scholarly journals Phylogenomic analyses of Snodgrassella isolates from honeybees and bumblebees reveals taxonomic and functional diversity

2021 ◽  
Author(s):  
Luc Cornet ◽  
Ilse Cleenwerck ◽  
Jessy Praet ◽  
Raphaël R. Leonard ◽  
Nicolas J. Vereecken ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Model Organism ◽  
Single Species ◽  
List Type ◽  
Inorganic Ion ◽  
Small Proteins ◽  
European Nucleotide Archive ◽  
Bee Health ◽  
Phylogenomic Analyses ◽  
Functional Analyses

AbstractSnodgrassella is a Betaproteobacteria genus found in the gut of honeybees (Apis spp.) and bumblebees (Bombus spp). It is part of a conserved microbiome that is composed of few core phylotypes and is essential for bee health and metabolism. Phylogenomic analyses using whole genome sequences of 75 Snodgrassella strains from 4 species of honey bees and 14 species of bumblebees showed that these strains formed a monophyletic lineage within the Neisseriaceae family, that Snodgrassella isolates from Asian honeybees diverged early on from the other species in their evolution, that isolates from honeybees and bumblebees were well separated and that this genus consists of at least seven species. We propose to formally name two new Snodgrassella species that were isolated from bumblebees, i.e. Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov. Possible evolutionary scenarios for 107 species or group specific genes revealed very limited evidence for horizontal gene transfer. Functional analyses revealed the importance of small proteins, defense mechanisms, amino acid transport and metabolism, inorganic ion transport and metabolism and carbohydrate transport and metabolism among these 107 specific genes.ImportanceThe microbiome of honeybees (Apis spp.) and bumblebees (Bombus spp.) is highly conserved and represented by few phylotypes. This simplicity in taxon composition makes the bee’s microbiome an emergent model organism for the study of gut microbial communities. Since the description of the Snodgrassella genus, which was isolated from the gut of honeybees and bumblebees in 2013, a single species, i.e. Snodgrassella alvi, has been named. Here we demonstrate that this genus is actually composed of at least seven species, two of them (Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov.) being formally described in the present publication. We also report the presence of 107 genes specific to Snodgrassella species, showing notably the importance of small proteins and defense mechanisms in this genus.Data summaryCornet L and Vandamme P, European Nucleotide Archive (ENA), Project accession: PRJEB47378Cornet L and Vandamme P, European Nucleotide Archive (ENA), Reads accessions: SAMEA9570070 - SAMEA9570078Cornet L and Vandamme P, European Nucleotide Archive (ENA), Genome accessions: GCA_914768015, GCA_914768025, GCA_914768035, GCA_914768045, GCA_914768055, GCA_914768065, GCA_914768075, GCA_914768085, GCA_914768095.

Parasite defense mechanisms in bees: behavior, immunity, antimicrobials, and symbionts

2019 ◽  
Vol 4 (1) ◽  
pp. 59-76 ◽  
Author(s):  
Alison E. Fowler ◽  
Rebecca E. Irwin ◽  
Lynn S. Adler
Keyword(s):  
Defense Mechanisms ◽  
Poor Quality ◽  
Future Research ◽  
Immune Priming ◽  
Social Bees ◽  
Bee Health ◽  
Landscape Scales ◽  
And Function ◽  
Solitary Species

Parasites are linked to the decline of some bee populations; thus, understanding defense mechanisms has important implications for bee health. Recent advances have improved our understanding of factors mediating bee health ranging from molecular to landscape scales, but often as disparate literatures. Here, we bring together these fields and summarize our current understanding of bee defense mechanisms including immunity, immunization, and transgenerational immune priming in social and solitary species. Additionally, the characterization of microbial diversity and function in some bee taxa has shed light on the importance of microbes for bee health, but we lack information that links microbial communities to parasite infection in most bee species. Studies are beginning to identify how bee defense mechanisms are affected by stressors such as poor-quality diets and pesticides, but further research on this topic is needed. We discuss how integrating research on host traits, microbial partners, and nutrition, as well as improving our knowledge base on wild and semi-social bees, will help inform future research, conservation efforts, and management.

