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Genetics and Genomics of Metabolism in Microorganisms
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Genetics and Genomics of Metabolism in Microorganisms

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (20 April 2021) | Viewed by 20847

Special Issue Editors

Dr. Dariusz Dziga

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Guest Editor
Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology,Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
Interests: toxic cyanobacteria; cyanotoxin biodegradation; cyanophages; physiology of cyanobacteria
Special Issues, Collections and Topics in MDPI journals
Dr. Benedykt Wladyka

E-Mail Website
Guest Editor
Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30387 Kraków, Poland
Interests: toxin–antitoxin systems; staphylococcal virulence; regulation of gene expression in bacteria

Special Issue Information

Dear Colleagues,

Microorganisms are a dominating form of life on Earth, found in virtually every environment. This dominance is achieved by the exceptional variety and plasticity of their genomes and gene expression mechanisms. In addition to basic metabolism, microorganisms are able to synthesize and/or degrade sophisticated molecules, such as toxins, antibiotics, and dyes. Many of these molecules play a crucial role in their interactions with the environment, as well as communication with other (micro)organisms. The growing availability of next-generation sequencing allows for tracking genetic bases of metabolisms not only in a single microbial cell, but also in whole communities. Genome-wide analysis provides information on evolutionary traits of microorganisms and the possible modes of life of the unculturable ones. Moreover, transcriptional profiling, which links genotype with phenotype, opens new avenues for studying networks of gene expression and the molecular mechanisms driving them. This Special Issue intends to address genes as a “cookbook” of microbial metabolism, providing an overview of recent developments in the field and their future implications in basic and environmental microbiology, as well as biotechnology. Particular attention is paid to metagenomic and metatranscriptomic diversity, the regulation of microbial transcriptomes by environmental factors and genetic bases, and the transcriptional regulation of synthesis/degradation of products by microorganisms.

Dr. Dariusz Dziga
Dr. Benedykt Wladyka
Guest Editors

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Keywords

  • Metagenomic and metatranscriptomic diversity
  • Gene expression in microbes
  • Regulation of microbial transcriptomes
  • Genetic bases of microbial metabolism

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Published Papers (7 papers)

