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
Interests: the studies of gene expression control and enzyme systems in laboratory strains of model bacterial species (Escherichia coli) and on construction and analysis of strains of industrial bacteria that are used in biotechnology-based syntheses of various compounds and environmental applications (e.g., Corynebacterium glutamicum, Rhodococcus erythropolis)
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Prof. Dr. Andreas Burkovski

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Microbiology Division, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
Interests: corynebacteria; host–pathogen interaction; nitrogen control; regulatory networks; secretome analyses; toxins
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Special Issue Information

Dear Colleagues,

Corynebacterium is a genus of Gram-positive bacteria that is classified as Actinobacteria and is phylogenetically related to mycobacteria, rhodococci, and nocardiae. This diverse group of rod-shaped or club-shaped (coryneform) microorganisms includes human, animal and plant pathogens, as well as saprophytes. The most notable human pathogen is Corynebacterium diphtheriae, which is the causative agent of diphtheria. Several species cause diseases in animals, most notably C. pseudotuberculosis, whereas other corynebacteria are opportunistic pathogens causing diseases in immunocompromised people. Numerous corynebacteria are innocuous commensals found in the mucosa and normal skin flora of humans and animals. A noteworthy positive side of corynebacteria is their broad range of biotechnological applications. C. glutamicum is considered a prominent workhorse in the biotechnology industry. This species, generally recognized as a safe bacterium, was initially used in the fermentative production of many amino acids. Currently, various C. glutamicum strains are efficient producers of fine chemicals, fuels, polymers, and pharmaceutical compounds. These strains are further improved by metabolic and genetic engineering. In addition to practical aspects, due to the application of advanced global techniques such as genomics, transcriptomics, metabolomics, and fluxomics in its research, C. glutamicum has become one of the best-studied model bacteria.

This Special Issue of Microorganisms invites you to submit manuscripts concerning any aspect of the genetics and physiology of both pathogenic and biotechnologically relevant corynebacteria.

Dr. Miroslav Pátek
Prof. Dr. Andreas Burkovski
Guest Editors

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Keywords

Corynebacterium diphtheria
Corynebacterium glutamicum
pathogen
biotechnology
zoonosis
antibiotic resistance
mycolic acids

Published Papers (9 papers)

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Research

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19 pages, 2423 KiB

Open AccessArticle

Corynebacterium glutamicum Regulation beyond Transcription: Organizing Principles and Reconstruction of an Extended Regulatory Network Incorporating Regulations Mediated by Small RNA and Protein–Protein Interactions

by Juan M. Escorcia-Rodríguez, Andreas Tauch and Julio A. Freyre-González

Microorganisms 2021, 9(7), 1395; https://doi.org/10.3390/microorganisms9071395 - 28 Jun 2021

Cited by 4 | Viewed by 2793

Abstract

Corynebacterium glutamicum is a Gram-positive bacterium found in soil where the condition changes demand plasticity of the regulatory machinery. The study of such machinery at the global scale has been challenged by the lack of data integration. Here, we report three regulatory network models for C. glutamicum: strong (3040 interactions) constructed solely with regulations previously supported by directed experiments; all evidence (4665 interactions) containing the strong network, regulations previously supported by nondirected experiments, and protein–protein interactions with a direct effect on gene transcription; sRNA (5222 interactions) containing the all evidence network and sRNA-mediated regulations. Compared to the previous version (2018), the strong and all evidence networks increased by 75 and 1225 interactions, respectively. We analyzed the system-level components of the three networks to identify how they differ and compared their structures against those for the networks of more than 40 species. The inclusion of the sRNA-mediated regulations changed the proportions of the system-level components and increased the number of modules but decreased their size. The C. glutamicum regulatory structure contrasted with other bacterial regulatory networks. Finally, we used the strong networks of three model organisms to provide insights and future directions of the C.glutamicum regulatory network characterization. Full article

(This article belongs to the Special Issue Genetics and Physiology of Corynebacteria)

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18 pages, 2774 KiB

Open AccessArticle

In Silico Prediction and Analysis of Unusual Lantibiotic Resistance Operons in the Genus Corynebacterium

by Oliver Goldbeck, Dominik Weixler, Bernhard J. Eikmanns and Christian U. Riedel

Microorganisms 2021, 9(3), 646; https://doi.org/10.3390/microorganisms9030646 - 19 Mar 2021