scholarly journals Evolutionarily recent dual obligatory symbiosis among adelgids indicates a transition between fungus- and insect-associated lifestyles

2021 ◽  
Author(s):  
Gitta Szabó ◽  
Frederik Schulz ◽  
Alejandro Manzano-Marín ◽  
Elena Rebecca Toenshoff ◽  
Matthias Horn
Keyword(s):  
Defense Mechanisms ◽  
Amino Acid Production ◽  
Evolutionary Transition ◽  
Evolutionary Time ◽  
Evolutionary Trajectories ◽  
Host Infection ◽  
Phylogenomic Analyses ◽  
Time Specific ◽  
High Level ◽  
Metagenomic Approach

AbstractAdelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of the Adelges laricis/Adelgestardus species complex containing betaproteobacterial (“Candidatus Vallotia tarda”) and gammaproteobacterial (“Candidatus Profftia tarda”) symbionts. Genomic characteristics and metabolic pathway reconstructions revealed that Vallotia and Profftia are evolutionary young endosymbionts, which complement each other’s role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts of Rhizopus fungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection, and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.

scholarly journals A Cryptic Non-Inducible Prophage Confers Phage-Immunity on the Streptococcus thermophilus M17PTZA496

Viruses ◽  
2018 ◽  
Vol 11 (1) ◽  
pp. 7 ◽  
Author(s):  
Vinícius da Silva Duarte ◽  
Sabrina Giaretta ◽  
Stefano Campanaro ◽  
Laura Treu ◽  
Andrea Armani ◽  
...  
Keyword(s):  
Mitomycin C ◽  
Defense Mechanisms ◽  
Large Subunit ◽  
Bacterial Species ◽  
Dairy Industry ◽  
Model Organism ◽  
Streptococcus Thermophilus ◽  
Starter Cultures ◽  
Economic Losses ◽  
Important Species

Streptococcus thermophilus is considered one of the most important species for the dairy industry. Due to their diffusion in dairy environments, bacteriophages can represent a threat to this widely used bacterial species. Despite the presence of a CRISPR-Cas system in the S. thermophilus genome, some lysogenic strains harbor cryptic prophages that can increase the phage-host resistance defense. This characteristic was identified in the dairy strain S. thermophilus M17PTZA496, which contains two integrated prophages 51.8 and 28.3 Kb long, respectively. In the present study, defense mechanisms, such as a lipoprotein-encoding gene and Siphovirus Gp157, the last associated to the presence of a noncoding viral DNA element, were identified in the prophage M17PTZA496 genome. The ability to overexpress genes involved in these defense mechanisms under specific stressful conditions, such as phage attack, has been demonstrated. Despite the addition of increasing amounts of Mitomycin C, M17PTZA496 was found to be non-inducible. However, the transcriptional activity of the phage terminase large subunit was detected in the presence of the antagonist phage vB_SthS-VA460 and of Mitomycin C. The discovery of an additional immune mechanism, associated with bacteriophage-insensitive strains, is of utmost importance, for technological applications and industrial processes. To our knowledge, this is the first study reporting the capability of a prophage integrated into the S. thermophilus genome expressing different phage defense mechanisms. Bacteriophages are widespread entities that constantly threaten starter cultures in the dairy industry. In cheese and yogurt manufacturing, the lysis of Streptococcus thermophilus cultures by viral attacks can lead to huge economic losses. Nowadays S. thermophilus is considered a well-stablished model organism for the study of natural adaptive immunity (CRISPR-Cas) against phage and plasmids, however, the identification of novel bacteriophage-resistance mechanisms, in this species, is strongly desirable. Here, we demonstrated that the presence of a non-inducible prophage confers phage-immunity to an S. thermophilus strain, by the presence of ltp and a viral noncoding region. S. thermophilus M17PTZA496 arises as an unconventional model to study phage resistance and potentially represents an alternative starter strain for dairy productions.

scholarly journals Evolutionary recent dual obligatory symbiosis among adelgids indicates a transition between fungus and insect associated lifestyles

