scholarly journals Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli

2021 ◽  
Vol 9 (6) ◽  
pp. 1123
Author(s):  
Hyun-Hee Lee ◽  
Jung-Wook Park ◽  
Hye-Jung Jung ◽  
Young-Su Seo
Keyword(s):  
Biosynthetic Gene Cluster ◽  
Ecological Niches ◽  
Repair System ◽  
Genome Sequences ◽  
Functional Roles ◽  
Pathway Enrichment ◽  
Pan Genome ◽  
Aromatic Compound Degradation ◽  
Burkholderia Gladioli

Burkholderia gladioli has high versatility and adaptability to various ecological niches. Here, we constructed a pan-genome using 14 genome sequences of B. gladioli, which originate from different niches, including gladiolus, rice, humans, and nature. Functional roles of core and niche-associated genomes were investigated by pathway enrichment analyses. Consequently, we inferred the uniquely important role of niche-associated genomes in (1) selenium availability during competition with gladiolus host; (2) aromatic compound degradation in seed-borne and crude oil-accumulated environments, and (3) stress-induced DNA repair system/recombination in the cystic fibrosis-niche. We also identified the conservation of the rhizomide biosynthetic gene cluster in all the B. gladioli strains and the concentrated distribution of this cluster in human isolates. It was confirmed the absence of complete CRISPR/Cas system in both plant and human pathogenic B. gladioli and the presence of the system in B. gladioli living in nature, possibly reflecting the inverse relationship between CRISPR/Cas system and virulence.

scholarly journals Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Sharon A. Huws ◽  
Joan E. Edwards ◽  
Wanchang Lin ◽  
Francesco Rubino ◽  
Mark Alston ◽  
...  
Keyword(s):  
Energy Harvesting ◽  
Perennial Ryegrass ◽  
Transcriptional Activity ◽  
Ecological Niches ◽  
Ecological Interactions ◽  
Carbohydrate Degradation ◽  
Host Nutrition ◽  
Role Based ◽  
Insight Into

Abstract Background Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling. Results Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be ‘cheating’ in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry. Conclusions In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants.

scholarly journals The Pleiotropic Function of Human Sirtuins as Modulators of Metabolic Pathways and Viral Infections

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 460
Author(s):  
Mohammed Hamed Alqarni ◽  
Ahmed Ibrahim Foudah ◽  
Magdy Mohamed Muharram ◽  
Nikolaos E. Labrou
Keyword(s):  
Metabolic Pathways ◽  
Histone Deacetylases ◽  
Viral Infections ◽  
Cell Physiology ◽  
Functional Roles ◽  
Regulatory Processes ◽  
Complex Functions ◽  
Natural Polyphenol ◽  
Antiviral Targets

Sirtuins (SIRTs) are nicotinamide adenine dinucleotide-dependent histone deacetylases that incorporate complex functions in the mechanisms of cell physiology. Mammals have seven distinct members of the SIRT family (SIRT1-7), which play an important role in a well-maintained network of metabolic pathways that control and adapt the cell to the environment, energy availability and cellular stress. Until recently, very few studies investigated the role of SIRTs in modulating viral infection and progeny. Recent studies have demonstrated that SIRT1 and SIRT2 are promising antiviral targets because of their specific connection to numerous metabolic and regulatory processes affected during infection. In the present review, we summarize some of the recent progress in SIRTs biochemistry and their emerging function as antiviral targets. We also discuss the potential of natural polyphenol-based SIRT modulators to control their functional roles in several diseases including viral infections.

scholarly journals Defining the niche for niche construction: evolutionary and ecological niches

2021 ◽  
Vol 36 (3) ◽  
Author(s):  
Rose Trappes
Keyword(s):  
Evolutionary Biology ◽  
Ecological Niche ◽  
Niche Construction ◽  
Habitat Degradation ◽  
Ecological Niches ◽  
Niche Concept ◽  
Definition Of ◽  
Compare And Contrast ◽  
Extreme Habitat

AbstractNiche construction theory (NCT) aims to transform and unite evolutionary biology and ecology. Much of the debate about NCT has focused on construction. Less attention has been accorded to the niche: what is it, exactly, that organisms are constructing? In this paper I compare and contrast the definition of the niche used in NCT with ecological niche definitions. NCT’s concept of the evolutionary niche is defined as the sum of selection pressures affecting a population. So defined, the evolutionary niche is narrower than the ecological niche. Moreover, when contrasted with a more restricted ecological niche concept, it has a slightly different extension. I point out three kinds of cases in which the evolutionary niche does not coincide with realized ecological niches: extreme habitat degradation, commensalism, and non-limiting or super-abundant resources. These conceptual differences affect the role of NCT in unifying ecology and evolutionary biology.

scholarly journals SOS2 Comes to the Fore: Differential Functionalities in Physiology and Pathology

