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PloS One 2021Essential genes, which form the basis of life activities, are crucial for the survival of organisms. Essential genes tend to be located in operons, but how they are...
Essential genes, which form the basis of life activities, are crucial for the survival of organisms. Essential genes tend to be located in operons, but how they are distributed in operons is still unclear for most prokaryotes. In order to clarify the general rule of position preference of essential genes in operons, an index of the average position of genes in an operon was proposed, and the distributions of essential and non-essential genes in operons in 51 bacterial genomes and two archaeal genomes were analyzed based on this new index. Consequently, essential genes were found to preferentially occupy the front positions of the operons, which tend to be expressed at higher levels.
Topics: Archaea; Bacteria; Computational Biology; Databases, Genetic; Genes, Archaeal; Genes, Bacterial; Genes, Essential; Operon
PubMed: 33886641
DOI: 10.1371/journal.pone.0250380 -
Nucleic Acids Research Jan 2012The Prokaryotic Operon DataBase (ProOpDB, http://operons.ibt.unam.mx/OperonPredictor) constitutes one of the most precise and complete repositories of operon predictions...
The Prokaryotic Operon DataBase (ProOpDB, http://operons.ibt.unam.mx/OperonPredictor) constitutes one of the most precise and complete repositories of operon predictions now available. Using our novel and highly accurate operon identification algorithm, we have predicted the operon structures of more than 1200 prokaryotic genomes. ProOpDB offers diverse alternatives by which a set of operon predictions can be retrieved including: (i) organism name, (ii) metabolic pathways, as defined by the KEGG database, (iii) gene orthology, as defined by the COG database, (iv) conserved protein domains, as defined by the Pfam database, (v) reference gene and (vi) reference operon, among others. In order to limit the operon output to non-redundant organisms, ProOpDB offers an efficient method to select the most representative organisms based on a precompiled phylogenetic distances matrix. In addition, the ProOpDB operon predictions are used directly as the input data of our Gene Context Tool to visualize their genomic context and retrieve the sequence of their corresponding 5' regulatory regions, as well as the nucleotide or amino acid sequences of their genes.
Topics: Bacteria; Bacterial Proteins; Databases, Genetic; Internet; Metabolic Networks and Pathways; Operon; Phylogeny; Protein Structure, Tertiary
PubMed: 22096236
DOI: 10.1093/nar/gkr1020 -
Nucleic Acids Research Feb 2022Operons are a hallmark of the genomic and regulatory architecture of prokaryotes. However, the mechanism by which two genes placed far apart gradually come close and...
Operons are a hallmark of the genomic and regulatory architecture of prokaryotes. However, the mechanism by which two genes placed far apart gradually come close and form operons remains to be elucidated. Here, we propose a new model of the origin of operons: Mobile genetic elements called insertion sequences can facilitate the formation of operons by consecutive insertion-deletion-excision reactions. This mechanism barely leaves traces of insertion sequences and thus difficult to detect in nature. In this study, as a proof-of-concept, we reproducibly demonstrated operon formation in the laboratory. The insertion sequence IS3 and the insertion sequence excision enhancer are genes found in a broad range of bacterial species. We introduced these genes into insertion sequence-less Escherichia coli and found that, supporting our hypothesis, the activity of the two genes altered the expression of genes surrounding IS3, closed a 2.7 kb gap between a pair of genes, and formed new operons. This study shows how insertion sequences can facilitate the rapid formation of operons through locally increasing the structural mutation rates and highlights how coevolution with mobile elements may shape the organization of prokaryotic genomes and gene regulation.
Topics: Catalysis; DNA Transposable Elements; Escherichia coli; Operon; Prokaryotic Cells
PubMed: 35066585
DOI: 10.1093/nar/gkac004 -
Nucleic Acids Research Aug 2022Many bacteria use CRISPR-Cas systems to defend against invasive mobile genetic elements (MGEs). In response, MGEs have developed strategies to resist CRISPR-Cas,...
Many bacteria use CRISPR-Cas systems to defend against invasive mobile genetic elements (MGEs). In response, MGEs have developed strategies to resist CRISPR-Cas, including the use of anti-CRISPR (Acr) proteins. Known acr genes may be followed in an operon by a putative regulatory Acr-associated gene (aca), suggesting the importance of regulation. Although ten families of helix-turn-helix (HTH) motif containing Aca proteins have been identified (Aca1-10), only three have been tested and shown to be transcriptional repressors of acr-aca expression. The AcrIIA1 protein (a Cas9 inhibitor) also contains a functionally similar HTH containing repressor domain. Here, we identified and analysed Aca and AcrIIA1 homologs across all bacterial genomes. Using HMM models we found aca-like genes are widely distributed in bacteria, both with and without known acr genes. The putative promoter regions of acr-aca operons were analysed and members of each family of bacterial Aca tested for regulatory function. For each Aca family, we predicted a conserved inverted repeat binding site within a core promoter. Promoters containing these sites directed reporter expression in E. coli and were repressed by the cognate Aca protein. These data demonstrate that acr repression by Aca proteins is widely conserved in nature.
