scholarly journals Toward a better understanding of the mechanisms of symbiosis: a comprehensive proteome map a nascent insect symbiont

2017 ◽  
Author(s):  
François Renoz ◽  
Antoine Champagne ◽  
Hervé Degand ◽  
Anne-Marie Faber ◽  
Pierre Morsomme ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Molecular Mechanisms ◽  
Symbiotic Bacteria ◽  
Primary Metabolism ◽  
Free Living ◽  
Molecular Features ◽  
Proteomic Approach ◽  
Insect Symbionts ◽  
Host Tissues

Symbiotic bacteria are common in insects and can affect various aspects of their hosts’ biology. Although the effects of insect symbionts have been clarified for various insect symbiosis models, due to the difficulty of cultivating them in vitro, there is still limited knowledge available on the molecular features that drive symbiosis. Serratia symbiotica is one of the most common symbionts found in aphids. The recent findings of free-living strains that are considered as nascent partners of aphids provide the opportunity to examine the molecular mechanisms that a symbiont can deployed at the early stages of the symbiosis (i.e., symbiotic factors). In this work, a proteomic approach was used to establish a comprehensive proteome map of the free-living S. symbiotica strain CWBI-2.3T. Most of the 720 proteins identified are related to housekeeping or primary metabolism. Of these, 76 were identified as candidate proteins possibly promoting host colonization. Our results provide strong evidence that S. symbiotica CWBI-2.3T is well-armed for invading insect host tissues, and suggest that certain molecular features usually harbored by pathogenic bacteria are no longer present. This comprehensive proteome map provides a series of candidate genes for further studies to understand the molecular cross-talk between insects and symbiotic bacteria.

scholarly journals Toward a better understanding of the mechanisms of symbiosis: a comprehensive proteome map a nascent insect symbiont

2017 ◽  
Author(s):  
François Renoz ◽  
Antoine Champagne ◽  
Hervé Degand ◽  
Anne-Marie Faber ◽  
Pierre Morsomme ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Molecular Mechanisms ◽  
Symbiotic Bacteria ◽  
Primary Metabolism ◽  
Free Living ◽  
Molecular Features ◽  
Proteomic Approach ◽  
Insect Symbionts ◽  
Host Tissues

Symbiotic bacteria are common in insects and can affect various aspects of their hosts’ biology. Although the effects of insect symbionts have been clarified for various insect symbiosis models, due to the difficulty of cultivating them in vitro, there is still limited knowledge available on the molecular features that drive symbiosis. Serratia symbiotica is one of the most common symbionts found in aphids. The recent findings of free-living strains that are considered as nascent partners of aphids provide the opportunity to examine the molecular mechanisms that a symbiont can deployed at the early stages of the symbiosis (i.e., symbiotic factors). In this work, a proteomic approach was used to establish a comprehensive proteome map of the free-living S. symbiotica strain CWBI-2.3T. Most of the 720 proteins identified are related to housekeeping or primary metabolism. Of these, 76 were identified as candidate proteins possibly promoting host colonization. Our results provide strong evidence that S. symbiotica CWBI-2.3T is well-armed for invading insect host tissues, and suggest that certain molecular features usually harbored by pathogenic bacteria are no longer present. This comprehensive proteome map provides a series of candidate genes for further studies to understand the molecular cross-talk between insects and symbiotic bacteria.

scholarly journals Toward a better understanding of the mechanisms of symbiosis: a comprehensive proteome map of a nascent insect symbiont

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3291 ◽  
Author(s):  
François Renoz ◽  
Antoine Champagne ◽  
Hervé Degand ◽  
Anne-Marie Faber ◽  
Pierre Morsomme ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Molecular Mechanisms ◽  
Symbiotic Bacteria ◽  
Primary Metabolism ◽  
Free Living ◽  
Molecular Features ◽  
Proteomic Approach ◽  
Insect Symbionts ◽  
Host Tissues