Cited by 5 | Viewed by 2811

Abstract

Post-translationally modified, (methyl-)lanthionine-containing peptides are produced by several Gram-positive bacteria. These so-called lantibiotics have potent activity against various bacterial pathogens including multidrug-resistant strains and are thus discussed as alternatives to antibiotics. Several naturally occurring mechanisms of resistance against lantibiotics have been described for bacteria, including cell envelope modifications, ABC-transporters, lipoproteins and peptidases. Corynebacterium species are widespread in nature and comprise important pathogens, commensals as well as environmentally and biotechnologically relevant species. Yet, little is known about lantibiotic biosynthesis and resistance in this genus. Here, we present a comprehensive in silico prediction of lantibiotic resistance traits in this important group of Gram-positive bacteria. Our analyses suggest that enzymes for cell envelope modification, peptidases as well as ABC-transporters involved in peptide resistance are widely distributed in the genus. Based on our predictions, we analyzed the susceptibility of six Corynebacterium species to nisin and found that those without dedicated resistance traits are more susceptible and unable to adapt to higher concentrations. In addition, we were able to identify lantibiotic resistance operons encoding for peptidases, ABC-transporters and two-component systems with an unusual predicted structure that are conserved in the genus Corynebacterium. Heterologous expression shows that these operons indeed confer resistance to the lantibiotic nisin. Full article

(This article belongs to the Special Issue Genetics and Physiology of Corynebacteria)

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16 pages, 2298 KiB

Open AccessArticle

The ldhA Gene Encoding Fermentative l-Lactate Dehydrogenase in Corynebacterium Glutamicum Is Positively Regulated by the Global Regulator GlxR

by Koichi Toyoda and Masayuki Inui

Microorganisms 2021, 9(3), 550; https://doi.org/10.3390/microorganisms9030550 - 06 Mar 2021

Cited by 5 | Viewed by 2795

Abstract

Bacterial metabolism shifts from aerobic respiration to fermentation at the transition from exponential to stationary growth phases in response to limited oxygen availability. Corynebacterium glutamicum, a Gram-positive, facultative aerobic bacterium used for industrial amino acid production, excretes l-lactate, acetate, and succinate as fermentation products. The ldhA gene encoding l-lactate dehydrogenase is solely responsible for l-lactate production. Its expression is repressed at the exponential phase and prominently induced at the transition phase. ldhA is transcriptionally repressed by the sugar-phosphate-responsive regulator SugR and l-lactate-responsive regulator LldR. Although ldhA expression is derepressed even at the exponential phase in the sugR and lldR double deletion mutant, a further increase in its expression is still observed at the stationary phase, implicating the action of additional transcription regulators. In this study, involvement of the cAMP receptor protein-type global regulator GlxR in the regulation of ldhA expression was investigated. The GlxR-binding site found in the ldhA promoter was modified to inhibit or enhance binding of GlxR. The ldhA promoter activity and expression of ldhA were altered in proportion to the binding affinity of GlxR. Similarly, l-lactate production was also affected by the binding site modification. Thus, GlxR was demonstrated to act as a transcriptional activator of ldhA. Full article

(This article belongs to the Special Issue Genetics and Physiology of Corynebacteria)

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12 pages, 1988 KiB

Open AccessArticle

Requirement of the LtsA Protein for Formation of the Mycolic Acid-Containing Layer on the Cell Surface of Corynebacterium glutamicum

by Yutaro Kumagai, Takashi Hirasawa and Masaaki Wachi

Microorganisms 2021, 9(2), 409; https://doi.org/10.3390/microorganisms9020409 - 16 Feb 2021

Viewed by 2786

Abstract

The ltsA gene of Corynebacterium glutamicum encodes a purF-type glutamine-dependent amidotransferase, and mutations in this gene result in increased susceptibility to lysozyme. Recently, it was shown that the LtsA protein catalyzes the amidation of diaminopimelate residues in the lipid intermediates of peptidoglycan biosynthesis. In this study, intracellular localization of wild-type and mutant LtsA proteins fused with green fluorescent protein (GFP) was investigated. The GFP-fused wild-type LtsA protein showed a peripheral localization pattern characteristic of membrane-associated proteins. The GFP-fusions with a mutation in the N-terminal domain of LtsA, which is necessary for the glutamine amido transfer reaction, exhibited a similar localization to the wild type, whereas those with a mutation or a truncation in the C-terminal domain, which is not conserved among the purF-type glutamine-dependent amidotransferases, did not. These results suggest that the C-terminal domain is required for peripheral localization. Differential staining of cell wall structures with fluorescent dyes revealed that formation of the mycolic acid-containing layer at the cell division planes was affected in the ltsA mutant cells. This was also confirmed by observation that bulge formation was induced at the cell division planes in the ltsA mutant cells upon lysozyme treatment. These results suggest that the LtsA protein function is required for the formation of a mycolic acid-containing layer at the cell division planes and that this impairment results in increased susceptibility to lysozyme. Full article

(This article belongs to the Special Issue Genetics and Physiology of Corynebacteria)

