Mechanisms of Genetic Instability in Mollicutes (Mycoplasmas)

Mollicutes are unique microorganisms characterized by a great extent for the reduction in genetic material, which retained the capability of independent division on acellular nutrient media. Phenotypically mycoplasmas differed from other bacteria by their small size and lack of a cell wall (mollis, soft; cutis, skin). High dependence on metabolism components utilized in the cultivation medium and high metabolic plasticity due to the absence of many genome regulatory elements make mycoplasmas perfect parasites for cells of the eukaryotic origin. The ability of these microorganisms to pass through host cells and their assumed participation in AIDS activation facilitate the study of mycoplasma pathogenesis. Another important feature of mycoplasmas, which is expressed during their interaction with a macroorganism, is their ability to escape from the immune response of a host due to surface antigen variation. These adaptation capacities of mycoplasmas ensuring their life in various biological niches, given a limited genome and the direct metabolic dependence on an environment, cannot be adequately explained at present. In this review, we attempted to collect and systematize data that contribute to our understanding of the important feature of mycoplasmas, genetic instability, which may underlie many of their adaptive responses.     

Peculiar properties of mycoplasmas: The smallest self-replicating prokaryotes

Mycoplasmas are the smallest and simplest prokaryotes capable of self-replication, with information provided by a genome which may be as small as 600 kb, estimated to carry less than 500 genes. Keeping the number of structural elements, metabolic pathways and components of the protein synthesizing machinery to an essential minimum places mycoplasmas closest to the concept of 'minimum cells'. Mycoplasmas are, therefore, most adequate candidates for the complete deciphering of the machinery of a self-replicating organism, and studies towards this goal are already underway. Living as 'minimum cells' was made possible by adopting a parasitic mode of life, securing from the host the many nutrients which cannot be synthesized by the mycoplasmas themselves. When pathogenic, infections by mycoplasmas usually follow a chronic course, with host immune reactions playing an important role in symptom production. Recent studies on the possible association of mycoplasmas with rheumatoid arthritis and AIDS are reviewed.     

Effects of mycoplasma infection on the host organism response via p53/NF-κB signaling

Mycoplasmas are bacteria lacking the cell wall, which is the major characteristic of this taxonomic class (Mollicutes). Among bacteria, mycoplasmas possess the smallest genome known for free-living organisms. This feature limits the autonomy of bacteria and makes them increasingly susceptible to changes in the host organism. Many mycoplasmas themselves cause pathological changes in the host organism, often complicated by immune disorders. Infection with certain strains of mycoplasma results in the activation of the nuclear factor kappa-light-chain-enhancer of activated B cells, which is the major mediator of the inflammatory response. Furthermore, mycoplasmas can inhibit p53-mediated checkpoint control of cell cycle and apoptosis. Collectively, these properties indicate that mycoplasmas might act as cancer-promoting factors. In this review, we summarize the information known to date on the role of mycoplasmas in the regulation of the host immune response and their functional interactions with p53.     

