Age-dependent decline in stress response capacity revealed by proteins dynamics analysis

Abstract The aging process is regarded as the progressive loss of physiological integrity, leading to impaired biological functions and the increased vulnerability to death. Among various biological functions, stress response capacity enables cells to alter gene expression patterns and survive when facing internal and external stresses. Here, we explored changes in stress response capacity during the replicative aging of Saccharomyces cerevisiae. To this end, we used a high-throughput microfluidic device to deliver intermittent pulses of osmotic stress and tracked the dynamic changes in the production of downstream stress-responsive proteins, in a large number of individual aging cells. Cells showed a gradual decline in stress response capacity of these osmotic-related downstream proteins during the aging process after the first 5 generations. Among the downstream stress-responsive genes and unrelated genes tested, the residual level of response capacity of Trehalose-6-Phosphate Synthase (TPS2) showed the best correlation with the cell remaining lifespan. By monitor dynamics of the upstream transcription factors and mRNA of Tps2, it was suggested that the decline in downstream stress response capacity was caused by the decline of translational rate of these proteins during aging.

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T-cell Activation Induces Dynamic Changes in miRNA Expression Patterns in CD4 and CD8 T-cell Subsets

MicroRNA ◽

10.2174/2211536604666150819194636 ◽

2015 ◽

Vol 4 (2) ◽

pp. 117-122 ◽

Cited By ~ 16

Author(s):

Nato Teteloshvili ◽

Katarzyna Smigielska-Czepiel ◽

Bart-Jan Kroesen ◽

Elisabeth Brouwer ◽

Joost Kluiver ◽

...

Keyword(s):

T Cell ◽

T Cell Activation ◽

Mirna Expression ◽

Cell Activation ◽

Expression Patterns ◽

Cd8 T Cell ◽

T Cell Subsets ◽

Dynamic Changes

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Metabolomics of aging in primary fibroblasts from small and large breed dogs

GeroScience ◽

10.1007/s11357-021-00388-0 ◽

2021 ◽

Author(s):

Paul S. Brookes ◽

Ana Gabriela Jimenez

Keyword(s):

Aging Process ◽

Tca Cycle ◽

Therapeutic Strategies ◽

Targeted Metabolomics ◽

The Tca Cycle ◽

Age Dependent ◽

Primary Fibroblasts ◽

Aging Rates ◽

Underlying Mechanisms ◽

Coenzyme A Biosynthesis

AbstractAmong several animal groups (eutherian mammals, birds, reptiles), lifespan positively correlates with body mass over several orders of magnitude. Contradicting this pattern are domesticated dogs, with small dog breeds exhibiting significantly longer lifespans than large dog breeds. The underlying mechanisms of differing aging rates across body masses are unclear, but it is generally agreed that metabolism is a significant regulator of the aging process. Herein, we performed a targeted metabolomics analysis on primary fibroblasts isolated from small and large breed young and old dogs. Regardless of size, older dogs exhibited lower glutathione and ATP, consistent with a role for oxidative stress and bioenergetic decline in aging. Furthermore, several size-specific metabolic patterns were observed with aging, including the following: (i) An apparent defect in the lower half of glycolysis in large old dogs at the level of pyruvate kinase. (ii) Increased glutamine anaplerosis into the TCA cycle in large old dogs. (iii) A potential defect in coenzyme A biosynthesis in large old dogs. (iv) Low nucleotide levels in small young dogs that corrected with age. (v) An age-dependent increase in carnitine in small dogs that was absent in large dogs. Overall, these data support the hypothesis that alterations in metabolism may underlie the different lifespans of small vs. large breed dogs, and further work in this area may afford potential therapeutic strategies to improve the lifespan of large dogs.

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Genome-Wide Identification and Expression Analyses of CONSTANS-Like Family Genes in Cucumber (Cucumis sativus L.)