Topics: CRISPR-Associated Proteins; Escherichia coli; CRISPR-Cas Systems; Operon; Helix-Turn-Helix Motifs; Bacteria; Bacterial Proteins
PubMed: 35947749
DOI: 10.1093/nar/gkac674 -
In Silico Biology 2015In this review, we survey work that has been carried out in the attempts of biomathematicians to understand the dynamic behaviour of simple bacterial operons starting... (Review)
Review
In this review, we survey work that has been carried out in the attempts of biomathematicians to understand the dynamic behaviour of simple bacterial operons starting with the initial work of the 1960's. We concentrate on the simplest of situations, discussing both repressible and inducible systems and then turning to concrete examples related to the biology of the lactose and tryptophan operons. We conclude with a brief discussion of the role of both extrinsic noise and so-called intrinsic noise in the form of translational and/or transcriptional bursting.
Topics: Algorithms; Animals; Gene Expression Regulation; Gene Regulatory Networks; Humans; Models, Biological; Operon; Prokaryotic Cells
PubMed: 25402755
DOI: 10.3233/ISB-140463 -
The Veterinary Quarterly Dec 2019Mammalian cell entry () genes are the components of the operon and play a vital role in the entry of Mycobacteria into the mammalian cell and their survival within... (Review)
Review
Mammalian cell entry () genes are the components of the operon and play a vital role in the entry of Mycobacteria into the mammalian cell and their survival within phagocytes and epithelial cells. operons are present in the DNA of Mycobacteria and translate proteins associated with the invasion and long-term existence of these pathogens in macrophages. The exact mechanism of action of genes and their functions are not clear yet. However, with the loss of these genes Mycobacteria lose their pathogenicity. subspecies (MAP), the etiological agent of Johne's disease, is the cause of chronic enteritis of animals and significantly affects economic impact on the livestock industry. Since MAP is not inactivated during pasteurization, human population is continuously at the risk of getting exposed to MAP infection through consumption of dairy products. There is need for new candidate genes and/or proteins for developing improved diagnostic assays for the diagnosis of MAP infection and for the control of disease. Increasing evidences showed that expression of genes is important for the virulence of MAP. Whole-genome DNA microarray representing MAP revealed that there are 14 large sequence polymorphisms with LSPP12 being the most widely conserved MAPspecific region that included a cluster of six homologs of -family involved in lipid metabolism. On the other hand, LSP11 comprising part of 2 operon was absent in MAP isolates. This review summarizes the advancement of research on genes of Mycobacteria with special reference to the MAP infection.
Topics: Animals; Bacterial Proteins; Mycobacterium avium subsp. paratuberculosis; Operon; Paratuberculosis; Virulence
PubMed: 31282842
DOI: 10.1080/01652176.2019.1641764 -
Nucleic Acids Research Oct 2022CRISPR-Cas systems are adaptive immune systems in bacteria and archaea that provide resistance against phages and other mobile genetic elements. To fight against...
CRISPR-Cas systems are adaptive immune systems in bacteria and archaea that provide resistance against phages and other mobile genetic elements. To fight against CRISPR-Cas systems, phages and archaeal viruses encode anti-CRISPR (Acr) proteins that inhibit CRISPR-Cas systems. The expression of acr genes is controlled by anti-CRISPR-associated (Aca) proteins encoded within acr-aca operons. AcrIF24 is a recently identified Acr that inhibits the type I-F CRISPR-Cas system. Interestingly, AcrIF24 was predicted to be a dual-function Acr and Aca. Here, we elucidated the crystal structure of AcrIF24 from Pseudomonas aeruginosa and identified its operator sequence within the regulated acr-aca operon promoter. The structure of AcrIF24 has a novel domain composition, with wing, head and body domains. The body domain is responsible for recognition of promoter DNA for Aca regulatory activity. We also revealed that AcrIF24 directly bound to type I-F Cascade, specifically to Cas7 via its head domain as part of its Acr mechanism. Our results provide new molecular insights into the mechanism of a dual functional Acr-Aca protein.
Topics: CRISPR-Cas Systems; CRISPR-Associated Proteins; Bacteriophages; Pseudomonas aeruginosa; Operon
PubMed: 36243977
DOI: 10.1093/nar/gkac880 -
Biological Research Jul 2015Salmonella enterica serovar Typhi (S. Typhi) stg operon, encoding a chaperone/usher fimbria (CU), contributes to an increased adherence to human epithelial cells....
