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Microbiology and Molecular Biology... Sep 2014The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme... (Review)
Review
The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme reductions of genomes, the last universal common ancestor (LUCA), the creation of semiartificial cells, and the design of protocells and chassis cells. Here we review these different areas of research and identify common and complementary aspects of each one. We focus on systems biology, a discipline that is greatly facilitating the classical top-down and bottom-up approaches toward minimal cells. In addition, we also review the so-called middle-out approach and its contributions to the field with mathematical and computational models. Owing to the advances in genomics technologies, much of the work in this area has been centered on minimal genomes, or rather minimal gene sets, required to sustain life. Nevertheless, a fundamental expansion has been taking place in the last few years wherein the minimal gene set is viewed as a backbone of a more complex system. Complementing genomics, progress is being made in understanding the system-wide properties at the levels of the transcriptome, proteome, and metabolome. Network modeling approaches are enabling the integration of these different omics data sets toward an understanding of the complex molecular pathways connecting genotype to phenotype. We review key concepts central to the mapping and modeling of this complexity, which is at the heart of research on minimal cells. Finally, we discuss the distinction between minimizing the number of cellular components and minimizing cellular complexity, toward an improved understanding and utilization of minimal and simpler cells.
Topics: Cyanobacteria; Genes, Bacterial; Genes, Essential; Genetic Engineering; Humans; Mycoplasma; Systems Biology
PubMed: 25184563
DOI: 10.1128/MMBR.00050-13 -
Veterinary Microbiology Aug 2015Bovine mycoplasmosis due to Mycoplasma bovis causes several important bovine diseases such as pneumonia, mastitis, arthritis, otitis, genital disorders or... (Review)
Review
Bovine mycoplasmosis due to Mycoplasma bovis causes several important bovine diseases such as pneumonia, mastitis, arthritis, otitis, genital disorders or keratoconjunctivitis. Variable surface lipoproteins, adhesion, invasion of host cells, modulation of the host immune system, biofilm formation and the release of secondary metabolites like hydrogen peroxide, as well as synergistic infections with other bacterial or viral pathogens are among the more significantly studied characteristics of the bacterium. The aim of this review is to summarize the current knowledge regarding the virulence of M. bovis and additionally, factors contributing to the dissemination and persistence of this pathogen in the bovine host will be discussed.
Topics: Animals; Cattle; Cattle Diseases; Mycoplasma Infections; Mycoplasma bovis; Virulence
PubMed: 25824130
DOI: 10.1016/j.vetmic.2015.02.024 -
The Journal of Molecular Diagnostics :... Nov 2023Bacterial commensals of the human genitourinary tract, Mycoplasma hominis and Ureaplasma species (parvum and urealyticum) can be sexually transmitted, and may cause...
Bacterial commensals of the human genitourinary tract, Mycoplasma hominis and Ureaplasma species (parvum and urealyticum) can be sexually transmitted, and may cause nongonococcal urethritis, pelvic inflammatory disease, and infertility. Mycoplasma hominis and Ureaplasma species may also cause severe invasive infections in immunocompromised patients. Current culture-based methods for Mycoplasma/Ureaplasma identification are costly and laborious, with a turnaround time between 1 and 2 weeks. We developed a high-throughput, real-time multiplex PCR assay for the rapid detection of M. hominis and Ureaplasma species in urine, genital swab, body fluid, and tissue. In total, 282 specimens were tested by PCR and compared with historic culture results; a molecular reference method was used to moderate discrepancies. Overall result agreement was 99% for M. hominis (97% positive percentage agreement and 100% negative percentage agreement) and 96% for Ureaplasma species (96% positive percentage agreement and 97% negative percentage agreement). Specimen stability was validated for up to 7 days at room temperature. This multiplex molecular assay was designed for implementation in a high-complexity clinical microbiology laboratory. With this method, >90 samples can be tested in one run, with a turnaround time of 4 to 5 hours from specimen extraction to reporting of results. This PCR test is also more labor effective and cheaper than the conventional culture-based test, thus improving laboratory efficiency and alleviating labor shortages.