2020 ◽  
Author(s):  
Gitta Szabó ◽  
Frederik Schulz ◽  
Alejandro Manzano-Marín ◽  
Elena Rebecca Toenshoff ◽  
Matthias Horn
Keyword(s):  
Defense Mechanisms ◽  
Amino Acid Production ◽  
Evolutionary Transition ◽  
Evolutionary Time ◽  
Evolutionary Trajectories ◽  
Host Infection ◽  
Phylogenomic Analyses ◽  
Time Specific ◽  
High Level ◽  
Metagenomic Approach

ABSTRACTAdelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of the Adelges laricis/tardus species complex containing betaproteobacterial (‘ Candidatus Vallotia tarda’) and gammaproteobacterial (‘Candidatus Profftia tarda’) symbionts. Genomic characteristics and metabolic pathway reconstructions revealed that Vallotia and Profftia are evolutionary young endosymbionts, which complement each other’s role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts of Rhizopus fungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.

scholarly journals The Nematode Caenorhabditis elegans A Model Animal “Made for Microscopy”

2004 ◽  
Vol 12 (2) ◽  
pp. 8-13
Author(s):  
David H. Hall
Keyword(s):  
Caenorhabditis Elegans ◽  
System Development ◽  
Scientific Discovery ◽  
Medical Science ◽  
Model Organism ◽  
Small Animal ◽  
Single Species ◽  
Fruit Fly ◽  
Nervous System Development ◽  
Model Animal

The small unassuming nematode, Caenorhabditis elegans is only one millimeter long and lives in the soil munching on bacteria. While many nematode (roundworm) species are parasites with medical or agricultural importance, C. elegans seems to harm no one. Yet, this animal has attained a status in medical science that compares to more complex organisms such as the mouse or fruit fly in its utility for scientific discovery. It has been the subject of thousands of studies dealing with topics as diverse as nutrition, aging, and nervous system development. About 5000 scientists are now pursuing this single species in hundreds of laboratories worldwide. In 2002, the Nobel Prize in Medicine was awarded to three of the pioneers in establishing C. elegans as a “model organism“: Sydney Brenner, John Sulston, and H. Robert Horvitz. Why study worms?Sydney Brenner first turned his attention to C. elegans in the 1960's. Working at the Medical Research Council in England, he was looking for a small animal with inexpensive tastes that could be easily cultured in the laboratory.

scholarly journals APEX-based proximity labeling in Plasmodium identifies a membrane protein with dual functions during mosquito infection

2020 ◽  
Author(s):  
Jessica Kehrer ◽  
Dominik Ricken ◽  
Leanne Strauss ◽  
Emma Pietsch ◽  
Julia M. Heinze ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Membrane Protein ◽  
Malaria Parasite ◽  
Model Organism ◽  
Subcellular Fractionation ◽  
Surface Proteins ◽  
List Type ◽  
Proximity Ligation ◽  
C Terminus ◽  
Mosquito Infection

AbstractTransmission of the malaria parasite Plasmodium to mosquitoes necessitates gamete egress from red blood cells to allow zygote formation and ookinete motility to enable penetration of the midgut epithelium. Both processes are dependent on the secretion of proteins from distinct sets of specialized vesicles. Inhibiting some of these proteins has shown potential for blocking parasite transmission to the mosquito. To identify new transmission blocking vaccine candidates, we defined the microneme content from ookinetes of the rodent model organism Plasmodium berghei using APEX2-mediated rapid proximity-dependent biotinylation. Besides known proteins of ookinete micronemes, this identified over 50 novel candidates and sharpened the list of a previous survey based on subcellular fractionation. Functional analysis of a first candidate uncovered a dual role for this membrane protein in male gametogenesis and ookinete midgut traversal. Mutation of a putative trafficking motif in the C-terminus led to its mis-localization in ookinetes and affected ookinete to oocyst transition but not gamete formation. This suggests the existence of distinct functional and transport requirements for Plasmodium proteins in different parasite stages.SignificanceThe genome of the malaria parasite Plasmodium contains over 5500 genes, of which over 30% have no assigned function. Transmission of Plasmodium spp. to the mosquito contains several essential steps that can be inhibited by antibodies or chemical compounds. Yet few proteins involved in these processes are characterized, thus limiting our capacity to generate transmission interfering tools. Here, we establish a method to rapidly identify proteins in a specific compartment within the parasite that is essential for establishment of an infection within the mosquito, and identify over 50 novel candidate proteins. Functional analysis of the top candidate identifies a protein with two independent essential functions in subsequent steps along the Plasmodium life cycle within the mosquito.Highlightsfirst use of APEX based proximity ligation in Apicomplexaidentification of >50 putative ookinete surface proteinsnovel membrane protein essential for microgamete egress and ookinete migrationputative trafficking motif essential in ookinetes but not gametes

scholarly journals Identifying small proteins by ribosome profiling with stalled initiation complexes

