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Mascarenhas Dos Santos AC, Julian AT, Liang P, Juárez O, Pombert JF. Telomere-to-Telomere genome assemblies of human-infecting Encephalitozoon species. BMC Genomics 2023; 24:237. [PMID: 37142951 PMCID: PMC10158259 DOI: 10.1186/s12864-023-09331-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Microsporidia are diverse spore forming, fungal-related obligate intracellular pathogens infecting a wide range of hosts. This diversity is reflected at the genome level with sizes varying by an order of magnitude, ranging from less than 3 Mb in Encephalitozoon species (the smallest known in eukaryotes) to more than 50 Mb in Edhazardia spp. As a paradigm of genome reduction in eukaryotes, the small Encephalitozoon genomes have attracted much attention with investigations revealing gene dense, repeat- and intron-poor genomes characterized by a thorough pruning of molecular functions no longer relevant to their obligate intracellular lifestyle. However, because no Encephalitozoon genome has been sequenced from telomere-to-telomere and since no methylation data is available for these species, our understanding of their overall genetic and epigenetic architectures is incomplete. METHODS In this study, we sequenced the complete genomes from telomere-to-telomere of three human-infecting Encephalitozoon spp. -E. intestinalis ATCC 50506, E. hellem ATCC 50604 and E. cuniculi ATCC 50602- using short and long read platforms and leveraged the data generated as part of the sequencing process to investigate the presence of epigenetic markers in these genomes. We also used a mixture of sequence- and structure-based computational approaches, including protein structure prediction, to help identify which Encephalitozoon proteins are involved in telomere maintenance, epigenetic regulation, and heterochromatin formation. RESULTS The Encephalitozoon chromosomes were found capped by TTAGG 5-mer telomeric repeats followed by telomere associated repeat elements (TAREs) flanking hypermethylated ribosomal RNA (rRNA) gene loci featuring 5-methylcytosines (5mC) and 5-hemimethylcytosines (5hmC), themselves followed by lesser methylated subtelomeres and hypomethylated chromosome cores. Strong nucleotide biases were identified between the telomeres/subtelomeres and chromosome cores with significant changes in GC/AT, GT/AC and GA/CT contents. The presence of several genes coding for proteins essential to telomere maintenance, epigenetic regulation, and heterochromatin formation was further confirmed in the Encephalitozoon genomes. CONCLUSION Altogether, our results strongly support the subtelomeres as sites of heterochromatin formation in Encephalitozoon genomes and further suggest that these species might shutdown their energy-consuming ribosomal machinery while dormant as spores by silencing of the rRNA genes using both 5mC/5hmC methylation and facultative heterochromatin formation at these loci.
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Affiliation(s)
| | | | - Pingdong Liang
- Department of Biology, Illinois Institute of Technology, Chicago, IL, USA
| | - Oscar Juárez
- Department of Biology, Illinois Institute of Technology, Chicago, IL, USA
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MraZ Transcriptionally Controls the Critical Level of FtsL Required for Focusing Z-Rings and Kickstarting Septation in Bacillus subtilis. J Bacteriol 2022; 204:e0024322. [PMID: 35943250 PMCID: PMC9487581 DOI: 10.1128/jb.00243-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial division and cell wall (dcw) cluster is a highly conserved region of the genome which encodes several essential cell division factors, including the central divisome protein FtsZ. Understanding the regulation of this region is key to our overall understanding of the division process. mraZ is found at the 5' end of the dcw cluster, and previous studies have described MraZ as a sequence-specific DNA binding protein. In this article, we investigate MraZ to elucidate its role in Bacillus subtilis. Through our investigation, we demonstrate that increased levels of MraZ result in lethal filamentation due to repression of its own operon (mraZ-mraW-ftsL-pbpB). We observed rescue of filamentation upon decoupling ftsL expression, but not other genes in the operon, from MraZ control. Our data suggest that regulation of the mra operon may be an alternative way for cells to quickly arrest cytokinesis, potentially during entry into the stationary phase and in the event of DNA replication arrest. Furthermore, through time-lapse microscopy, we were able to identify that overexpression of mraZ or depletion of FtsL results in decondensation of the FtsZ ring (Z-ring). Using fluorescent d-amino acid labeling, we also observed that coordinated peptidoglycan insertion at the division site is dysregulated in the absence of FtsL. Thus, we reveal that the precise role of FtsL is in Z-ring maturation and focusing septal peptidoglycan synthesis. IMPORTANCE MraZ is a highly conserved protein found in a diverse range of bacteria, including genome-reduced Mycoplasma. We investigated the role of MraZ in Bacillus subtilis and found that overproduction of MraZ is toxic due to cell division inhibition. Upon further analysis, we observed that MraZ is a repressor of its own operon, which includes genes that encode the essential cell division factors FtsL and PBP2B. We noted that decoupling of ftsL alone was sufficient to abolish MraZ-mediated cell division inhibition. Using time-lapse microscopy, we showed that under conditions where the FtsL level is depleted, the cell division machinery is unable to initiate cytokinesis. Thus, our results pinpoint that the precise role of FtsL is in concentrating septal cell wall synthesis to facilitate cell division.