BACKGROUND
Salmonella enterica serovar Typhi (S. Typhi) stg operon, encoding a chaperone/usher fimbria (CU), contributes to an increased adherence to human epithelial cells. However, one report suggests that the presence of the Stg fimbria impairs the monocyte--bacteria association, as deduced by the lower level of invasion to macrophage-like cells observed when the stg fimbrial cluster was overexpressed. Nevertheless, since other CU fimbrial structures increase the entry of S. Typhi into macrophages, and considering that transcriptomic analyses revealed that stg operon is indeed expressed in macrophages, we reassessed the role of the stg operon in the interaction between S. Typhi strain STH2370 and human cells, including macrophage-like cells and mononuclear cells directly taken from human peripheral blood.
RESULTS
We compared S. Typhi STH2370 WT, a Chilean clinical strain, and the S. Typhi STH2370 Δstg mutant with respect to association and invasion using epithelial and macrophage-like cells. We observed that deletion of stg operon reduced the association and invasion of S. Typhi, in both cellular types. The presence of the cloned stg operon restored the WT phenotype in all the cases. Moreover, we compared Salmonella enterica sv. Typhimurium 14028s (S. Typhimurium, a serovar lacking stg operon) and S. Typhimurium heterologously expressing S. Typhi stg. We found that the latter presents an increased cell disruption of polarized epithelial cells and an increased association in both epithelial and macrophage-like cells.
CONCLUSIONS
S. Typhi stg operon encodes a functional adhesin that participates in the interaction bacteria-eukaryotic cells, including epithelial cells and macrophages-like cells. The phenotypes associated to stg operon include increased association and consequent invasion in bacteria-eukaryotic cells, and cell disruption.
Topics: Cell Adhesion; Epithelial Cells; Fimbriae, Bacterial; Humans; Macrophages; Operon; Salmonella typhi
PubMed: 26149381
DOI: 10.1186/s40659-015-0024-9 -
MBio Jun 2022What do programmed cell death (PCD) and carbohydrate metabolism by-product transport have in common? Intriguingly, both processes involve the and operons in the major...
What do programmed cell death (PCD) and carbohydrate metabolism by-product transport have in common? Intriguingly, both processes involve the and operons in the major human pathogen Staphylococcus aureus. Previously, CidA and LrgA have been studied in the context of programmed cell death, but a second function in overflow metabolism is increasingly evident. New work from J. L. Endres, S. S. Chaudhari, X. Zhang, J. Prahlad, et al. (mBio 13:e02827-21, 2022, https://doi.org/10.1128/mBio.02827-21) combining a lysis cassette, mutagenesis, and classic microbiology demonstrates that CidA and LrgA function as holins to support endolysin-induced lysis. But that's not all-the operon also facilitates pyruvate uptake during microaerobic and anaerobic growth. This commentary highlights the main findings from this work and places them in context of the literature to date. Finally, as these proteins are highly conserved and carry out disparate functions of great importance, it is tempting to speculate future work will elucidate the link between S. aureus lysis and pyruvate metabolism.
Topics: Apoptosis; Bacterial Proteins; Gene Expression Regulation, Bacterial; Humans; Operon; Pyruvates; Staphylococcus aureus
PubMed: 35608302
DOI: 10.1128/mbio.00761-22 -
Molecular Microbiology Jan 2021When Streptococcus mutans is transferred from a preferred carbohydrate (glucose or fructose) to lactose, initiation of growth can take several hours, and substantial...
When Streptococcus mutans is transferred from a preferred carbohydrate (glucose or fructose) to lactose, initiation of growth can take several hours, and substantial amounts of glucose are released during growth. Here, S. mutans strains UA159 and GS-5 were examined for stochastic behaviors in transcription of the lac operon. Using a gfp reporter fusion, we demonstrated that induction of the lac operon occurs in only a fraction of the population, with prior exposure to carbohydrate source and strain influencing the magniture of the sub-population response. Lower glucokinase activity in GS-5 was associated with release of substantially more glucose than UA159 and significantly lower lac expression. Mutants unable to use lactose grew on lactose as the sole carbohydrate when strains with an intact lac operon were also present in the cultures, indicative of the potential for population cheating. Utilizing a set of engineered obligate cheating and non-cheating strains, we confirmed that cheating can sustain a heterogeneous population. Futher, obligate cheaters of GS-5 competed well with the non-cheaters and showed a high degree of competitive fitness in a human-derived consortium biofilm model. The results show that bet-hedging behaviors in carbohydrate metabolism may substantially influence the composition and pathogenic potential of oral biofilms.
Topics: Biofilms; Carbohydrate Metabolism; Fructose; Gene Expression; Gene Expression Regulation, Bacterial; Glucose; Lac Operon; Lactose; Operon; Streptococcus mutans
PubMed: 32881164
DOI: 10.1111/mmi.14596