2019 ◽  
Author(s):  
Jeremy Weaver ◽  
Fuad Mohammad ◽  
Allen R. Buskirk ◽  
Gisela Storz
Keyword(s):  
Amino Acids ◽  
Model Organism ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Genomic Context ◽  
True Prevalence ◽  
New Genes ◽  
Small Proteins ◽  
Intergenic Regions ◽  
Reading Frames

ABSTRACTSmall proteins consisting of 50 or fewer amino acids have been identified as regulators of larger proteins in bacteria and eukaryotes. Despite the importance of these molecules, the true prevalence of small proteins remains unknown because conventional annotation pipelines usually exclude small open reading frames (smORFs). We previously identified several dozen small proteins in the model organism Escherichia coli using theoretical bioinformatic approaches based on sequence conservation and matches to canonical ribosome binding sites. Here, we present an empirical approach for discovering new proteins, taking advantage of recent advances in ribosome profiling in which antibiotics are used to trap newly-initiated 70S ribosomes at start codons. This approach led to the identification of many novel initiation sites in intergenic regions in E. coli. We tagged 41 smORFs on the chromosome and detected protein synthesis for all but three. The corresponding genes are not only intergenic, but are also found antisense to other genes, in operons, and overlapping other open reading frames (ORFs), some impacting the translation of larger downstream genes. These results demonstrate the utility of this method for identifying new genes, regardless of their genomic context.IMPORTANCEProteins comprised of 50 or fewer amino acids have been shown to interact with and modulate the function of larger proteins in a range of organisms. Despite the possible importance of small proteins, the true prevalence and capabilities of these regulators remain unknown as the small size of the proteins places serious limitations on their identification, purification and characterization. Here, we present a ribosome profiling approach with stalled initiation complexes that led to the identification of 38 new small proteins.

scholarly journals Genetics in the Honey Bee: Achievements and Prospects toward the Functional Analysis of Molecular and Neural Mechanisms Underlying Social Behaviors

Insects ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 348 ◽  
Author(s):  
Hiroki Kohno ◽  
Takeo Kubo
Keyword(s):  
Candidate Genes ◽  
Honey Bee ◽  
Genetic Manipulation ◽  
Expression Profiles ◽  
Model Organism ◽  
Social Behaviors ◽  
Forward Genetics ◽  
Mushroom Bodies ◽  
Functional Analyses ◽  
The Brain

The European honey bee is a model organism for studying social behaviors. Comprehensive analyses focusing on the differential expression profiles of genes between the brains of nurse bees and foragers, or in the mushroom bodies—the brain structure related to learning and memory, and multimodal sensory integration—has identified candidate genes related to honey bee behaviors. Despite accumulating knowledge on the expression profiles of genes related to honey bee behaviors, it remains unclear whether these genes actually regulate social behaviors in the honey bee, in part because of the scarcity of genetic manipulation methods available for application to the honey bee. In this review, we describe the genetic methods applied to studies of the honey bee, ranging from classical forward genetics to recently developed gene modification methods using transposon and CRISPR/Cas9. We then discuss future functional analyses using these genetic methods targeting genes identified by the preceding research. Because no particular genes or neurons unique to social insects have been found yet, further exploration of candidate genes/neurons correlated with sociality through comprehensive analyses of mushroom bodies in the aculeate species can provide intriguing targets for functional analyses, as well as insight into the molecular and neural bases underlying social behaviors.

scholarly journals Adaptation of Porphyromonas gingivalis to microaerophilic conditions involves increased consumption of formate and reduced utilization of lactate

