scholarly journals REPINs are facultative genomic symbionts of bacterial genomes

2021 ◽  
Author(s):  
Frederic Bertels ◽  
Paul B Rainey
Keyword(s):  
Population Biology ◽  
Distribution Patterns ◽  
Host Cells ◽  
Symbiotic Relationship ◽  
Short Sequence ◽  
Bacterial Genomes ◽  
Theoretical Predictions ◽  
Biological World ◽  
Genome Space ◽  
Living Organisms

Relationships among organisms, in which one lives inside of another, with benefits accruing to both partners, are referred to as endosymbiotic. Such relationships are common in the biological world, yet descriptions are confined to organismal life. Here we argue that short sequence repeats known as REPINs - whose replication is dependent on a non-jumping RAYT transposase - form a similar facultative symbiotic relationship with the bacterial chromosome. Evidence stems from distribution patterns across the eubacteria: persistence times of many millions of years, exceedingly rare duplication rates, vertical transmission, and population biology typical of living organisms, including population size fluctuations that correlate with available genome space. Additional analysis of patterns of REPIN evolution conform with theoretical predictions of conflict (and resolution) arising from the effects of selection operating simultaneously on REPINs and host cells. A search for similar kinds of genomic symbionts suggests that the REPIN-RAYT system is not unique.

scholarly journals Dealing with PET radiometabolites

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Krishna Kanta Ghosh ◽  
Parasuraman Padmanabhan ◽  
Chang-Tong Yang ◽  
Sachin Mishra ◽  
Christer Halldin ◽  
...  
Keyword(s):  
Pet Imaging ◽  
Distribution Patterns ◽  
The Body ◽  
Analysis Process ◽  
Pet Tracer ◽  
Positron Emission ◽  
Structural Identity ◽  
Available Technology ◽  
Living Organisms ◽  
Entire Amount

Abstract Positron emission tomography (PET) offers the study of biochemical, physiological, and pharmacological functions at a cellular and molecular level. The performance of a PET study mostly depends on the used radiotracer of interest. However, the development of a novel PET tracer is very difficult, as it is required to fulfill a lot of important criteria. PET radiotracers usually encounter different chemical modifications including redox reaction, hydrolysis, decarboxylation, and various conjugation processes within living organisms. Due to this biotransformation, different chemical entities are produced, and the amount of the parent radiotracer is declined. Consequently, the signal measured by the PET scanner indicates the entire amount of radioactivity deposited in the tissue; however, it does not offer any indication about the chemical disposition of the parent radiotracer itself. From a radiopharmaceutical perspective, it is necessary to quantify the parent radiotracer’s fraction present in the tissue. Hence, the identification of radiometabolites of the radiotracers is vital for PET imaging. There are mainly two reasons for the chemical identification of PET radiometabolites: firstly, to determine the amount of parent radiotracers in plasma, and secondly, to rule out (if a radiometabolite enters the brain) or correct any radiometabolite accumulation in peripheral tissue. Besides, radiometabolite formations of the tracer might be of concern for the PET study, as the radiometabolic products may display considerably contrasting distribution patterns inside the body when compared with the radiotracer itself. Therefore, necessary information is needed about these biochemical transformations to understand the distribution of radioactivity throughout the body. Various published review articles on PET radiometabolites mainly focus on the sample preparation techniques and recently available technology to improve the radiometabolite analysis process. This article essentially summarizes the chemical and structural identity of the radiometabolites of various radiotracers including [11C]PBB3, [11C]flumazenil, [18F]FEPE2I, [11C]PBR28, [11C]MADAM, and (+)[18F]flubatine. Besides, the importance of radiometabolite analysis in PET imaging is also briefly summarized. Moreover, this review also highlights how a slight chemical modification could reduce the formation of radiometabolites, which could interfere with the results of PET imaging. Graphical abstract

scholarly journals Pathways of DNA Transfer to Plants fromAgrobacterium tumefaciensand Related Bacterial Species

2019 ◽  
Vol 57 (1) ◽  
pp. 231-251 ◽  
Author(s):  
Benoît Lacroix ◽  
Vitaly Citovsky
Keyword(s):  
Genetic Transformation ◽  
Host Plants ◽  
Virulence Genes ◽  
Bacterial Species ◽  
Dna Transfer ◽  
Plant Biology ◽  
Host Cells ◽  
Bacterial Genomes ◽  
Unique Model ◽  
Complete Set