Topics: Mycoplasma hominis; Humans; Ureaplasma; Multiplex Polymerase Chain Reaction; Real-Time Polymerase Chain Reaction; Ureaplasma Infections; Mycoplasma Infections; Sensitivity and Specificity; High-Throughput Screening Assays; DNA, Bacterial; Reproducibility of Results
PubMed: 37683891
DOI: 10.1016/j.jmoldx.2023.07.004 -
Virulence Dec 2021Mycoplasmas, the smallest bacteria lacking a cell wall, can cause various diseases in both humans and animals. Mycoplasmas harbor a variety of virulence factors that... (Review)
Review
Mycoplasmas, the smallest bacteria lacking a cell wall, can cause various diseases in both humans and animals. Mycoplasmas harbor a variety of virulence factors that enable them to overcome numerous barriers of entry into the host; using accessory proteins, mycoplasma adhesins can bind to the receptors or extracellular matrix of the host cell. Although the host immune system can eradicate the invading mycoplasma in most cases, a few sagacious mycoplasmas employ a series of invasion and immune escape strategies to ensure their continued survival within their hosts. For instance, capsular polysaccharides are crucial for anti-phagocytosis and immunomodulation. Invasive enzymes degrade reactive oxygen species, neutrophil extracellular traps, and immunoglobulins. Biofilm formation is important for establishing a persistent infection. During proliferation, successfully surviving mycoplasmas generate numerous metabolites, including hydrogen peroxide, ammonia and hydrogen sulfide; or secrete various exotoxins, such as community-acquired respiratory distress syndrome toxin, and hemolysins; and express various pathogenic enzymes, all of which have potent toxic effects on host cells. Furthermore, some inherent components of mycoplasmas, such as lipids, membrane lipoproteins, and even mycoplasma-generated superantigens, can exert a significant pathogenic impact on the host cells or the immune system. In this review, we describe the proposed virulence factors in the toolkit of notorious mycoplasmas to better understand the pathogenic features of these bacteria, along with their pathogenic mechanisms.
Topics: Animals; Biofilms; Host-Pathogen Interactions; Humans; Mice; Mycoplasma; Phagocytosis; Virulence; Virulence Factors
PubMed: 33704021
DOI: 10.1080/21505594.2021.1889813 -
Genes & Genomics Nov 2021The Gram-negative intracellular bacterium Mycoplasma anatis is a pathogen of respiratory infectious diseases in ducks and has caused significant economic losses in the...
BACKGROUND
The Gram-negative intracellular bacterium Mycoplasma anatis is a pathogen of respiratory infectious diseases in ducks and has caused significant economic losses in the poultry industry.
OBJECTIVE
This study, as the first report of the structure and function of the pan-genome of Mycoplasma anatis, may provide a valuable genetic basis for many aspects of future research on the pathogens of waterfowl.
METHODS
We sequenced the whole genomes of 15 Mycoplasma anatis isolated from ducks in China. Draft genome sequencing was carried out and whole-genome sequencing was performed by the sequencers of the PacBio Sequel and an IonTorrent Personal Genome Machine (PGM). Then the common genic elements of protein-coding genes, tRNAs, and rRNAs of Mycoplasma anatis genomes were predicted by using the pipeline Prokka v1.13.7. To investigate homologous protein clusters across Mycoplasma anatis genomes, we adopted Roary v3.13.0 to cluster orthologous genes (OGs) based on the following criteria.
RESULTS
We obtained one complete genome and 14 genome sketches. Microbial mobile genetic element analysis revealed the distribution of insertion sequences (IS30, IS3, and IS1634), prophage regions, and CRISPR arrays in the genome of Mycoplasma anatis. Comparative genomic analysis decoded the genetic components and functional classification of the pan-genome of Mycoplasma anatis that comprised 646 core genes, 231 dispensable genes and among them 110 was strain-specific. Virulence-related gene profiles of Mycoplasma anatis were systematically identified, and the products of these genes included bacterial ABC transporter systems, iron transport proteins, toxins, and secretion systems.