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17 pages, 2570 KiB

Open AccessArticle

Ribonuclease J-Mediated mRNA Turnover Modulates Cell Shape, Metabolism and Virulence in Corynebacterium diphtheriae

by Truc Thanh Luong, Minh Tan Nguyen, Yi-Wei Chen, Chungyu Chang, Ju Huck Lee, Manuel Wittchen, HyLam Ton-That, Melissa Cruz, Danielle A. Garsin, Asis Das, Andreas Tauch and Hung Ton-That

Microorganisms 2021, 9(2), 389; https://doi.org/10.3390/microorganisms9020389 - 14 Feb 2021

Cited by 6 | Viewed by 2573

Abstract

Controlled RNA degradation is a crucial process in bacterial cell biology for maintaining proper transcriptome homeostasis and adaptation to changing environments. mRNA turnover in many Gram-positive bacteria involves a specialized ribonuclease called RNase J (RnJ). To date, however, nothing is known about this process in the diphtheria-causative pathogen Corynebacterium diphtheriae, nor is known the identity of this ribonuclease in this organism. Here, we report that C. diphtheriae DIP1463 encodes a predicted RnJ homolog, comprised of a conserved N-terminal β-lactamase domain, followed by β-CASP and C-terminal domains. A recombinant protein encompassing the β-lactamase domain alone displays 5′-exoribonuclease activity, which is abolished by alanine-substitution of the conserved catalytic residues His¹⁸⁶ and His¹⁸⁸. Intriguingly, deletion of DIP1463/rnj in C. diphtheriae reduces bacterial growth and generates cell shape abnormality with markedly augmented cell width. Comparative RNA-seq analysis revealed that RnJ controls a large regulon encoding many factors predicted to be involved in biosynthesis, regulation, transport, and iron acquisition. One upregulated gene in the ∆rnj mutant is ftsH, coding for a membrane protease (FtsH) involved in cell division, whose overexpression in the wild-type strain also caused cell-width augmentation. Critically, the ∆rnj mutant is severely attenuated in virulence in a Caenorhabditis elegans model of infection, while the FtsH-overexpressing and toxin-less strains exhibit full virulence as the wild-type strain. Evidently, RNase J is a key ribonuclease in C. diphtheriae that post-transcriptionally influences the expression of numerous factors vital to corynebacterial cell physiology and virulence. Our findings have significant implications for basic biological processes and mechanisms of corynebacterial pathogenesis. Full article

(This article belongs to the Special Issue Genetics and Physiology of Corynebacteria)

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15 pages, 616 KiB

Open AccessArticle

Improved Plasmid-Based Inducible and Constitutive Gene Expression in Corynebacterium glutamicum

by Nadja A. Henke, Irene Krahn and Volker F. Wendisch

Microorganisms 2021, 9(1), 204; https://doi.org/10.3390/microorganisms9010204 - 19 Jan 2021

Cited by 15 | Viewed by 5331

Abstract

Corynebacterium glutamicum has been safely used in white biotechnology for the last 60 years and the portfolio of new pathways and products is increasing rapidly. Hence, expression vectors play a central role in discovering endogenous gene functions and in establishing heterologous gene expression. In this work, new expression vectors were designed based on two strategies: (i) a library screening of constitutive native and synthetic promoters and (ii) an increase of the plasmid copy number. Both strategies were combined and resulted in a very strong expression and overproduction of the fluorescence protein GfpUV. As a second test case, the improved vector for constitutive expression was used to overexpress the endogenous xylulokinase gene xylB in a synthetic operon with xylose isomerase gene xylA from Xanthomonas campestris. The xylose isomerase activity in crude extracts was increased by about three-fold as compared to that of the parental vector. In terms of application, the improved vector for constitutive xylA and xylB expression was used for production of the N-methylated amino acid sarcosine from monomethylamine, acetate, and xylose. As a consequence, the volumetric productivity of sarcosine production was 50% higher as compared to that of the strain carrying the parental vector. Full article

(This article belongs to the Special Issue Genetics and Physiology of Corynebacteria)

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23 pages, 1882 KiB

Open AccessArticle

Physiological Response of Corynebacterium glutamicum to Indole

by Tatjana Walter, Kareen H. Veldmann, Susanne Götker, Tobias Busche, Christian Rückert, Arman Beyraghdar Kashkooli, Jannik Paulus, Katarina Cankar and Volker F. Wendisch

Microorganisms 2020, 8(12), 1945; https://doi.org/10.3390/microorganisms8121945 - 08 Dec 2020

