scholarly journals Positive Selection and Gene Expression Analyses from Salivary Glands Reveal Discrete Adaptations within the Ecologically Diverse Bat Family Phyllostomidae

2020 ◽  
Vol 12 (8) ◽  
pp. 1419-1428
Author(s):  
Michael W Vandewege ◽  
Cibele G Sotero-Caio ◽  
Caleb D Phillips
Keyword(s):  
Gene Expression ◽  
Positive Selection ◽  
Salivary Glands ◽  
Acid Synthesis ◽  
Functional Diversification ◽  
Amino Acid Synthesis ◽  
The Family ◽  
Gene Expression Analyses ◽  
Dietary Strategies ◽  
Vampire Bat

Abstract The leaf-nosed bats (Phyllostomidae) are outliers among chiropterans with respect to the unusually high diversity of dietary strategies within the family. Salivary glands, owing to their functions and high ultrastructural variability among lineages, are proposed to have played an important role during the phyllostomid radiation. To identify genes underlying salivary gland functional diversification, we sequenced submandibular gland transcriptomes from phyllostomid species representative of divergent dietary strategies. From the assembled transcriptomes, we performed an array of selection tests and gene expression analyses to identify signatures of adaptation. Overall, we identified an enrichment of immunity-related gene ontology terms among 53 genes evolving under positive selection. Lineage-specific selection tests revealed several endomembrane system genes under selection in the vampire bat. Many genes that respond to insulin were under selection and differentially expressed genes pointed to modifications of amino acid synthesis pathways in plant-visitors. Results indicate salivary glands have diversified in various ways across a functional diverse clade of mammals in response to niche specializations.

scholarly journals Unearthing LTR retrotransposon gag genes co-opted in the deep evolution of eukaryotes

2021 ◽  
Author(s):  
Jianhua Wang ◽  
Guan-Zhu Han
Keyword(s):  
Gene Expression ◽  
Selective Pressure ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Cellular Functions ◽  
The Family ◽  
Family Level ◽  
Gene Expression Analyses ◽  
Comprehensive Picture ◽  
Gypsy Retrotransposons

Abstract LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes, and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.

scholarly journals Positive selection on secretory and structural components of salivary glands within the ecologically diverse bat family Phyllostomidae

2019 ◽  
Author(s):  
Michael Vandewege ◽  
Cibele G. Sotero-Caio ◽  
Caleb D. Phillips
Keyword(s):  
Salivary Gland ◽  
Positive Selection ◽  
Salivary Glands ◽  
Single Gene ◽  
Go Annotation ◽  
Exact Function ◽  
Secretory Products ◽  
Cellular Components ◽  
Dietary Strategies ◽  
Extracellular Environment

Abstract The leaf-nosed bats (Phyllostomidae) are outliers among chiropterans with respect to the unusually high diversity of dietary strategies within the family. Salivary glands, owing to their functions and high ultrastructural variability among lineages, are proposed to have played an important role during the phyllostomid radiation. Salivary gland secretory products directly interact with food materials and pathogens which can provide selective interactions. To identify genes underlying salivary gland functional diversification, we sequenced submandibular gland transcriptomes from phyllostomid species representative of divergent dietary strategies. From the assembled transcriptomes, we identified and tested 3,266 single gene orthologs and identified 57 evolving under positive selection. All enriched gene ontology terms were related to defense against other organisms and the cell membrane/extracellular environment. Based on GO annotation, many of the defense-related loci under selection form secretory products. Salivary glands perform a complex array of tasks, and we identified positive selection on additional proteins bound to membranes and in the extracellular environment with multiple functions. Although illuminating exact function is difficult, results suggest that regulatory release of secretory products, not the products themselves, is disproportionately shaped by positive selection on coding sequence. Identified instances of selection on such cellular components may help explain the ultrastructural variability of salivary glands previously documented.

scholarly journals Ohm's Law for increasing fitness gene expression with selection pressure

2019 ◽  
Author(s):  
Marta Ciechonska ◽  
Marc Sturrock ◽  
Alice Grob ◽  
Gerald Larrouy-Maumus ◽  
Vahid Shahrezaei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Selection Process ◽  
Antibiotic Resistance Gene ◽  
Phenotypic Selection ◽  
Acid Synthesis ◽  
General Nature ◽  
Amino Acid Synthesis ◽  
Positive Feedbacks ◽  
Ohm’S Law ◽  
Ohm's Law

Natural selection relies on genotypic and phenotypic adaptation in response to fluctuating environmental conditions and is the key to predicting and preventing drug resistance. Whereas classic persistence is all-or-nothing, here we show for the first time that an antibiotic resistance gene displays linear dose-responsive selection for increased expression in proportion to rising antibiotic concentration in E. coli. Furthermore, we observe the general nature of an instantaneous phenotypic selection process upon bactericidal and bacteriostatic antibiotic treatment, as well as an amino acid synthesis pathway enzyme under a range of auxotrophic conditions. To explain this phenomenon, we propose an analogy to Ohm's law in electricity (V=IR) where fitness pressure acts similarly to voltage (V), gene expression to current (I), and resistance (R) to cellular machinery constraints. Lastly, mathematical modelling approaches reveal that the emergent gene expression mechanism requires variation in mRNA and protein production within an isogenic population, and cell 'memory' from positive feedbacks between growth and expression of any fitness-inducing gene.

scholarly journals Molecular and Histologic Adaptation of Horned Gall Induced by the Aphid Schlechtendalia chinensis (Pemphigidae)