Symbiotic bacteria are common in insects and can affect various aspects of their hosts’ biology. Although the effects of insect symbionts have been clarified for various insect symbiosis models, due to the difficulty of cultivating themin vitro, there is still limited knowledge available on the molecular features that drive symbiosis.Serratia symbioticais one of the most common symbionts found in aphids. The recent findings of free-living strains that are considered as nascent partners of aphids provide the opportunity to examine the molecular mechanisms that a symbiont can deploy at the early stages of the symbiosis (i.e., symbiotic factors). In this work, a proteomic approach was used to establish a comprehensive proteome map of the free-livingS. symbioticastrain CWBI-2.3T. Most of the 720 proteins identified are related to housekeeping or primary metabolism. Of these, 76 were identified as candidate proteins possibly promoting host colonization. Our results provide strong evidence thatS. symbioticaCWBI-2.3Tis well-armed for invading insect host tissues, and suggest that certain molecular features usually harbored by pathogenic bacteria are no longer present. This comprehensive proteome map provides a series of candidate genes for further studies to understand the molecular cross-talk between insects and symbiotic bacteria.

scholarly journals Oxygen-Dependent Changes in the N-Glycome of Murine Pulmonary Endothelial Cells

Antioxidants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1947
Author(s):  
Akos Tiboldi ◽  
Johannes Führer ◽  
Wolfgang Schaubmayr ◽  
Eva Hunyadi-Gulyas ◽  
Marie Louise Zach ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Lectin Binding ◽  
Supplemental Oxygen ◽  
Redox Status ◽  
Blood Oxygenation ◽  
Glycan Structure ◽  
Pulmonary Endothelium ◽  
Proteomic Approach ◽  
Oxygen Conditions

Supplemental oxygen is frequently used together with mechanical ventilation to achieve sufficient blood oxygenation. Despite the undoubted benefits, it is vigorously debated whether too much oxygen can also have unpredicted side-effects. Uncertainty is also due to the fact that the molecular mechanisms are still insufficiently understood. The lung endothelium is covered with an exceptionally broad glycocalyx, carrying N- and O-glycans, proteoglycans, glycolipids and glycosaminoglycans. Glycan structures are not genetically determined but depend on the metabolic state and the expression level and activity of biosynthetic and glycan remodeling enzymes, which can be influenced by oxygen and the redox status of the cell. Altered glycan structures can affect cell interactions and signaling. In this study, we investigated the effect of different oxygen conditions on aspects of the glycobiology of the pulmonary endothelium with an emphasis on N-glycans and terminal sialylation using an in vitro cell culture system. We combined a proteomic approach with N-glycan structure analysis by LC-MS, qRT-PCR, sialic acid analysis and lectin binding to show that constant and intermittent hyperoxia induced time dependent changes in global and surface glycosylation. An siRNA approach identified St6gal1 as being primarily responsible for the early transient increase of α2-6 sialylated structures in response to hyperoxia.

scholarly journals Challenges and perspectives for structural biology of lncRNAs—the example of the Xist lncRNA A-repeats

2019 ◽  
Vol 11 (10) ◽  
pp. 845-859 ◽  
Author(s):  
Alisha N Jones ◽  
Michael Sattler
Keyword(s):  
High Resolution ◽  
Structural Biology ◽  
Recent Progress ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Structural Features ◽  
Molecular Features