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Research

18 pages, 1826 KiB  
Article
Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics
by Sigitas Šulčius, Gediminas Alzbutas, Viktorija Juknevičiūtė, Eugenijus Šimoliūnas, Petras Venckus, Monika Šimoliūnienė and Ričardas Paškauskas
Genes 2021, 12(6), 886; https://doi.org/10.3390/genes12060886 - 8 Jun 2021
Cited by 5 | Viewed by 3382
Abstract
Little is known about the diversity and distribution of viruses infecting green sulfur bacteria (GSB) thriving in euxinic (sulfuric and anoxic) habitats, including gypsum karst lake ecosystems. In this study, we used targeted cell sorting combined with single-cell sequencing to gain insights into [...] Read more.
Little is known about the diversity and distribution of viruses infecting green sulfur bacteria (GSB) thriving in euxinic (sulfuric and anoxic) habitats, including gypsum karst lake ecosystems. In this study, we used targeted cell sorting combined with single-cell sequencing to gain insights into the gene content and genomic potential of viruses infecting sulfur-oxidizing bacteria Chlorobium clathratiforme, obtained from water samples collected during summer stratification in gypsum karst Lake Kirkilai (Lithuania). In total, 82 viral contigs were bioinformatically identified in 62 single amplified genomes (SAGs) of C. clathratiforme. The majority of viral gene and protein sequences showed little to no similarity with phage sequences in public databases, uncovering the vast diversity of previously undescribed GSB viruses. We observed a high level of lysogenization in the C. clathratiforme population, as 87% SAGs contained intact prophages. Among the thirty identified auxiliary metabolic genes (AMGs), two, thiosulfate sulfurtransferase (TST) and thioredoxin-dependent phosphoadenosine phosphosulfate (PAPS) reductase (cysH), were found to be involved in the oxidation of inorganic sulfur compounds, suggesting that viruses can influence the metabolism and cycling of this essential element. Finally, the analysis of CRISPR spacers retrieved from the consensus C. clathratiforme genome imply persistent and active virus–host interactions for several putative phages prevalent among C. clathratiforme SAGs. Overall, this study provides a glimpse into the diversity of phages associated with naturally occurring and highly abundant sulfur-oxidizing bacteria. Full article
(This article belongs to the Special Issue Genetics and Genomics of Metabolism in Microorganisms)
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14 pages, 1571 KiB  
Article
Are Bacterio- and Phytoplankton Community Compositions Related in Lakes Differing in Their Cyanobacteria Contribution and Physico-Chemical Properties?
by Mikołaj Kokociński, Dariusz Dziga, Adam Antosiak and Janne Soininen
Genes 2021, 12(6), 855; https://doi.org/10.3390/genes12060855 - 2 Jun 2021
Cited by 6 | Viewed by 2567
Abstract
Bacterioplankton community composition has become the center of research attention in recent years. Bacteria associated with toxic cyanobacteria blooms have attracted considerable interest. However, little is known about the environmental factors driving the bacteria community, including the impact of invasive cyanobacteria. Therefore, our [...] Read more.
Bacterioplankton community composition has become the center of research attention in recent years. Bacteria associated with toxic cyanobacteria blooms have attracted considerable interest. However, little is known about the environmental factors driving the bacteria community, including the impact of invasive cyanobacteria. Therefore, our aim has been to determine the relationships between heterotrophic bacteria and phytoplankton community composition across 24 Polish lakes with different contributions of cyanobacteria including the invasive species Raphidiopsis raciborskii. This analysis revealed that cyanobacteria were present in 16 lakes, while R. raciborskii occurred in 14 lakes. Our results show that bacteria communities differed between lakes dominated by cyanobacteria and lakes with minor contributions of cyanobacteria but did not differ between lakes with R. raciborskii and other lakes. Physical factors, including water and Secchi depth, were the major drivers of bacteria and phytoplankton community composition. However, in lakes dominated by cyanobacteria, bacterial community composition was also influenced by biotic factors such as the amount of R. raciborskii, chlorophyll-a and total phytoplankton biomass. Thus, our study provides novel evidence on the influence of environmental factors and R. raciborskii on lake bacteria communities. Full article
(This article belongs to the Special Issue Genetics and Genomics of Metabolism in Microorganisms)
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19 pages, 783 KiB  
Article
Impacts of the Type I Toxin–Antitoxin System, SprG1/SprF1, on Staphylococcus aureus Gene Expression
by Kinga Chlebicka, Emilia Bonar, Piotr Suder, Emeline Ostyn, Brice Felden, Benedykt Wladyka and Marie-Laure Pinel-Marie
Genes 2021, 12(5), 770; https://doi.org/10.3390/genes12050770 - 18 May 2021
Cited by 3 | Viewed by 2970
Abstract
Type I toxin–antitoxin (TA) systems are widespread genetic modules in bacterial genomes. They express toxic peptides whose overexpression leads to growth arrest or cell death, whereas antitoxins regulate the expression of toxins, acting as labile antisense RNAs. The Staphylococcus aureus (S. aureus [...] Read more.