Symbiogenesis as Evolution of Open Genetic Systems

The evolution of intracellular symbioses formed by bacteria with plants and animals is addressed as a model for reconstructing the origin of eukaryotic cells as a symbiosis between different forms of prokaryotes (symbiogenesis). In microorganisms that are in facultative or conditionally obligatory (ecologically obligatory) dependence on symbiosis, their gene networks arise on the basis of host-activated intragenomic rearrangements and horizontal gene transfer. The latter factor determines the evolution of the genomes of symbiotic bacteria as open genetic systems (OGSs), in which the ratio of accessory genome regions to its core regions is increased compared to free-living relatives. Coevolution of bacteria and eukaryotic hosts results in the formation of higher rank OGSs, symbiogenomes, the integrity of which is mediated by signaling interactions that determine cross-regulation of partner genes. Increasing the effectiveness of their cooperation is achieved with the transition of bacteria to strictly obligatory (genetically obligatory) dependence on hosts, determined by (a) the loss of considerable regions of the microbial genome encoding the functions of autonomous development and (b) adaptation of bacteria to permanent intracellular existence, endocytobiosis. At this stage, symbiogenomes acquire the status of inheritance systems, determined by vertical (as a rule, transovarial) transfer of microsymbionts through host generations. The transformation of endocytobionts into cellular organelles is associated with the loss of their genetic autonomy, i.e., the ability to maintain and express their rudimentary genomes, until their complete loss. However, organelles partially retain phenotypic identity of ancestral bacteria, which is determined by the importation from the host cell of the gene products (proteins, RNA) obtained earlier from microsymbionts, which led to the formation of structurally integrated hologenomes. The gene loss and gain strategy realized in this way led to the formation of different patterns of eukaryotic cell organization in accordance with the mosaic scenario, which includes sequential introduction of several symbionts into the host cell, or with the matryoshka doll scenario, in which new symbionts are introduced into the cells of previously acquired symbionts.     

靶向宿主代谢重编程的溶瘤病毒调控策略

溶瘤病毒是一类天然的或经过基因编辑后能特异性在肿瘤细胞中复制、发挥抗肿瘤效应的病毒。溶瘤病毒的抗肿瘤效应主要通过以下两个方面实现：a. 直接的溶瘤效应，例如诱导肿瘤细胞发生凋亡、促使细胞裂解等；b. 溶瘤病毒作为一种激活免疫的药物，通过诱导机体产生强烈的抗肿瘤免疫，达到清除肿瘤的目的。溶瘤病毒疗法作为免疫疗法的一个重要分支，因其具有肿瘤特异性，便于基因改造等优点，成为该领域的研究热点。截至目前，处在临床实验招募和完成阶段的溶瘤病毒疗法虽然已达100多例，但已批准上市的产品仅有4款。溶瘤疗法应用于肿瘤治疗领域还面临着诸多挑战。因此，系统性回顾溶瘤病毒的改造策略，深入了解溶瘤病毒的生物学过程显得尤为必要。病毒依赖于宿主完成复制、增殖过程，其生物学过程与宿主的代谢状态密切相关。肿瘤的标志性特征为代谢重编程，即肿瘤细胞重新构建代谢网络以满足指数生长和增殖的需求并防止氧化应激的过程。通常包括糖酵解的增强和谷氨酰胺分解，以及线粒体功能和氧化还原稳态的变化。通过靶向宿主代谢重编程增强溶瘤病毒的复制、溶瘤能力是当前极具前景的方向。本文综述溶瘤病毒的临床应用现状及与代谢相关的调控机制，为进一步开发新型溶瘤病毒以及联用方式提供新的思路。     

Highlights of mycoplasma research—An historical perspective

This brief historical development of the biology of the mycoplasmas begins with their discovery in 1898 to the present. Mycoplasmas are the smallest free-living microorganisms and for years were thought to be viruses because they passed through the usual bacterial filters. They lack a cell wall, are widespread in nature and many are animal, plantand human pathogens. The extensive use of cell cultures in the last fifty years and their frequent contamination with mycoplasmas, together with their possession of the smallest genome of any free-living organism, has drawn enormous attention to these organisms and has revealed considerably more about their biology.     

Adherence of Pathogenic Mycoplasmas to Host Cells

The significant genome compaction in mycoplasmas was made possible by adoption of a parasitic lifestyle. During their evolution and adaptation to a parasitic mode of life the mycoplasmas have developed various genetic systems enabling their attachment to host tissues as well as a highly plastic set of variable surface proteins. The generation of a versatile surface coat through high-frequency phase and size variation provides the organism with a useful tool for immune system avoidance, allowing the mycoplasmas to escape antibody attack, explaining why these minute organisms are such successful parasites.     