Abstract Following the discovery of numerous long non-coding RNA (lncRNA) transcripts in the human genome, their important roles in biology and human disease are emerging. Recent progress in experimental methods has enabled the identification of structural features of lncRNAs. However, determining high-resolution structures is challenging as lncRNAs are expected to be dynamic and adopt multiple conformations, which may be modulated by interaction with protein binding partners. The X-inactive specific transcript (Xist) is necessary for X inactivation during dosage compensation in female placental mammals and one of the best-studied lncRNAs. Recent progress has provided new insights into the domain organization, molecular features, and RNA binding proteins that interact with distinct regions of Xist. The A-repeats located at the 5′ end of the transcript are of particular interest as they are essential for mediating silencing of the inactive X chromosome. Here, we discuss recent progress with elucidating structural features of the Xist lncRNA, focusing on the A-repeats. We discuss the experimental and computational approaches employed that have led to distinct structural models, likely reflecting the intrinsic dynamics of this RNA. The presence of multiple dynamic conformations may also play an important role in the formation of the associated RNPs, thus influencing the molecular mechanism underlying the biological function of the Xist A-repeats. We propose that integrative approaches that combine biochemical experiments and high-resolution structural biology in vitro with chemical probing and functional studies in vivo are required to unravel the molecular mechanisms of lncRNAs.

scholarly journals Protein Expression Profiles in an Endosymbiotic Cyanobacterium Revealed by a Proteomic Approach

2006 ◽  
Vol 19 (11) ◽  
pp. 1251-1261 ◽  
Author(s):  
Martin Ekman ◽  
Petter Tollbäck ◽  
Johan Klint ◽  
Birgitta Bergman
Keyword(s):  
Mass Spectrometry ◽  
Protein Expression ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Calvin Cycle ◽  
Pentose Phosphate ◽  
Free Living ◽  
Two Dimensional Gel Electrophoresis ◽  
Proteomic Approach ◽  
Nostoc Strain

Molecular mechanisms behind adaptations in the cyano-bacterium (Nostoc sp.) to a life in endosymbiosis with plants are still not clarified, nor are the interactions between the partners. To get further insights, the proteome of a Nostoc strain, freshly isolated from the symbiotic gland tissue of the angiosperm Gunnera manicata Linden, was analyzed and compared with the proteome of the same strain when free-living. Extracted proteins were separated by two-dimensional gel electrophoresis and were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry combined with tandem mass spectrometry. Even when the higher percentage of differentiated cells (heterocysts) in symbiosis was compensated for, the majority of the proteins detected in the symbiotic cyanobacteria were present in the free-living counterpart, indicating that most cellular processes were common for both stages. However, differential expression profiling revealed a significant number of proteins to be down-regulated or missing in the symbiotic stage, while others were more abundant or only expressed in symbiosis. The differential protein expression was primarily connected to i) cell envelope-associated processes, including proteins involved in exopolysaccharide synthesis and surface and membrane associated proteins, ii) to changes in growth and metabolic activities (C and N), including upregulation of nitrogenase and proteins involved in the oxidative pentose phosphate pathway and downregu-lation of Calvin cycle enzymes, and iii) to the dark, micro-aerobic conditions offered inside the Gunnera gland cells, including changes in relative phycobiliprotein concentrations. This is the first comprehensive analysis of proteins in the symbiotic state.

scholarly journals OmpA-Mediated Biofilm Formation Is Essential for the Commensal Bacterium Sodalis glossinidius To Colonize the Tsetse Fly Gut

2012 ◽  
Vol 78 (21) ◽  
pp. 7760-7768 ◽  
Author(s):  
Michele A. Maltz ◽  
Brian L. Weiss ◽  
Michelle O'Neill ◽  
Yineng Wu ◽  
Serap Aksoy
Keyword(s):  
Immune System ◽  
Pathogenic Bacteria ◽  
Tsetse Fly ◽  
Symbiotic Bacteria ◽  
Tsetse Flies ◽  
Host Immune System ◽  
Content Type ◽  
African Trypanosomes ◽  
Sodalis Glossinidius