Type I toxin–antitoxin (TA) systems are widespread genetic modules in bacterial genomes. They express toxic peptides whose overexpression leads to growth arrest or cell death, whereas antitoxins regulate the expression of toxins, acting as labile antisense RNAs. The Staphylococcus aureus (S. aureus) genome contains and expresses several functional type I TA systems, but their biological functions remain unclear. Here, we addressed and challenged experimentally, by proteomics, if the type I TA system, the SprG1/SprF1 pair, influences the overall gene expression in S. aureus. Deleted and complemented S. aureus strains were analyzed for their proteomes, both intracellular and extracellular, during growth. Comparison of intracellular proteomes among the strains points to the SprF1 antitoxin as moderately downregulating protein expression. In the strain naturally expressing the SprG1 toxin, cytoplasmic proteins are excreted into the medium, but this is not due to unspecific cell leakages. Such a toxin-driven release of the cytoplasmic proteins may modulate the host inflammatory response that, in turn, could amplify the S. aureus infection spread. Full article
(This article belongs to the Special Issue Genetics and Genomics of Metabolism in Microorganisms)
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14 pages, 1620 KiB  
Article
ATP-Dependent Ligases and AEP Primases Affect the Profile and Frequency of Mutations in Mycobacteria under Oxidative Stress
by Anna Brzostek, Filip Gąsior, Jakub Lach, Lidia Żukowska, Ewelina Lechowicz, Małgorzata Korycka-Machała, Dominik Strapagiel and Jarosław Dziadek
Genes 2021, 12(4), 547; https://doi.org/10.3390/genes12040547 - 9 Apr 2021
Cited by 1 | Viewed by 2103
Abstract
The mycobacterial nonhomologous end-joining pathway (NHEJ) involved in double-strand break (DSB) repair consists of the multifunctional ATP-dependent ligase LigD and the DNA bridging protein Ku. The other ATP-dependent ligases LigC and AEP-primase PrimC are considered as backup in this process. The engagement of [...] Read more.
The mycobacterial nonhomologous end-joining pathway (NHEJ) involved in double-strand break (DSB) repair consists of the multifunctional ATP-dependent ligase LigD and the DNA bridging protein Ku. The other ATP-dependent ligases LigC and AEP-primase PrimC are considered as backup in this process. The engagement of LigD, LigC, and PrimC in the base excision repair (BER) process in mycobacteria has also been postulated. Here, we evaluated the sensitivity of Mycolicibacterium smegmatis mutants defective in the synthesis of Ku, Ku-LigD, and LigC1-LigC2-PrimC, as well as mutants deprived of all these proteins to oxidative and nitrosative stresses, with the most prominent effect observed in mutants defective in the synthesis of Ku protein. Mutants defective in the synthesis of LigD or PrimC/LigC presented a lower frequency of spontaneous mutations than the wild-type strain or the strain defective in the synthesis of Ku protein. As identified by whole-genome sequencing, the most frequent substitutions in all investigated strains were T→G and A→C. Double substitutions, as well as insertions of T or CG, were exclusively identified in the strains carrying functional Ku and LigD proteins. On the other hand, the inactivation of Ku/LigD increased the efficiency of the deletion of G in the mutant strain. Full article
(This article belongs to the Special Issue Genetics and Genomics of Metabolism in Microorganisms)
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13 pages, 2153 KiB  
Article
Identification of the Gene Responsible for Lignin-Derived Low-Molecular-Weight Compound Catabolism in Pseudomonas sp. Strain LLC-1
by Jun Hirose, Ryusei Tsukimata, Munetoshi Miyatake and Haruhiko Yokoi
Genes 2020, 11(12), 1416; https://doi.org/10.3390/genes11121416 - 27 Nov 2020
Cited by 4 | Viewed by 2331
Abstract
Pseudomonas sp. strain LLC-1 (NBRC 111237) is capable of degrading lignin-derived low-molecular-weight compounds (LLCs). The genes responsible for the catabolism of LLCs were characterized in this study using whole-genome sequencing. Despite the close phylogenetic relationship with Pseudomonas putida, strain LLC-1 lacked the [...] Read more.
Pseudomonas sp. strain LLC-1 (NBRC 111237) is capable of degrading lignin-derived low-molecular-weight compounds (LLCs). The genes responsible for the catabolism of LLCs were characterized in this study using whole-genome sequencing. Despite the close phylogenetic relationship with Pseudomonas putida, strain LLC-1 lacked the genes usually found in the P. putida genome, which included fer, encoding an enzyme for ferulic acid catabolism, and vdh encoding an NAD+-dependent aldehyde dehydrogenase specific for its catabolic intermediate, vanillin. Cloning and expression of the 8.5 kb locus adjacent to the van operon involved in vanillic acid catabolism revealed the bzf gene cluster, which is involved in benzoylformic acid catabolism. One of the structural genes identified, bzfC, expresses the enzyme (BzfC) having the ability to transform vanillin and syringaldehyde to corresponding acids, indicating that BzfC is a multifunctional enzyme that initiates oxidization of LLCs in strain LLC-1. Benzoylformic acid is a catabolic intermediate of (R,S)-mandelic acid in P. putida. Strain LLC-1 did not possess the genes for mandelic acid racemization and oxidation, suggesting that the function of benzoylformic acid catabolic enzymes is different from that in P. putida. Genome-wide characterization identified the bzf gene responsible for benzoylformate and vanillin catabolism in strain LLC-1, exhibiting a unique mode of dissimilation for biomass-derived aromatic compounds by this strain. Full article