Genetic transformation of host plants by Agrobacterium tumefaciens and related species represents a unique model for natural horizontal gene transfer. Almost five decades of studying the molecular interactions between Agrobacterium and its host cells have yielded countless fundamental insights into bacterial and plant biology, even though several steps of the DNA transfer process remain poorly understood. Agrobacterium spp. may utilize different pathways for transferring DNA, which likely reflects the very wide host range of Agrobacterium. Furthermore, closely related bacterial species, such as rhizobia, are able to transfer DNA to host plant cells when they are provided with Agrobacterium DNA transfer machinery and T-DNA. Homologs of Agrobacterium virulence genes are found in many bacterial genomes, but only one non- Agrobacterium bacterial strain, Rhizobium etli CFN42, harbors a complete set of virulence genes and can mediate plant genetic transformation when carrying a T-DNA-containing plasmid.

scholarly journals The coevolution of toxin and antitoxin genes drives the dynamics of bacterial addiction complexes and intragenomic conflict

2012 ◽  
Vol 279 (1743) ◽  
pp. 3706-3715 ◽  
Author(s):  
Daniel J. Rankin ◽  
Leighton A. Turner ◽  
Jack A. Heinemann ◽  
Sam P. Brown
Keyword(s):  
Theoretical Model ◽  
Kin Selection ◽  
Population Biology ◽  
Bacterial Genomes ◽  
Daughter Cells ◽  
Intragenomic Conflict ◽  
Bacterial Chromosomes ◽  
Gene Complexes ◽  
Deleterious Genes

Bacterial genomes commonly contain ‘addiction’ gene complexes that code for both a toxin and a corresponding antitoxin. As long as both genes are expressed, cells carrying the complex can remain healthy. However, loss of the complex (including segregational loss in daughter cells) can entail death of the cell. We develop a theoretical model to explore a number of evolutionary puzzles posed by toxin–antitoxin (TA) population biology. We first extend earlier results demonstrating that TA complexes can spread on plasmids, as an adaptation to plasmid competition in spatially structured environments, and highlight the role of kin selection. We then considered the emergence of TA complexes on plasmids from previously unlinked toxin and antitoxin genes. We find that one of these traits must offer at least initially a direct advantage in some but not all environments encountered by the evolving plasmid population. Finally, our study predicts non-transitive ‘rock-paper-scissors’ dynamics to be a feature of intragenomic conflict mediated by TA complexes. Intragenomic conflict could be sufficient to select deleterious genes on chromosomes and helps to explain the previously perplexing observation that many TA genes are found on bacterial chromosomes.

scholarly journals Effects of Mycoplasmas on the Host Cell Signaling Pathways

Pathogens ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 308
Author(s):  
Sergei N. Borchsenius ◽  
Innokentii E. Vishnyakov ◽  
Olga A. Chernova ◽  
Vladislav M. Chernov ◽  
Nikolai A. Barlev
Keyword(s):  
Host Cell ◽  
Intracellular Signaling ◽  
Nuclear Translocation ◽  
Inflammatory Responses ◽  
Cell Interaction ◽  
Host Cells ◽  
Nuclear Factor ◽  
New Therapeutic Approaches ◽  
Anti Inflammatory ◽  
Living Organisms

Mycoplasmas are the smallest free-living organisms. Reduced sizes of their genomes put constraints on the ability of these bacteria to live autonomously and make them highly dependent on the nutrients produced by host cells. Importantly, at the organism level, mycoplasmal infections may cause pathological changes to the host, including cancer and severe immunological reactions. At the molecular level, mycoplasmas often activate the NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) inflammatory response and concomitantly inhibit the p53-mediated response, which normally triggers the cell cycle and apoptosis. Thus, mycoplasmal infections may be considered as cancer-associated factors. At the same time, mycoplasmas through their membrane lipoproteins (LAMPs) along with lipoprotein derivatives (lipopeptide MALP-2, macrophage-activating lipopeptide-2) are able to modulate anti-inflammatory responses via nuclear translocation and activation of Nrf2 (the nuclear factor-E2-related anti-inflammatory transcription factor 2). Thus, interactions between mycoplasmas and host cells are multifaceted and depend on the cellular context. In this review, we summarize the current information on the role of mycoplasmas in affecting the host’s intracellular signaling mediated by the interactions between transcriptional factors p53, Nrf2, and NF-κB. A better understanding of the mechanisms underlying pathologic processes associated with reprogramming eukaryotic cells that arise during the mycoplasma-host cell interaction should facilitate the development of new therapeutic approaches to treat oncogenic and inflammatory processes.