ABSTRACTMany bacteria successfully colonize animals by forming protective biofilms. Molecular processes that underlie the formation and function of biofilms in pathogenic bacteria are well characterized. In contrast, the relationship between biofilms and host colonization by symbiotic bacteria is less well understood. Tsetse flies (Glossinaspp.) house 3 maternally transmitted symbionts, one of which is a commensal (Sodalis glossinidius) found in several host tissues, including the gut. We determined thatSodalisforms biofilms in the tsetse gut and that this process is influenced by theSodalisouter membrane protein A (OmpA). MutantSodalisstrains that do not produce OmpA (SodalisΔOmpA mutants) fail to form biofilmsin vitroand are unable to colonize the tsetse gut unless endogenous symbiotic bacteria are present. Our data indicate that in the absence of biofilms,SodalisΔOmpA mutant cells are exposed to and eliminated by tsetse's innate immune system, suggesting that biofilms helpSodalisevade the host immune system. Tsetse is the sole vector of pathogenic African trypanosomes, which also reside in the fly gut. Acquiring a better understanding of the dynamics that promoteSodaliscolonization of the tsetse gut may enhance the development of novel disease control strategies.

Epigenetic Mechanisms of Stem Cell Aging and Rejuvenation

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. SCI-44-SCI-44
Author(s):  
Thomas A. Rando
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Molecular Mechanisms ◽  
Conflicts Of Interest ◽  
Cell Aging ◽  
Molecular Characteristics ◽  
Molecular Features ◽  
Functional Features

Abstract For most tissues, stem cell numbers decline negligibly with age; nevertheless, there is an age-dependent decline in stem cell functionality. Many molecular, biochemical, and functional features of stem cells have been characterized across a broad range of tissues, and these changes have been assumed to be largely irreversible and inevitable accompaniments of aging. However, in studies both in vivo and in vitro we have demonstrated a reversibility of the functional and, in some cases, molecular characteristics of aged stem cells. Supported by compelling data from studies of heterochronic parabiotic pairings of mice, it is clear that the aged phenotype can be modified when aged cells are exposed to a youthful systemic milieu. These findings challenge the fundamental tenet of aging as an irreversible process and raises the question of whether, or to what extent, the aged phenotype is epigenetically determined. We have begun to examine the epigenetic profiles of young, old, and “rejuvenated” old stem cells to attempt to define youthfulness and aging in epigenetic terms. To the extent that aging can be “reprogrammed” back to youthfulness in somatic tissues, it has parallels to the resetting of the aging clock that occurs with somatic cell nuclear transfer. Elucidating the underlying molecular features, both genetic and epigenetic, of aged stem cells will provide a framework for understanding the fundamental molecular mechanisms of aging and the mechanisms by which environmental influences, such as those that occur in the setting of heterochronic parabiosis, can reverse the mechanisms of aging. Disclosures No relevant conflicts of interest to declare.

scholarly journals High-Throughput Phenotyping Toolkit for Characterizing Cellular Models of Hypertrophic Cardiomyopathy in Vitro

2019 ◽  
Vol 2 (4) ◽  
pp. 83 ◽  
Author(s):  
Mosqueira ◽  
Lis-Slimak ◽  
Denning
Keyword(s):  
Hypertrophic Cardiomyopathy ◽  
High Throughput ◽  
Molecular Mechanisms ◽  
Clinical Manifestations ◽  
Cellular Models ◽  
Molecular Features ◽  
High Throughput Drug Screening ◽  
High Throughput Phenotyping ◽  
Screening Approaches

Hypertrophic cardiomyopathy (HCM) is a prevalent and complex cardiovascular disease characterised by multifarious hallmarks, a heterogeneous set of clinical manifestations, and several molecular mechanisms. Various disease models have been developed to study this condition, but they often show contradictory results, due to technical constraints and/or model limitations. Therefore, new tools are needed to better investigate pathological features in an unbiased and technically refined approach, towards improving understanding of disease progression. Herein, we describe three simple protocols to phenotype cellular models of HCM in vitro, in a high-throughput manner where technical artefacts are minimized. These are aimed at investigating: (1) Hypertrophy, by measuring cell volume by flow cytometry; (2) HCM molecular features, through the analysis of a hypertrophic marker, multinucleation, and sarcomeric disarray by high-content imaging; and (3) mitochondrial respiration and content via the Seahorse™ platform. Collectively, these protocols comprise straightforward tools to evaluate molecular and functional parameters of HCM phenotypes in cardiomyocytes in vitro. These facilitate greater understanding of HCM and high-throughput drug screening approaches and are accessible to all researchers of cardiac disease modelling. Whilst HCM is used as an exemplar, the approaches described are applicable to other cellular models where the investigation of identical biological changes is paramount.