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Sun H, Wang M, Liu Y, Wu P, Yao T, Yang W, Yang Q, Yan J, Yang B. Regulation of flagellar motility and biosynthesis in enterohemorrhagic Escherichia coli O157:H7. Gut Microbes 2022; 14:2110822. [PMID: 35971812 PMCID: PMC9387321 DOI: 10.1080/19490976.2022.2110822] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
ABSTARCTEnterohemorrhagic Escherichia coli (EHEC) O157:H7 is a human pathogen that causes a variety of diseases, such as hemorrhagic colitis and lethal hemolytic uremic syndrome. Flagellum-dependent motility plays diverse roles in the pathogenesis of EHEC O157:H7, including its migration to an optimal host site, adherence and colonization, survival at the infection site, and post-infection dispersal. However, it is very expensive for cellular economy in terms of the number of genes and the energy required for flagellar biosynthesis and functioning. Furthermore, the flagellar filament bears strong antigenic properties that induce a strong host immune response. Consequently, the flagellar gene expression and biosynthesis are highly regulated to occur at the appropriate time and place by different regulatory influences. The present review focuses on the regulatory mechanisms of EHEC O157:H7 motility and flagellar biosynthesis, especially in terms of flagellar gene regulation by environmental factors, regulatory proteins, and small regulatory RNAs.
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Affiliation(s)
- Hongmin Sun
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Min Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Yutao Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Pan Wu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Ting Yao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Wen Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Qian Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Jun Yan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Bin Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China,CONTACT Bin Yang TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin300457, P. R. China
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Zhang S, Ma X, Yu H, Lu X, Liu J, Zhang L, Wang G, Ye J, Ning G. Silver(I) metal-organic framework-embedded polylactic acid electrospun fibrous membranes for efficient inhibition of bacteria. Dalton Trans 2022; 51:6673-6681. [PMID: 35411886 DOI: 10.1039/d1dt04234c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
With recent outbreaks of fatal strains of diseases and the emergency of antibiotic resistance, there is a pressing demand to discover bactericidal materials that can effectively reduce or prevent infections by pathogenic bacteria. Herein, silver(I) metal organic frameworks Ag2(HBTC) were embedded into biocompatible polylactic acid (PLA) fibrous membranes through an electrospinning process as an antibiotic-free material for effective bacterial killing. The as-synthesized Ag2(HBTC)/PLA composite membrane showed an inactivation efficiency of more than 99.9% against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) at a concentration of 200-250 mg L-1. Mechanistic investigation indicated that the steady release of Ag+ ions and ˙OH generation from the composites contributed to the efficient antibacterial activities through irreversible damage to the bacterial cell membranes. In-depth proteomic analysis demonstrated that Ag2(HBTC)/PLA exerted a biological effect towards bacterial cells through down-regulating functional proteins, thereby destroying the central biochemical pathways of the cellular energy metabolism process, reducing resistance to oxidative damage and inhibiting cell division. In general, this study shows a promising perspective on designing MOF/PLA membranes with broad-spectrum disinfection capability for potential environmental sterilization and public healthcare protection.
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Affiliation(s)
- Siqi Zhang
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning, 116024, PR China
| | - Xiao Ma
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning, 116024, PR China
| | - Hailong Yu
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning, 116024, PR China
| | - Xinyi Lu
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning, 116024, PR China.,CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China.
| | - Jianhui Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China.
| | - Lihua Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China.
| | - Guangyao Wang
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning, 116024, PR China
| | - Junwei Ye
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning, 116024, PR China
| | - Guiling Ning
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning, 116024, PR China
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Comparative Analysis of Three Bradyrhizobium diazoefficiens Genomes Show Specific Mutations Acquired during Selection for a Higher Motility Phenotype and Adaption to Laboratory Conditions. Microbiol Spectr 2021; 9:e0056921. [PMID: 34762518 PMCID: PMC8585493 DOI: 10.1128/spectrum.00569-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial genomes are being extensively studied using next-generation sequencing technologies in order to understand the changes that occur under different selection regimes. In this work, the number and type of mutations that have occurred in three Bradyrhizobium diazoefficiens USDA 110T strains under laboratory conditions and during selection for a more motile phenotypic variant were analyzed. Most of the mutations found in both processes consisted of single nucleotide polymorphisms, single nucleotide deletions or insertions. In the case of adaptation to laboratory conditions, half of the changes occurred within intergenic regions, and around 80% were insertions. When the more motile phenotypic variant was evaluated, eight single nucleotide polymorphisms and an 11-bp deletion were found, although none of them was directly related to known motility or chemotaxis genes. Two mutants were constructed to evaluate the 11-bp deletion affecting the alpha subunit of 2-oxoacid:acceptor oxidoreductase (AAV28_RS30705-blr6743). The results showed that this single deletion was not responsible for the enhanced motility phenotype. IMPORTANCE The genetic and genomic changes that occur under laboratory conditions in Bradyrhizobium diazoefficiens genomes remain poorly studied. Only a few genome sequences of this important nitrogen-fixing species are available, and there are no genome-wide comparative analyses of related strains. In the present work, we sequenced and compared the genomes of strains derived from a parent strain, B. diazoefficiens USDA 110, that has undergone processes of repeated culture in the laboratory environment, or phenotypic selection toward antibiotic resistance and enhanced motility. Our results represent the first analysis in B. diazoefficiens that provides insights into the specific mutations that are acquired during these processes.