scholarly journals On the Life Cycle and Natural History of Hymenitis Nero (Lepidoptera: Ithomiinae) in Costa Rica

1972 ◽  
Vol 79 (4) ◽  
pp. 284-294 ◽  
Author(s):  
Allen M. Young
Keyword(s):  
Life Cycle ◽  
Costa Rica ◽  
Natural History ◽  
Population Biology ◽  
Distribution Patterns ◽  
Broad Distribution ◽  
Tropical Plant ◽  
History Of ◽  
Local Patterns ◽  
Tropical Plant Communities

A knowledge of life cycle and natural history are often important prerequisites to studies of population biology in butterflies. Although studies on the systematics and broad distribution patterns of that familiar New World Tropical group, the Ithomiinae, have been conducted (Seitz, 194; Fox, 1956; Fox, 1968), a lot remains to be known about the biology of many species in Central America. This is surprising in light of the considerable interest in these butterflies as members of mimicry complexes. In this spirit, this paper summarizes life cycle and natural history data on a clear wing ithoreiine Hymenitis nero (Hewitson) (Nymphalidae: Ithomiinae) in Costa Rica. Similar studies of several other sympatric ithomiines have either been completed (Young, in prep.) or begun, as a preliminary step towards understanding the local patterns of diversity of this family in selected tropical plant communities.

scholarly journals An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic networks of symbiotic organisms

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Mariana Reyes-Prieto ◽  
Carlos Vargas-Chávez ◽  
Mercè Llabrés ◽  
Pere Palmer ◽  
Amparo Latorre ◽  
...  
Keyword(s):  
Metabolic Networks ◽  
Directed Acyclic Graphs ◽  
Symbiotic Relationship ◽  
Bacterial Genomes ◽  
Individual Organism ◽  
Symbiotic Relationships ◽  
Public Resource ◽  
Acyclic Graphs ◽  
Symbiotic Organisms ◽  
Relevant Range

Abstract The Symbiotic Genomes Database (SymGenDB; http://symbiogenomesdb.uv.es/) is a public resource of manually curated associations between organisms involved in symbiotic relationships, maintaining a catalog of completely sequenced/finished bacterial genomes exclusively. It originally consisted of three modules where users could search for the bacteria involved in a specific symbiotic relationship, their genomes and their genes (including their orthologs). In this update, we present an additional module that includes a representation of the metabolic network of each organism included in the database, as Directed Acyclic Graphs (MetaDAGs). This module provides unique opportunities to explore the metabolism of each individual organism and/or to evaluate the shared and joint metabolic capabilities of the organisms of the same genera included in our listing, allowing users to construct predictive analyses of metabolic associations and complementation between systems. We also report a ~25% increase in manually curated content in the database, i.e. bacterial genomes and their associations, with a final count of 2328 bacterial genomes associated to 498 hosts. We describe new querying possibilities for all the modules, as well as new display features for the MetaDAGs module, providing a relevant range of content and utility. This update continues to improve SymGenDB and can help elucidate the mechanisms by which organisms depend on each other.

scholarly journals The Potassium Transporter Trk and External Potassium Modulate Salmonella enterica Protein Secretion and Virulence

2008 ◽  
Vol 77 (2) ◽  
pp. 667-675 ◽  
Author(s):  
Jing Su ◽  
Hao Gong ◽  
Jeff Lai ◽  
Andrew Main ◽  
Sangwei Lu
Keyword(s):  
Salmonella Enterica ◽  
Bacterial Pathogen ◽  
Effector Proteins ◽  
Host Cells ◽  
Infection Model ◽  
Human Pathogens ◽  
Food Borne ◽  
External Potassium ◽  
Living Organisms ◽  
External K

ABSTRACT Potassium (K+) is the most abundant intracellular cation and is essential for many physiological functions of all living organisms; however, its role in the pathogenesis of human pathogens is not well understood. In this study, we characterized the functions of the bacterial Trk K+ transport system and external K+ in the pathogenesis of Salmonella enterica, a major food-borne bacterial pathogen. Here we report that Trk is important for Salmonella to invade and grow inside epithelial cells. It is also necessary for the full virulence of Salmonella in an animal infection model. Analysis of proteins of Salmonella indicated that Trk is involved in the expression and secretion of effector proteins of the type III secretion system (TTSS) encoded by Salmonella pathogenicity island 1 (SPI1) that were previously shown to be necessary for Salmonella invasion. In addition to the role of the Trk transporter in the pathogenesis of Salmonella, we discovered that external K+ modulates the pathogenic properties of Salmonella by increasing the expression and secretion of effector proteins of the SPI1-encoded TTSS and by enhancing epithelial cell invasion. Our studies demonstrated that K+ is actively involved in the pathogenesis of Salmonella and indicated that Salmonella may take advantage of the high K+ content inside host cells and in the intestinal fluid during diarrhea to become more virulent.