2021 ◽  
Vol 22 (12) ◽  
pp. 6613
Author(s):  
Fernando C. Baltanás ◽  
Rósula García-Navas ◽  
Eugenio Santos
Keyword(s):  
Expression Patterns ◽  
Critical Role ◽  
Ras Signaling ◽  
Epidermal Stem Cell ◽  
Functional Specificity ◽  
Functional Roles ◽  
Signaling Axis ◽  
Therapy Target ◽  
External Stimuli

The SOS family of Ras-GEFs encompasses two highly homologous and widely expressed members, SOS1 and SOS2. Despite their similar structures and expression patterns, early studies of constitutive KO mice showing that SOS1-KO mutants were embryonic lethal while SOS2-KO mice were viable led to initially viewing SOS1 as the main Ras-GEF linking external stimuli to downstream RAS signaling, while obviating the functional significance of SOS2. Subsequently, different genetic and/or pharmacological ablation tools defined more precisely the functional specificity/redundancy of the SOS1/2 GEFs. Interestingly, the defective phenotypes observed in concomitantly ablated SOS1/2-DKO contexts are frequently much stronger than in single SOS1-KO scenarios and undetectable in single SOS2-KO cells, demonstrating functional redundancy between them and suggesting an ancillary role of SOS2 in the absence of SOS1. Preferential SOS1 role was also demonstrated in different RASopathies and tumors. Conversely, specific SOS2 functions, including a critical role in regulation of the RAS–PI3K/AKT signaling axis in keratinocytes and KRAS-driven tumor lines or in control of epidermal stem cell homeostasis, were also reported. Specific SOS2 mutations were also identified in some RASopathies and cancer forms. The relevance/specificity of the newly uncovered functional roles suggests that SOS2 should join SOS1 for consideration as a relevant biomarker/therapy target.

scholarly journals Species functional traits and abundance as drivers of multiplex ecological networks: first empirical quantification of inter-layer edge weights

2020 ◽  
Vol 287 (1939) ◽  
pp. 20202127
Author(s):  
S. Hervías-Parejo ◽  
C. Tur ◽  
R. Heleno ◽  
M. Nogales ◽  
S. Timóteo ◽  
...  
Keyword(s):  
Species Traits ◽  
Abundant Species ◽  
Modular Organization ◽  
Vertebrate Species ◽  
Multilayer Network ◽  
Functional Roles ◽  
Different Types ◽  
Seed Dispersers ◽  
Natural Communities

Many vertebrate species act as both plant pollinators and seed-dispersers, thus interconnecting these processes, particularly on islands. Ecological multilayer networks are a powerful tool to explore interdependencies between processes; however, quantifying the links between species engaging in different types of interactions (i.e. inter-layer edges) remains a great challenge. Here, we empirically measured inter-layer edge weights by quantifying the role of individually marked birds as both pollinators and seed-dispersers of Galápagos plant species over an entire year. Although most species (80%) engaged in both functions, we show that only a small proportion of individuals actually linked the two processes, highlighting the need to further consider intra-specific variability in individuals' functional roles. Furthermore, we found a high variation among species in linking both processes, i.e. some species contribute more than others to the modular organization of the multilayer network. Small and abundant species are particularly important for the cohesion of pollinator seed-dispersal networks, demonstrating the interplay between species traits and neutral processes structuring natural communities.

scholarly journals Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton

2008 ◽  
Vol 74 (10) ◽  
pp. 2933-2939 ◽  
Author(s):  
Erin J. Biers ◽  
Kui Wang ◽  
Catherine Pennington ◽  
Robert Belas ◽  
Feng Chen ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Sequence Data ◽  
Genome Sequences ◽  
Metagenomic Sequence ◽  
Marine Bacterioplankton ◽  
Extracellular Release ◽  
Gene Transfer Agent ◽  
Metagenomic Sequence Data ◽  
Search For Homologs

ABSTRACT Genes with homology to the transduction-like gene transfer agent (GTA) were observed in genome sequences of three cultured members of the marine Roseobacter clade. A broader search for homologs for this host-controlled virus-like gene transfer system identified likely GTA systems in cultured Alphaproteobacteria, and particularly in marine bacterioplankton representatives. Expression of GTA genes and extracellular release of GTA particles (∼50 to 70 nm) was demonstrated experimentally for the Roseobacter clade member Silicibacter pomeroyi DSS-3, and intraspecific gene transfer was documented. GTA homologs are surprisingly infrequent in marine metagenomic sequence data, however, and the role of this lateral gene transfer mechanism in ocean bacterioplankton communities remains unclear.