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Martínez-Torró C, Torres-Puig S, Marcos-Silva M, Huguet-Ramón M, Muñoz-Navarro C, Lluch-Senar M, Serrano L, Querol E, Piñol J, Pich OQ. Functional Characterization of the Cell Division Gene Cluster of the Wall-less Bacterium Mycoplasma genitalium. Front Microbiol 2021; 12:695572. [PMID: 34589065 PMCID: PMC8475190 DOI: 10.3389/fmicb.2021.695572] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/10/2021] [Indexed: 12/03/2022] Open
Abstract
It is well-established that FtsZ drives peptidoglycan synthesis at the division site in walled bacteria. However, the function and conservation of FtsZ in wall-less prokaryotes such as mycoplasmas are less clear. In the genome-reduced bacterium Mycoplasma genitalium, the cell division gene cluster is limited to four genes: mraZ, mraW, MG_223, and ftsZ. In a previous study, we demonstrated that ftsZ was dispensable for growth of M. genitalium under laboratory culture conditions. Herein, we show that the entire cell division gene cluster of M. genitalium is non-essential for growth in vitro. Our analyses indicate that loss of the mraZ gene alone is more detrimental for growth of M. genitalium than deletion of ftsZ or the entire cell division gene cluster. Transcriptional analysis revealed a marked upregulation of ftsZ in the mraZ mutant. Stable isotope labeling by amino acids in cell culture (SILAC)-based proteomics confirmed the overexpression of FtsZ in MraZ-deprived cells. Of note, we found that ftsZ expression was upregulated in non-adherent cells of M. genitalium, which arise spontaneously at relatively high rates. Single cell analysis using fluorescent markers showed that FtsZ localization varied throughout the cell cycle of M. genitalium in a coordinated manner with the chromosome and the terminal organelle (TMO). In addition, our results indicate a possible role for the RNA methyltransferase MraW in the regulation of FtsZ expression at the post-transcriptional level. Altogether, this study provides an extensive characterization of the cell division gene cluster of M. genitalium and demonstrates the existence of regulatory elements controlling FtsZ expression at the temporal and spatial level in mycoplasmas.
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Affiliation(s)
- Carlos Martínez-Torró
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sergi Torres-Puig
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marina Marcos-Silva
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marta Huguet-Ramón
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Carmen Muñoz-Navarro
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Enrique Querol
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jaume Piñol
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Oscar Q. Pich
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Institut d’Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, Sabadell, Spain
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Critical discovery and synthesis of novel antibacterial and resistance-modifying agents inspired by plant phytochemical defense mechanisms. Chem Biol Interact 2020; 333:109318. [PMID: 33186599 DOI: 10.1016/j.cbi.2020.109318] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/17/2020] [Accepted: 11/06/2020] [Indexed: 01/19/2023]
Abstract
Antimicrobial resistance is at increasing risk worldwide since it is threatening the ability to control common infectious diseases, resulting in prolonged illness, disability, and death. Herein, we inspired by the effective plant phytochemical mechanisms evolved to overcome microbial pathogenesis and evolved resistance. Cuminaldehyde is previously reported as the main antibacterial component in Calligonum comosum essential oil. The toxicity of cuminaldehyde limits its medical application for human use. On the other hand, compared to cuminaldehyde, the plant total extract showed similar antibacterial activities, while maintained lower toxicity, although it contains 22 times less cuminaldehyde. Thus, we assumed that other components in the plant extracts specifically affect bacteria but not mammalian cells. Bioassay-guided fractionations combined with comparative metabolomics analysis of different plant extracts were employed. The results revealed the presence of bacterial species-specific phytochemicals. Cinnamyl linoleate and linoleic acid enhanced the antibacterial activities of cuminaldehyde and ampicillin against S. aureus including MRSA, while decanal and cinnamyl linoleate enhanced the activities against E. coli. Computational modeling and enzyme inhibition assays indicated that cinnamyl linoleate selectively bind to bacterial ribosomal RNA methyltransferase, an important enzyme involved in the virulence and resistance of multidrug resistant bacteria. The results obtained can be employed for the future preparation of pharmaceutical formula containing cinnamyl linoleate in order to overcome evolved multidrug resistance behaviors by microbes.
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