scholarly journals Prospective stem cell lines as in vitro neurodegenerative disease models for natural product research

2019 ◽  
Vol 2 (1) ◽  
pp. 16-30
Author(s):  
Nur Izzati Mansor ◽  
Nuratiqah Azmi ◽  
King Hwa Ling ◽  
Rozita Rosli ◽  
Zurina Hassan ◽  
...  
Keyword(s):  
Natural Products ◽  
Stem Cell ◽  
Cell Lines ◽  
Molecular Mechanisms ◽  
Vital Role ◽  
Common Source ◽  
Molecular Features ◽  
Natural Product Research ◽  
Stem Cell Lines

The use of in vitro model for screening pharmacological compounds or natural products has gained global interest.  The choice of cells to be manipulated plays a vital role in coming up with the best-suited model for specific diseases, including neurodegenerative diseases (ND). A good in vitro ND model should provide appropriate morphological and molecular features that mimic ND conditions where it can be used to screen potential properties of natural products in addition to unravelling the molecular mechanisms of ND.  In this mini review, we intend to demonstrate two prospective stem cell lines as the potential cell source for in vitro ND model and compare them to the commonly used cells.  The common source of cells that have been used as the in vitro ND models is discussed before going into details talking about the two prospective stem cell lines.

scholarly journals Metabolic reprogramming associated with aggressiveness occurs in the G-CIMP-high molecular subtypes of IDH1mut lower grade gliomas

2019 ◽  
Vol 22 (4) ◽  
pp. 480-492 ◽  
Author(s):  
Victor Ruiz-Rodado ◽  
Tathiane M Malta ◽  
Tomohiro Seki ◽  
Adrian Lita ◽  
Tyrone Dowdy ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Molecular Subtype ◽  
Tumor Biology ◽  
Metabolic Reprogramming ◽  
The Cancer Genome Atlas ◽  
Model Systems ◽  
Lower Grade ◽  
Molecular Features

Abstract Background Early detection of increased aggressiveness of brain tumors is a major challenge in the field of neuro-oncology because of the inability of traditional imaging to uncover it. Isocitrate dehydrogenase (IDH)-mutant gliomas represent an ideal model system to study the molecular mechanisms associated with tumorigenicity because they appear indolent and non-glycolytic initially, but eventually a subset progresses toward secondary glioblastoma with a Warburg-like phenotype. The mechanisms and molecular features associated with this transformation are poorly understood. Methods We employed model systems for IDH1 mutant (IDH1mut) gliomas with different growth and proliferation rates in vivo and in vitro. We described the metabolome, transcriptome, and epigenome of these models in order to understand the link between their metabolism and the tumor biology. To verify whether this metabolic reprogramming occurs in the clinic, we analyzed data from The Cancer Genome Atlas. Results We reveal that the aggressive glioma models have lost DNA methylation in the promoters of glycolytic enzymes, especially lactate dehydrogenase A (LDHA), and have increased mRNA and metabolite levels compared with the indolent model. We find that the acquisition of the high glycolytic phenotype occurs at the glioma cytosine-phosphate-guanine island methylator phenotype (G-CIMP)-high molecular subtype in patients and is associated with the worst outcome. Conclusion We propose very early monitoring of lactate levels as a biomarker of metabolic reprogramming and tumor aggressiveness.

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