Quantitative Assessment of Mycoplasma Hemadsorption Activity by Flow Cytometry

A number of adherent mycoplasmas have developed highly complex polar structures that are involved in diverse aspects of the biology of these microorganisms and play a key role as virulence factors by promoting adhesion to host cells in the first stages of infection. Attachment activity of mycoplasma cells has been traditionally investigated by determining their hemadsorption ability to red blood cells and it is a distinctive trait widely examined when characterizing the different mycoplasma species. Despite the fact that protocols to qualitatively determine the hemadsorption or hemagglutination of mycoplasmas are straightforward, current methods when investigating hemadsorption at the quantitative level are expensive and poorly reproducible. By using flow cytometry, we have developed a procedure to quantify rapidly and accurately the hemadsorption activity of mycoplasmas in the presence of SYBR Green I, a vital fluorochrome that stains nucleic acids, allowing to resolve erythrocyte and mycoplasma cells by their different size and fluorescence. This method is very reproducible and permits the kinetic analysis of the obtained data and a precise hemadsorption quantification based on standard binding parameters such as the dissociation constant K _d. The procedure we developed could be easily implemented in a standardized assay to test the hemadsorption activity of the growing number of clinical isolates and mutant strains of different mycoplasma species, providing valuable data about the virulence of these microorganisms.     

Proteomic response of bacteria during the interaction with a host cell in a model of <Emphasis Type="Italic">Mycoplasma gallisepticum</Emphasis>

Parasitism, which is a way of the coexistence of bacteria with a host, is a very interesting phenomenon. Although the pathogenicity of many microorganisms has been studied in detail, many aspects of this phenomenon remain poorly understood for most bacteria. Among interesting objects for studying pathogen–host interactions are the members of the Mycoplasma genus. Despite a very broad geographical range of habitat of these bacteria, their pathogenicity has been poorly studied. Almost all living beings are the hosts of mycoplasmas, and the reduced genome of these microorganisms makes them a convenient object for model studies. Here, we have described for the first time an experimental label-free method for the analysis of the protein profile of a bacterium immediately during its interaction with a host cell, which made it possible to understand what changes the pathogen undergoes at this stage of infection. The method involves the sampling of eukaryotic cells at different times of cultivation with the pathogen, the sedimentation of infected cells, the preparation of a cell lysate, the hydrolytic cleavage of cell proteins, and their identification by mass spectrometry (HPLC–MS). Changes in the protein abundance were analyzed by the method of multiple reaction monitoring (MRM). In the present work, a model of the interaction of the bacterium Mycoplasma gallisepticum with chicken erythroblasts (HD3 cells) at the stage of acute infection was studied. A panel of 100 proteins was taken for the analysis, which were chosen based on their functions and literature data. To obtain the greatest number of identified proteins, several methods of their hydrolytic cleavage with subsequent preparation of the peptide extract were used: digestion in solution using the RapiGest SF surfactant, digestion using sodium deoxycholate and urea, and the digestion of proteins in gel. As a result, proteins were identified that, probably, are involved in the interaction of M. gallisepticum with the host cell at early infection stages; most of them were the proteins of adhesion, glycolysis, and ribosomal proteins.     

Internalization and intracellular survival of Mycoplasma pneumoniae by non-phagocytic cells

Current theory holds that mycoplasmas remain attached to the surface of epithelial cells although some mycoplasmas have evolved mechanisms for entering host cells that are not naturally phagocytic. The ability of Mycoplasma pneumoniae strain M129 to invade and survive within host cells was studied using a HeLa cell line and a human lung carcinoma cell line (A549). The invasion process into the eukaryotic cells was studied qualitatively by confocal laser scanning microscopy and quantitatively by the gentamicin resistance assay. Internalization was found with A549 cells but not with HeLa cells. Internalization was dependent on the duration of the infection and on temperature. The organism, detected in the cytoplasm and perinuclear regions, survived within the host cells for prolonged periods of time. The intracellular location of M. pneumoniae is obviously a privileged niche, well protected from the immune system and from the action of many antibiotics and may explain the pathogenic potential of this organism.     