CONCLUSION
A complete virulence-related gene profile of Mycoplasma anatis has been identified, most of the genes are highly conserved in all strains. Sequencing results are relevant to the molecular mechanisms of drug resistance, adaptive evolution of pathogens, population structure, and vaccine development.
Topics: Base Sequence; China; Comparative Genomic Hybridization; Genome, Bacterial; Molecular Sequence Annotation; Mycoplasma; Phylogeny; Prophages; Sequence Analysis, DNA; Vaccine Development; Virulence; Virulence Factors; Whole Genome Sequencing
PubMed: 34181213
DOI: 10.1007/s13258-021-01129-5 -
Veterinaria Italiana Nov 2022Testudo hermanni is included as near‑threatened in the Red List of the International Union for Conservation of Nature, while T. hermanni hermanni is considered...
Testudo hermanni is included as near‑threatened in the Red List of the International Union for Conservation of Nature, while T. hermanni hermanni is considered endangered in the Italian Red List. Appropriate management of smuggled or seized wild individuals is recommended before their reintroduction into the wild. Accordingly, a health monitoring study was carried out. During 2014‑2016, 133 oral swabs and 121 cloacal swabs were collected from a total of approximately 180 free‑ranging and rescued T. hermanni hermanni from eight different Italian regions to investigate the presence of DNA of Testudinid alphaherpesvirus (TeAHV), Chlamydia spp. and Mycoplasma spp. in the oral cavity, and Salmonella spp. isolates in the cloaca. Mycoplasma spp. was detected in 52 out of 87 (59.77%) of rescued and in 1 out of 46 free‑ranging (2.17%) individuals; 33 out of 53 (62.26%) Mycoplasma spp. positive samples were typed as M. agassizii by PCR. Salmonella spp. was isolated from 45 out of 121 (37.19%) cloacal swabs, typed into 14 serovars, and characterized for complete antimicrobial susceptibility. A significantly different distribution of Salmonella spp. isolates was found in 2016 in comparison with 2014 and 2015, without any difference between free‑ranging and rescued tortoises. All the tested tortoises were negative for TeAHV and Chlamydia spp. These results are considered a baseline information critical to monitor the dynamics of these microorganisms in free‑ranging and rescued populations of T. h. hermanni, and to correctly approach the management of rescued animals and possible relocation programs.
Topics: Animals; Mycoplasma; Turtles; Salmonella; Chlamydia; Italy
PubMed: 36398674
DOI: 10.12834/VetIt.1915.13833.1 -
Science (New York, N.Y.) Jul 2020Structural biology studies performed inside cells can capture molecular machines in action within their native context. In this work, we developed an integrative in-cell...
Structural biology studies performed inside cells can capture molecular machines in action within their native context. In this work, we developed an integrative in-cell structural approach using the genome-reduced human pathogen We combined whole-cell cross-linking mass spectrometry, cellular cryo-electron tomography, and integrative modeling to determine an in-cell architecture of a transcribing and translating expressome at subnanometer resolution. The expressome comprises RNA polymerase (RNAP), the ribosome, and the transcription elongation factors NusG and NusA. We pinpointed NusA at the interface between a NusG-bound elongating RNAP and the ribosome and propose that it can mediate transcription-translation coupling. Translation inhibition dissociated the expressome, whereas transcription inhibition stalled and rearranged it. Thus, the active expressome architecture requires both translation and transcription elongation within the cell.
Topics: Bacterial Proteins; DNA-Directed RNA Polymerases; Genome, Bacterial; Humans; Mycoplasma pneumoniae; Peptide Chain Elongation, Translational; Peptide Elongation Factors; Protein Interaction Maps; Ribosomes; Transcription, Genetic; Transcriptome
PubMed: 32732422
DOI: 10.1126/science.abb3758 -
Journal of Molecular Biology Jan 2022Building structural models of entire cells has been a long-standing cross-discipline challenge for the research community, as it requires an unprecedented level of...