(This article belongs to the Special Issue Genetics and Genomics of Metabolism in Microorganisms)
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16 pages, 1765 KiB  
Article
IurV, Encoded by ORF VCA0231, Is Involved in the Regulation of Iron Uptake Genes in Vibrio cholerae
by Bernardo Sachman-Ruiz, José Antonio Ibarra, Paulina Estrada-de los Santos, Alexia Torres Muñoz, Begoña Giménez, Juan Carlos Salazar and Víctor Antonio García-Angulo
Genes 2020, 11(10), 1184; https://doi.org/10.3390/genes11101184 - 12 Oct 2020
Cited by 3 | Viewed by 3033
Abstract
The pathogen Vibrio cholerae has multiple iron acquisition systems which allow bacteria to exploit a variety of iron sources across the different environments on which it thrives. The expression of such iron uptake systems is highly regulated, mainly by the master iron homeostasis [...] Read more.
The pathogen Vibrio cholerae has multiple iron acquisition systems which allow bacteria to exploit a variety of iron sources across the different environments on which it thrives. The expression of such iron uptake systems is highly regulated, mainly by the master iron homeostasis regulator Fur but also by other mechanisms. Recently, we documented that the expression of many of the iron-responsive genes is also modulated by riboflavin. Among them, the open reading frame VCA0231, repressed both by riboflavin and iron, encodes a putative transcriptional regulator of the AraC/XylS family. Nonetheless, the genes or functions affected by this factor are unknown. In the present study, a series of in silico analyses was performed in order to identify the putative functions associated with the product of VCA0231. The STRING database predicted many iron uptake genes as functional partners for the product of VCA0231. In addition, a genomic neighborhood analysis with the Enzyme Function Initiative tools detected many Pfam families involved in iron homeostasis genetically associated with VCA0231. Moreover, a phylogenetic tree showed that other AraC/XylS members known to regulate siderophore utilization in bacteria clustered together and the product of VCA0231 localized in this cluster. This suggested that the product of VCA0231, here named IurV, is involved in the regulation of iron uptake processes. RNAseq was performed to determine the transcriptional effects of a deletion in VCA0231. A total of 52 genes were overexpressed and 21 genes were downregulated in response to the iurV deletion. Among these, several iron uptake genes and other iron homeostasis-related genes were found. Six gene ontology (GO) functional terms were enriched in the upregulated genes, of which five were related to iron metabolism. The regulatory pattern observed in the transcriptomics of a subset of genes was independently confirmed by quantitative real time PCR analysis. The results indicate that IurV is a novel regulator of the AraC/XylS family involved in the repression of iron uptake genes. Whether this effect is direct or indirect remains to be determined. Full article
(This article belongs to the Special Issue Genetics and Genomics of Metabolism in Microorganisms)
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13 pages, 2058 KiB  
Article
The Role of Metabolites in the Link between DNA Replication and Central Carbon Metabolism in Escherichia coli
by Klaudyna Krause, Monika Maciąg-Dorszyńska, Anna Wosinski, Lidia Gaffke, Joanna Morcinek-Orłowska, Estera Rintz, Patrycja Bielańska, Agnieszka Szalewska-Pałasz, Georgi Muskhelishvili and Grzegorz Węgrzyn
Genes 2020, 11(4), 447; https://doi.org/10.3390/genes11040447 - 19 Apr 2020
Cited by 7 | Viewed by 3305
Abstract
A direct link between DNA replication regulation and central carbon metabolism (CCM) has been previously demonstrated in Bacillus subtilis and Escherichia coli, as effects of certain mutations in genes coding for replication proteins could be specifically suppressed by particular mutations in genes [...] Read more.
A direct link between DNA replication regulation and central carbon metabolism (CCM) has been previously demonstrated in Bacillus subtilis and Escherichia coli, as effects of certain mutations in genes coding for replication proteins could be specifically suppressed by particular mutations in genes encoding CCM enzymes. However, specific molecular mechanism(s) of this link remained unknown. In this report, we demonstrate that various CCM metabolites can suppress the effects of mutations in different replication genes of E. coli on bacterial growth, cell morphology, and nucleoid localization. This provides evidence that the CCM-replication link is mediated by metabolites rather than direct protein-protein interactions. On the other hand, action of metabolites on DNA replication appears indirect rather than based on direct influence on the replication machinery, as rate of DNA synthesis could not be corrected by metabolites in short-term experiments. This corroborates the recent discovery that in B. subtilis, there are multiple links connecting CCM to DNA replication initiation and elongation. Therefore, one may suggest that although different in detail, the molecular mechanisms of CCM-dependent regulation of DNA replication are similar in E. coli and B. subtilis, making this regulation an important and common constituent of the control of cell physiology in bacteria. Full article
(This article belongs to the Special Issue Genetics and Genomics of Metabolism in Microorganisms)
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