Cited by 14 | Viewed by 4354

Abstract

The aromatic heterocyclic compound indole is widely spread in nature. Due to its floral odor indole finds application in dairy, flavor, and fragrance products. Indole is an inter- and intracellular signaling molecule influencing cell division, sporulation, or virulence in some bacteria that synthesize it from tryptophan by tryptophanase. Corynebacterium glutamicum that is used for the industrial production of amino acids including tryptophan lacks tryptophanase. To test if indole is metabolized by C. glutamicum or has a regulatory role, the physiological response to indole by this bacterium was studied. As shown by RNAseq analysis, indole, which inhibited growth at low concentrations, increased expression of genes involved in the metabolism of iron, copper, and aromatic compounds. In part, this may be due to iron reduction as indole was shown to reduce Fe³⁺ to Fe²⁺ in the culture medium. Mutants with improved tolerance to indole were selected by adaptive laboratory evolution. Among the mutations identified by genome sequencing, mutations in three transcriptional regulator genes were demonstrated to be causal for increased indole tolerance. These code for the regulator of iron homeostasis DtxR, the regulator of oxidative stress response RosR, and the hitherto uncharacterized Cg3388. Gel mobility shift analysis revealed that Cg3388 binds to the intergenic region between its own gene and the iolT2-rhcM2D2 operon encoding inositol uptake system IolT2, maleylacetate reductase, and catechol 1,2-dioxygenase. Increased RNA levels of rhcM2 in a cg3388 deletion strain indicated that Cg3388 acts as repressor. Indole, hydroquinone, and 1,2,4-trihydroxybenzene may function as inducers of the iolT2-rhcM2D2 operon in vivo as they interfered with DNA binding of Cg3388 at physiological concentrations in vitro. Cg3388 was named IhtR. Full article

(This article belongs to the Special Issue Genetics and Physiology of Corynebacteria)

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Review

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15 pages, 1248 KiB

Open AccessReview

Current Evidence for Corynebacterium on the Ocular Surface

by Takanori Aoki, Koji Kitazawa, Hideto Deguchi and Chie Sotozono

Microorganisms 2021, 9(2), 254; https://doi.org/10.3390/microorganisms9020254 - 27 Jan 2021

Cited by 19 | Viewed by 4568

Abstract

Corynebacterium species are commonly found in the conjunctiva of healthy adults and are recognized as non-pathogenic bacteria. In recent years, however, Corynebacterium species have been reported to be potentially pathogenic in various tissues. We investigated Corynebacterium species on the ocular surface and reviewed various species of Corynebacterium in terms of their antimicrobial susceptibility and the underlying molecular resistance mechanisms. We identified a risk for Corynebacterium-related ocular infections in patients with poor immunity, such as patients with diabetes or long-term users of topical steroids, and in those with corneal epithelial damage due to trauma, contact lens wear, lagophthalmos, and trichiasis. The predominant strain in the conjunctiva was C. macginleyi, and the species associated with keratitis and conjunctivitis were C. macginleyi, C. propinquum, C. mastitidis, C. pseudodiphtheriticum, C. accolens, C. striatum, C. xerosis, and C. bovis. Overall, Corynebacterium species present on the ocular surface were resistant to quinolones, whereas those in the nasal cavity were more susceptible. The prevalence of fluoroquinolone-resistant Corynebacterium has not changed in the past 10 years; however, Corynebacterium species remain susceptible to third-generation cephems. In conclusion, the use of third-generation cephems should be a reasonable and pragmatic approach for treatment of ocular infections caused by Corynebacterium species. Full article

(This article belongs to the Special Issue Genetics and Physiology of Corynebacteria)

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19 pages, 2870 KiB

Open AccessReview

Corynebacterium glutamicum Mechanosensing: From Osmoregulation to L-Glutamate Secretion for the Avian Microbiota-Gut-Brain Axis

by Yoshitaka Nakayama

Microorganisms 2021, 9(1), 201; https://doi.org/10.3390/microorganisms9010201 - 19 Jan 2021

Cited by 14 | Viewed by 6167

Abstract

After the discovery of Corynebacterium glutamicum from avian feces-contaminated soil, its enigmatic L-glutamate secretion by corynebacterial MscCG-type mechanosensitive channels has been utilized for industrial monosodium glutamate production. Bacterial mechanosensitive channels are activated directly by increased membrane tension upon hypoosmotic downshock; thus; the physiological significance of the corynebacterial L-glutamate secretion has been considered as adjusting turgor pressure by releasing cytoplasmic solutes. In this review, we present information that corynebacterial mechanosensitive channels have been evolutionally specialized as carriers to secrete L-glutamate into the surrounding environment in their habitats rather than osmotic safety valves. The lipid modulation activation of MscCG channels in L-glutamate production can be explained by the “Force-From-Lipids” and “Force-From-Tethers” mechanosensing paradigms and differs significantly from mechanical activation upon hypoosmotic shock. The review also provides information on the search for evidence that C. glutamicum was originally a gut bacterium in the avian host with the aim of understanding the physiological roles of corynebacterial mechanosensing. C. glutamicum is able to secrete L-glutamate by mechanosensitive channels in the gut microbiota and help the host brain function via the microbiota–gut–brain axis. Full article

(This article belongs to the Special Issue Genetics and Physiology of Corynebacteria)

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