2021 ◽  
Vol 22 (10) ◽  
pp. 5166
Author(s):  
Qin Lu ◽  
Xiaoming Chen ◽  
Zixiang Yang ◽  
Nawaz Haider Bashir ◽  
Juan Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Amino Acid ◽  
Host Plants ◽  
Acid Synthesis ◽  
Essential Amino Acids ◽  
Amino Acid Synthesis ◽  
Glucose Content ◽  
Anatomical Structures ◽  
Synthesis And Degradation

Chinese galls are the result of hyperplasia in host plants induced by aphids. The metabolism and gene expression of these galls are modified to accommodate the aphids. Here, we highlight the molecular and histologic features of horned galls according to transcriptome and anatomical structures. In primary pathways, genes were found to be unevenly shifted and selectively expressed in the galls and leaves near the galls (LNG). Pathways for amino acid synthesis and degradation were also unevenly shifted, favoring enhanced accumulation of essential amino acids in galls for aphids. Although galls enhanced the biosynthesis of glucose, which is directly available to aphids, glucose content in the gall tissues was lower due to the feeding of aphids. Pathways of gall growth were up-regulated to provide enough space for aphids. In addition, the horned gall has specialized branched schizogenous ducts and expanded xylem in the stalk, which provide a broader feeding surface for aphids and improve the efficiency of transportation and nutrient exchange. Notably, the gene expression in the LNG showed a similar pattern to that of the galls, but on a smaller scale. We suppose the aphids manipulate galls to their advantage, and galls lessen competition by functioning as a medium between the aphids and their host plants.

Influence of increased nutrient supply on Microcystis aeruginosa at cellular and proteomic levels

2020 ◽  
Vol 85 ◽  
pp. 47-58
Author(s):  
Y Jiang ◽  
Y Liu
Keyword(s):  
Microcystis Aeruginosa ◽  
Regulatory Protein ◽  
Acid Synthesis ◽  
Nutrient Supply ◽  
Nitrogen Supply ◽  
Nitrogen And Phosphorus ◽  
Comprehensive Description ◽  
Amino Acid Synthesis ◽  
High Nutrient ◽  
Proteomic Responses

Various studies have observed that increased nutrient supply promotes the growth of bloom-forming cyanobacteria, but only a limited number of studies have investigated the influence of increased nutrient supply on bloom-forming cyanobacteria at the proteomic level. We investigated the cellular and proteomic responses of Microcystis aeruginosa to elevated nitrogen and phosphorus supply. Increased supply of both nutrients significantly promoted the growth of M. aeruginosa and the synthesis of chlorophyll a, protein, and microcystins. The release of microcystins and the synthesis of polysaccharides negatively correlated with the growth of M. aeruginosa under high nutrient levels. Overexpressed proteins related to photosynthesis, and amino acid synthesis, were responsible for the stimulatory effects of increased nutrient supply in M. aeruginosa. Increased nitrogen supply directly promoted cyanobacterial growth by inducing the overexpression of the cell division regulatory protein FtsZ. NtcA, that regulates gene transcription related to both nitrogen assimilation and microcystin synthesis, was overexpressed under the high nitrogen condition, which consequently induced overexpression of 2 microcystin synthetases (McyC and McyF) and promoted microcystin synthesis. Elevated nitrogen supply induced the overexpression of proteins involved in gas vesicle organization (GvpC and GvpW), which may increase the buoyancy of M. aeruginosa. Increased phosphorus level indirectly affected growth and the synthesis of cellular substances in M. aeruginosa through the mediation of differentially expressed proteins related to carbon and phosphorus metabolism. This study provides a comprehensive description of changes in the proteome of M. aeruginosa in response to an increased supply of 2 key nutrients.

O-AcylTEMPOs, a Modified and Fundamental, but Unexplored Carboxylic Derivative: Recent Progress in Synthetic Applications

2019 ◽  
Vol 23 (19) ◽  
pp. 2102-2121
Author(s):  
Hiroyuki Kawafuchi ◽  
Lijian Ma ◽  
Md Imran Hossain ◽  
Tsutomu Inokuchi
Keyword(s):  
Organic Synthesis ◽  
Recent Progress ◽  
Knoevenagel Condensation ◽  
Acid Synthesis ◽  
Amino Acid Synthesis ◽  
Electrophilic Amination ◽  
Weinreb Amides ◽  
Anionic Species ◽  
Diastereoselective Addition ◽  
Carbonyl Function

O-Acylated 2,2,6,6-tetramethylpiperidine-N-oxyls (abbr. O-AcylTEMPOs) are easily available and stable carboxylic derivatives, but their utility in organic synthesis is unexplored in contrast to analogues, such as the N-methoxy-N-methylamides, known as Weinreb amides. Especially, the O–N unit of the O-acylTEMPOs dictates a fairly electronwithdrawing character for the carbonyl function. This enhances the reactivity and stability of the resulting enolate ions. Accordingly, O-acylTEMPOs allow various transformations and this review encompasses seven topics: (1) Reactivity of O-acylTEMPOs towards nucleophiles and chemoselective transformations, (2) Reactivity of anionic species derived from O-acylTEMPOs, (3) E-Selective Knoevenagel condensation of acetoacetylTEMPOs and synthesis of furans, (4) Electrocyclization of 2,4-dienones derived from acetoacetic derivatives and 2-substituted enals, (5) Diastereoselective addition of amide anion to O-(2-alkenoyl)TEMPOs and β-amino acid synthesis, (6) Thermolysis of O-acylTEMPOs, and (7) Applications for Umpolung reactions using O-benzoylTEMPOs, useful for the electrophilic amination of alkenes and alkynes.

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