Prevalence of schistosome infections within molluscan populations: observed patterns and theoretical predictions

Parasitology ◽  
1979 ◽  
Vol 79 (1) ◽  
pp. 63-94 ◽  
Author(s):  
R. M. Anderson ◽  
R. M. May
Keyword(s):  
Latent Period ◽  
Quantitative Data ◽  
Population Biology ◽  
Infected Snail ◽  
Parasite Prevalence ◽  
Mortality Rates ◽  
Snail Infection ◽  
Theoretical Predictions ◽  
Low Levels ◽  
Field And Laboratory Conditions

SUMMARYThe paper draws together a large and scattered body of empirical evidence concerning the prevalence of snail infection with schistosome parasites in field situations, the duration of the latent period of infection in snails (and its dependence on temperature), and the mortality rates of infected and uninfected snails in field and laboratory conditions. A review and synthesis of quantitative data on the population biology of schistosome infections within the molluscan host is attempted and observed patterns of infection are compared with predictions of a schistosomiasis model developed by May (1977) which incorporates differential snail mortality (between infected and uninfected snails) and latent periods of infection. It is suggested that the low levels of prevalence within snail populations in endemic areas of schistosomiasis are closely associated with high rates of infected snail mortality and the duration of the latent period of infection within the mollusc. In certain instances, the expected life-span of an infected snail may be less than the duration of the latent period of infection. Such patterns generate very low levels of parasite prevalence. A new age prevalence model for schistosome infections within snail populations is developed and its predictions compared with observed patterns.The implications of this study of observed and predicted patterns of snail infection within molluscan populations are discussed in relation to the overall transmission dynamics of schistosomiasis.

scholarly journals Cu Homeostasis in Bacteria: The Ins and Outs

Membranes ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 242
Author(s):  
Andreea Andrei ◽  
Yavuz Öztürk ◽  
Bahia Khalfaoui-Hassani ◽  
Juna Rauch ◽  
Dorian Marckmann ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Host Cells ◽  
Microbial Pathogens ◽  
Host Immune System ◽  
Biological Processes ◽  
Multiple Strategies ◽  
Relay Systems ◽  
Bacterial Response ◽  
Cu Homeostasis ◽  
Living Organisms

Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.

scholarly journals Enhanced Symbiotic Characteristics in Bacterial Genomes with the Disruption of rRNA Operon

Biology ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 440
Author(s):  
Hyeonju Ahn ◽  
Donghyeok Seol ◽  
Seoae Cho ◽  
Heebal Kim ◽  
Woori Kwak
Keyword(s):  
Ribosomal Rna ◽  
Dynamic Range ◽  
Rrna Operon ◽  
Reproduction Rate ◽  
Bacterial Genomes ◽  
Positive Effects ◽  
Living Organisms ◽  
Low Dynamic Range ◽  
Growth And Reproduction ◽  
Adenine Thymine

Ribosomal RNA is an indispensable molecule in living organisms that plays an essential role in protein synthesis. Especially in bacteria, 16S, 23S, and 5S rRNAs are usually co-transcribed as operons. Despite the positive effects of rRNA co-transcription on growth and reproduction rate, a recent study revealed that bacteria with unlinked rRNA operons are more widespread than expected. However, it is still unclear why the rRNA operon is broken. Here, we explored rRNA operon linkage status in 15,898 bacterial genomes and investigated whether they have common features or lifestyles; 574 genomes were found to have unlinked rRNA operons and tended to be phylogenetically conserved. Most of them were symbionts and showed enhanced symbiotic genomic features such as reduced genome size and high adenine–thymine (AT) content. In an eggNOG-mapper analysis, they were also found to have significantly fewer genes than rRNA operon-linked bacteria in the “transcription” and “energy production and conversion in metabolism” categories. These genomes also tend to decrease RNases related to the synthesis of ribosomes and tRNA processing. Based on these results, the disruption of the rRNA operon seems to be one of the tendencies associated with the characteristics of bacteria requiring a low dynamic range.

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