The Relation of Scent-Marking, Olfactory Investigation, and Specific Postures in the Isolation-Induced Fighting of Rats

Behaviour ◽  
1976 ◽  
Vol 56 (3-4) ◽  
pp. 286-297 ◽  
Author(s):  
David B. Adams
Keyword(s):  
Scent Marking ◽  
Functional Roles ◽  
Threat Behavior ◽  
Typical Sequence ◽  
Strange Male ◽  
Familiar Environment ◽  
And Performance ◽  
Temporal Sequences ◽  
Defensive Mechanism

AbstractThe temporal sequences of acts and postures of rats during tests for isolation-induced fighting were recorded and analyzed. Scent-marking and olfactory investigation, which have been related to fighting by previous studies, were particularly emphasized. From the data a model was constructed for the sequence of behaviors which lead to and maintain isolation-induced fighting. The typical sequence begins with olfactory investigation and scent-marking; the home rat initially investigates the intruder, and the intruder initially investigates the cage. The combination of olfactory perception of a strange male and a familiar environment, it was suggested, serves to trigger an offensive mechanism in the home rat which leads to bite-and-kick attack and offensive sideways posture. The pain of the attack then triggers defensive mechanism in the intruder rat which leads to defensive upright posture and submissive posture. Whereas the functional role of the bite-and-kick attack appears to be simply the infliction of pain and elicitation of defense in the intruder, the function of offensive sideways posture as a threat behavior may be more complex. It is possible that it becomes a conditioned pain stimulus due to its close temporal pairing with bite-and-kick attack, but it is more likely that it produces defense by a process of sensitization. In any case, following the initial attack, the offensive sideways posture continues to elicit defensive behavior by the intruder even when there are no further attacks. The functional roles of the defensive postures were interpreted as positioning the intruder in such a way that the home rat cannot assume the aggressive posture from which attack is launched. Scent-marking behavior was consistent within strains, within individuals, and across different types of measures (accumulation of scent-marking marking material and performance of the stereotyped scent-marking act, crawl-over-dish). Amount of scent-marking was not correlated with attack, however, and its role in isolation-induced fighting remains unclear. In parallel to findings in other rodents, it was observed that scent-marking was diminished in animals after they had been subjected to attack.

scholarly journals Exploring the multiple roles of guardian of the genome: P53

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Wasim Feroz ◽  
Arwah Mohammad Ali Sheikh
Keyword(s):  
Cell Cycle ◽  
Dna Repair ◽  
Crucial Role ◽  
Cellular Response ◽  
Genotoxic Stress ◽  
Specific Response ◽  
Main Body ◽  
Repair System ◽  
Tumour Suppression

Abstract Background Cells have evolved balanced mechanisms to protect themselves by initiating a specific response to a variety of stress. The TP53 gene, encoding P53 protein, is one of the many widely studied genes in human cells owing to its multifaceted functions and complex dynamics. The tumour-suppressing activity of P53 plays a principal role in the cellular response to stress. The majority of the human cancer cells exhibit the inactivation of the P53 pathway. In this review, we discuss the recent advancements in P53 research with particular focus on the role of P53 in DNA damage responses, apoptosis, autophagy, and cellular metabolism. We also discussed important P53-reactivation strategies that can play a crucial role in cancer therapy and the role of P53 in various diseases. Main body We used electronic databases like PubMed and Google Scholar for literature search. In response to a variety of cellular stress such as genotoxic stress, ischemic stress, oncogenic expression, P53 acts as a sensor, and suppresses tumour development by promoting cell death or permanent inhibition of cell proliferation. It controls several genes that play a role in the arrest of the cell cycle, cellular senescence, DNA repair system, and apoptosis. P53 plays a crucial role in supporting DNA repair by arresting the cell cycle to purchase time for the repair system to restore genome stability. Apoptosis is essential for maintaining tissue homeostasis and tumour suppression. P53 can induce apoptosis in a genetically unstable cell by interacting with many pro-apoptotic and anti-apoptotic factors. Furthermore, P53 can activate autophagy, which also plays a role in tumour suppression. P53 also regulates many metabolic pathways of glucose, lipid, and amino acid metabolism. Thus under mild metabolic stress, P53 contributes to the cell’s ability to adapt to and survive the stress. Conclusion These multiple levels of regulation enable P53 to perform diversified roles in many cell responses. Understanding the complete function of P53 is still a work in progress because of the inherent complexity involved in between P53 and its target proteins. Further research is required to unravel the mystery of this Guardian of the genome “TP53”.

scholarly journals Nematode Hsp90: highly conserved but functionally diverse

Parasitology ◽  
2014 ◽  
Vol 141 (9) ◽  
pp. 1203-1215 ◽  
Author(s):  
VICTORIA GILLAN ◽  
EILEEN DEVANEY
Keyword(s):  
Life Cycle ◽  
Heat Shock Protein 90 ◽  
Ecological Niches ◽  
Actual Number ◽  
Host Organism ◽  
Free Living ◽  
Parasitic Species ◽  
Free Living Nematode ◽  
Functionally Diverse

SUMMARYNematodes are amongst the most successful and abundant organisms on the planet with approximately 30 000 species described, although the actual number of species is estimated to be one million or more. Despite sharing a relatively simple and invariant body plan, there is considerable diversity within the phylum. Nematodes have evolved to colonize most ecological niches, and can be free-living or can parasitize plants or animals to the detriment of the host organism. In this review we consider the role of heat shock protein 90 (Hsp90) in the nematode life cycle. We describe studies on Hsp90 in the free-living nematode Caenorhabditis elegans and comparative work on the parasitic species Brugia pahangi, and consider whether a dependence upon Hsp90 can be exploited for the control of parasitic species.

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