Metabolic interdependence of obligate intracellular bacteria and their insect hosts.

Mutualistic associations of obligate intracellular bacteria and insects have attracted much interest in the past few years due to the evolutionary consequences for their genome structure. However, much less attention has been paid to the metabolic ramifications for these endosymbiotic microorganisms, which have to compete with but also to adapt to another metabolism--that of the host cell. This review attempts to provide insights into the complex physiological interactions and the evolution of metabolic pathways of several mutualistic bacteria of aphids, ants, and tsetse flies and their insect hosts.     

Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution

We present here the hologenome theory of evolution, which considers the holobiont (the animal or plant with all of its associated microorganisms) as a unit of selection in evolution. The hologenome is defined as the sum of the genetic information of the host and its microbiota. The theory is based on four generalizations: (1) All animals and plants establish symbiotic relationships with microorganisms. (2) Symbiotic microorganisms are transmitted between generations. (3) The association between host and symbionts affects the fitness of the holobiont within its environment. (4) Variation in the hologenome can be brought about by changes in either the host or the microbiota genomes; under environmental stress, the symbiotic microbial community can change rapidly. These points taken together suggest that the genetic wealth of diverse microbial symbionts can play an important role both in adaptation and in evolution of higher organisms. During periods of rapid changes in the environment, the diverse microbial symbiont community can aid the holobiont in surviving, multiplying and buying the time necessary for the host genome to evolve. The distinguishing feature of the hologenome theory is that it considers all of the diverse microbiota associated with the animal or the plant as part of the evolving holobiont. Thus, the hologenome theory fits within the framework of the 'superorganism' proposed by Wilson and Sober.     

Impact of genomics and genetics on the elucidation of bacterial metabolism

In the last few years, the emergence of complete genome sequences has had profound effects on all fields of biology. While the existence of these genome sequences has served to facilitate experimental work, it has also highlighted the gaps in our knowledge of bacterial metabolism. Our current knowledge of metabolism is primarily the result of data accumulated from decades of study by biochemists and geneticists. In general these studies focused on discrete pathways and their regulation. The technical innovations of the last decade, culminating with the sequencing of complete genomes, provide us with the ability to address the next frontier in physiology, metabolic integration. Herein we describe current approaches that can be used to complement classic genetic approaches and further our understanding of both novel metabolic functions and metabolic integration in microorganisms.     

藤黄微球菌V017基因组测序及对辐照的转录组响应

[背景]耐辐射微生物是一类重要的极端微生物资源,在研究其耐受机制以及环境保护等方面具有重大的意义.[目的]从基因组和转录组角度解析耐辐射藤黄微球菌(Micrococcus luteus) V017的抗性遗传背景以及对辐照的转录组响应.[方法]利用PacBio平台对菌株V017进行基因组测序,通过比较基因组分析菌株V01...     

Auditioning of CHO host cell lines using the artificial chromosome expression (ACE) technology