Building structural models of entire cells has been a long-standing cross-discipline challenge for the research community, as it requires an unprecedented level of integration between multiple sources of biological data and enhanced methods for computational modeling and visualization. Here, we present the first 3D structural models of an entire Mycoplasma genitalium (MG) cell, built using the CellPACK suite of computational modeling tools. Our model recapitulates the data described in recent whole-cell system biology simulations and provides a structural representation for all MG proteins, DNA and RNA molecules, obtained by combining experimental and homology-modeled structures and lattice-based models of the genome. We establish a framework for gathering, curating and evaluating these structures, exposing current weaknesses of modeling methods and the boundaries of MG structural knowledge, and visualization methods to explore functional characteristics of the genome and proteome. We compare two approaches for data gathering, a manually-curated workflow and an automated workflow that uses homologous structures, both of which are appropriate for the analysis of mesoscale properties such as crowding and volume occupancy. Analysis of model quality provides estimates of the regularization that will be required when these models are used as starting points for atomic molecular dynamics simulations.
Topics: Bacteria; Computational Biology; Genome, Bacterial; Models, Structural; Molecular Dynamics Simulation; Mycoplasma; Mycoplasma genitalium; Proteome; Transcriptome
PubMed: 34774566
DOI: 10.1016/j.jmb.2021.167351 -
Clinical Microbiology Reviews Jan 2017The human Ureaplasma species are the most frequently isolated microorganisms from the amniotic fluid and placentae of women who deliver preterm and are also associated... (Review)
Review
The human Ureaplasma species are the most frequently isolated microorganisms from the amniotic fluid and placentae of women who deliver preterm and are also associated with spontaneous abortions or miscarriages, neonatal respiratory diseases, and chorioamnionitis. Despite the fact that these microorganisms have been habitually found within placentae of pregnancies with chorioamnionitis, the role of Ureaplasma species as a causative agent has not been satisfactorily explained. There is also controversy surrounding their role in disease, particularly as not all women infected with Ureaplasma spp. develop chorioamnionitis. In this review, we provide evidence that Ureaplasma spp. are associated with diseases of pregnancy and discuss recent findings which demonstrate that Ureaplasma spp. are associated with chorioamnionitis, regardless of gestational age at the time of delivery. Here, we also discuss the proposed major virulence factors of Ureaplasma spp., with a focus on the multiple-banded antigen (MBA), which may facilitate modulation/alteration of the host immune response and potentially explain why only subpopulations of infected women experience adverse pregnancy outcomes. The information presented within this review confirms that Ureaplasma spp. are not simply "innocent bystanders" in disease and highlights that these microorganisms are an often underestimated pathogen of pregnancy.
Topics: Chorioamnionitis; Female; Humans; Infant, Newborn; Obstetric Labor, Premature; Pregnancy; Ureaplasma; Ureaplasma Infections; Virulence Factors
PubMed: 27974410
DOI: 10.1128/CMR.00091-16 -
Emerging Infectious Diseases Oct 2017We evaluated isolates obtained from children with Mycoplasma pneumoniae infection throughout Japan during 2008-2015. The highest prevalence of macrolide-resistant M....
We evaluated isolates obtained from children with Mycoplasma pneumoniae infection throughout Japan during 2008-2015. The highest prevalence of macrolide-resistant M. pneumoniae was 81.6% in 2012, followed by 59.3% in 2014 and 43.6% in 2015. The prevalence of macrolide-resistant M. pneumoniae among children in Japan has decreased.
Topics: Adolescent; Anti-Bacterial Agents; Child; Child, Preschool; Drug Resistance, Bacterial; Female; Humans; Infant; Infant, Newborn; Japan; Macrolides; Male; Microbial Sensitivity Tests; Mutation Rate; Mycoplasma pneumoniae; Pneumonia, Mycoplasma; Prevalence; RNA, Ribosomal, 23S
PubMed: 28930026
DOI: 10.3201/eid2310.170106