Microbiology ◽  
2009 ◽  
Vol 155 (11) ◽  
pp. 3758-3774 ◽  
Author(s):  
Janina P. Lewis ◽  
Divya Iyer ◽  
Cecilia Anaya-Bergman
Keyword(s):  
Gene Expression ◽  
Porphyromonas Gingivalis ◽  
Model Organism ◽  
Oxygen Metabolism ◽  
Exponential Growth Phase ◽  
Transcriptional Level ◽  
Gene Encoding ◽  
Aerobic Conditions ◽  
Small Proteins ◽  
Genes Encoding

Porphyromonas gingivalis, previously classified as a strict anaerobe, can grow in the presence of low concentrations of oxygen. Microarray analysis revealed alteration in gene expression in the presence of 6 % oxygen. During the exponential growth phase, 96 genes were upregulated and 79 genes were downregulated 1.4-fold. Genes encoding proteins that play a role in oxidative stress protection were upregulated, including alkyl hydroperoxide reductase (ahpCF), superoxide dismutase (sod) and thiol peroxidase (tpx). Significant changes in gene expression of proteins that mediate oxidative metabolism, such as cytochrome d ubiquinol oxidase-encoding genes, cydA and cydB, were detected. The expression of genes encoding formate uptake transporter (PG0209) and formate tetrahydrofolate ligase (fhs) was drastically elevated, which indicates that formate metabolism plays a major role under aerobic conditions. The concomitant reduction of expression of a gene encoding the lactate transporter PG1340 suggests decreased utilization of this nutrient. The concentrations of both formate and lactate were assessed in culture supernatants and cells, and they were in agreement with the results obtained at the transcriptional level. Also, genes encoding gingipain protease secretion/maturation regulator (porR) and protease transporter (porT) had reduced expression in the presence of oxygen, which also correlated with reduced protease activities under aerobic conditions. In addition, metal transport was affected, and while iron-uptake genes such as the genes encoding the haemin uptake locus (hmu) were downregulated, expression of manganese transporter genes, such as feoB2, was elevated in the presence of oxygen. Finally, genes encoding putative regulatory proteins such as extracellular function (ECF) sigma factors as well as small proteins had elevated expression levels in the presence of oxygen. As P. gingivalis is distantly related to the well-studied model organism Escherichia coli, results from our work may provide further understanding of oxygen metabolism and protection in other related bacteria belonging to the phylum Bacteroidetes.

scholarly journals A functional screen of translated pancreatic lncRNAs identifies a microprotein-independent role for LINC00261 in endocrine cell differentiation

2020 ◽  
Author(s):  
Bjoern Gaertner ◽  
Sebastiaan van Heesch ◽  
Valentin Schneider-Lunitz ◽  
Jana Felicitas Schulz ◽  
Franziska Witte ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Endocrine Cell ◽  
Small Scale ◽  
List Type ◽  
Pancreas Development ◽  
Human Pancreas ◽  
Loss Of Function ◽  
Developmentally Regulated ◽  
Small Proteins ◽  
Heterogenous Group

AbstractLong noncoding RNAs (lncRNAs) are a heterogenous group of RNAs, which can encode small proteins. The extent to which developmentally regulated lncRNAs are translated and whether the produced microproteins are relevant for human development is unknown. Here, we show that many lncRNAs in direct vicinity of lineage-determining transcription factors (TFs) are dynamically regulated, predominantly cytosolic, and highly translated during pancreas development. We genetically ablated ten such lncRNAs, most of them translated, and found that nine are dispensable for endocrine cell differentiation. However, deletion of LINC00261 diminishes generation of insulin+ endocrine cells, in a manner independent of the nearby TF FOXA2. Systematic deletion of each of LINC00261’s seven poorly conserved microproteins shows that the RNA, rather than the microproteins, is required for endocrine development. Our work highlights extensive translation of lncRNAs into recently evolved microproteins during human pancreas development and provides a blueprint for dissection of their coding and noncoding roles.Graphical AbstractHighlightsExtensive lncRNA translation and microprotein production during human pancreas developmentA small-scale loss-of-function screen shows most translated lncRNAs are dispensableLINC00261 is highly translated and regulates endocrine cell differentiationDeleting LINC00261’s evolutionary young microproteins reveals no essential roles

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