In order to maximize recombinant protein expression in mammalian cells many factors need to be considered such as transfection method, vector construction, screening techniques and culture conditions. In addition, the host cell line can have a profound effect on the protein expression. However, auditioning or directly comparing host cell lines for optimal protein expression may be difficult since most transfection methods are based on random integration of the gene of interest into the host cell genome. Thus it is not possible to determine whether differences in expression between various host cell lines are due to the phenotype of the host cell itself or genetic factors such as gene copy number or gene location. To improve cell line generation, the ACE System was developed based on pre‐engineered artificial chromosomes with multiple recombination acceptor sites. This system allows for targeted transfection and has been effectively used to rapidly generate stable CHO cell lines expressing high levels of monoclonal antibody. A key feature of the ACE System is the ability to isolate and purify ACEs containing the gene(s) of interest and transfect the same ACEs into different host cell lines. This feature allows the direct auditioning of host cells since the host cells have been transfected with ACEs that contain the same number of gene copies in the same genetic environment. To investigate this audition feature, three CHO host cell lines (CHOK1SV, CHO‐S and DG44) were transfected with the same ACE containing gene copies of a human monoclonal IgG1 antibody. Clonal cell lines were generated allowing a direct comparison of antibody expression and stability between the CHO host cells. Results showed that the CHOK1SV host cell line expressed antibody at levels of more than two to five times that for DG44 and CHO‐S host cell lines, respectively. To confirm that the ACE itself was not responsible for the low antibody expression seen in the CHO‐S based clones, the ACE was isolated and purified from these cells and transfected back into fresh CHOK1SV cells. The resulting expression of the antibody from the ACE newly transfected into CHOK1SV increased fivefold compared to its expression in CHO‐S and confirmed that the differences in expression between the different CHO host cells was due to the cell phenotype rather than differences in gene copy number and/or location. These results demonstrate the utility of the ACE System in providing a rapid and direct technique for auditioning host cell lines for optimal recombinant protein expression. Biotechnol. Bioeng. 2009; 104: 526–539 © 2009 Wiley Periodicals, Inc.     

CRISPR/Cas9技术在工业微生物中的应用

近年来,通过基因编辑技术对工业微生物底盘细胞改造从而获得的优良细胞工厂,促进了农业、医学、环境、能源等领域的可持续发展,提高了人民的生活水平。微生物底盘细胞的改造离不开基因编辑,作为现阶段主要的基因编辑技术,规律间隔成簇短回文重复序列（clustered regularly interspaced short palindromic repeats,CRISPR）/Cas9系统自被发现以来,依靠其低成本、高效率等编辑优点,被广泛用于工业微生物底盘细胞的改造。本文主要简述了以CRISPR/Cas9为基础而衍伸出的各种基因编辑技术,提出了常用的工业微生物对应底盘细胞的改造策略,以期为研究者在进行微生物底盘细胞改造时选择出合适的基因编辑方法。最后指出了CRISPR基因编辑技术面临的PAM位点的依赖性、脱靶效应和应用广泛性等问题。     

Novel clades of soil biphenyl degraders revealed by integrating isotope probing,multi-omics,and single-cell analyses

Most microorganisms in the biosphere remain uncultured and poorly characterized. Although the surge in genome sequences has enabled insights into the genetic and metabolic properties of uncultured microorganisms, their physiology and ecological roles cannot be determined without direct probing of their activities in natural habitats. Here we employed an experimental framework coupling genome reconstruction and activity assays to characterize the largely uncultured microorganisms responsible for aerobic biodegradation of biphenyl as a proxy for a large class of environmental pollutants, polychlorinated biphenyls. We used ¹³C-labeled biphenyl in contaminated soils and traced the flow of pollutant-derived carbon into active cells using single-cell analyses and protein–stable isotope probing. The detection of ¹³C-enriched proteins linked biphenyl biodegradation to the uncultured Alphaproteobacteria clade {"type":"entrez-protein","attrs":{"text":"UBA11222","term_id":"2096922005"}}UBA11222, which we found to host a distinctive biphenyl dioxygenase gene widely retrieved from contaminated environments. The same approach indicated the capacity of Azoarcus species to oxidize biphenyl and suggested similar metabolic abilities for species of Rugosibacter. Biphenyl oxidation would thus represent formerly unrecognized ecological functions of both genera. The quantitative role of these microorganisms in pollutant degradation was resolved using single-cell-based uptake measurements. Our strategy advances our understanding of microbially mediated biodegradation processes and has general application potential for elucidating the ecological roles of uncultured microorganisms in their natural habitats.Subject terms: Microbial ecology, Biogeochemistry, Biogeochemistry, Soil microbiology, Biogeochemistry