Journal of Plant Growth Regulation ◽

10.1007/s00344-021-10420-4 ◽

2021 ◽

Author(s):

Zhen Tian ◽

Xiaodong Qin ◽

Hui Wang ◽

Ji Li ◽

Jinfeng Chen

Keyword(s):

Floral Induction ◽

Structural Characteristics ◽

Expression Patterns ◽

Evolutionary Relationship ◽

Biological Functions ◽

Promoter Regions ◽

Cucumis Sativus L ◽

Cis Acting ◽

Genome Wide ◽

Induction Process

AbstractThe CONSTANS-like (COL) gene family is one of the plant-specific transcription factor families that play important roles in plant growth and development. However, the knowledge of COLs related in cucumber is limited, and their biological functions, especially in the photoperiod-dependent flowering process, are still unclear. In this study, twelve CsaCOL genes were identified in the cucumber genome. Phylogenetic and conserved motif analyses provided insights into the evolutionary relationship between the CsaCOLs. Further, the comparative genome analysis revealed that COL genes are conserved in different plant species, especially collinearity gene pairs related to CsaCOL5. Ten kinds of cis-acting elements were vividly detected in CsaCOLs promoter regions, including five light-responsive elements, which echo the diurnal rhythm expression patterns of seven CsaCOL genes under SD and LD photoperiod regimes. Combined with the expression data of developmental stage, three CsaCOL genes are involved in the flowering network and play pivotal roles for the floral induction process. Our results provide useful information for further elucidating the structural characteristics, expression patterns, and biological functions of COL family genes in many plants

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The Divergent Roles of the Rice bcl-2 Associated Athanogene (BAG) Genes in Plant Development and Environmental Responses

Plants ◽

10.3390/plants10102169 ◽

2021 ◽

Vol 10 (10) ◽

pp. 2169

Author(s):

Hailian Zhou ◽

Jiaying Li ◽

Xueyuan Liu ◽

Xiaoshuang Wei ◽

Ziwei He ◽

...

Keyword(s):

Plant Development ◽

Stress Responses ◽

Expression Profiles ◽

Expression Patterns ◽

Brown Planthopper ◽

Protein Structures ◽

Secondary Growth ◽

Primary Cell Wall ◽

Biological Functions ◽

Group I

Bcl-2-associated athanogene (BAG), a group of proteins evolutionarily conserved and functioned as co-chaperones in plants and animals, is involved in various cell activities and diverse physiological processes. However, the biological functions of this gene family in rice are largely unknown. In this study, we identified a total of six BAG members in rice. These genes were classified into two groups, OsBAG1, -2, -3, and -4 are in group I with a conserved ubiquitin-like structure and OsBAG5 and -6 are in group Ⅱ with a calmodulin-binding domain, in addition to a common BAG domain. The BAG genes exhibited diverse expression patterns, with OsBAG4 showing the highest expression level, followed by OsBAG1 and OsBAG3, and OsBAG6 preferentially expressed in the panicle, endosperm, and calli. The co-expression analysis and the hierarchical cluster analysis indicated that the OsBAG1 and OsBAG3 were co-expressed with primary cell wall-biosynthesizing genes, OsBAG4 was co-expressed with phytohormone and transcriptional factors, and OsBAG6 was co-expressed with disease and shock-associated genes. β-glucuronidase (GUS) staining further indicated that OsBAG3 is mainly involved in primary young tissues under both primary and secondary growth. In addition, the expression of the BAG genes under brown planthopper (BPH) feeding, N, P, and K deficiency, heat, drought and plant hormones treatments was investigated. Our results clearly showed that OsBAGs are multifunctional molecules as inferred by their protein structures, subcellular localizations, and expression profiles. BAGs in group I are mainly involved in plant development, whereas BAGs in group II are reactive in gene regulations and stress responses. Our results provide a solid basis for the further elucidation of the biological functions of plant BAG genes.

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Respiratory Microbiota Profiles Associated With the Progression From Airway Inflammation to Remodeling in Mice With OVA-Induced Asthma

Frontiers in Microbiology ◽

10.3389/fmicb.2021.723152 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jun Zheng ◽

Qian Wu ◽

Ya Zou ◽

Meifen Wang ◽

Li He ◽

...

Keyword(s):

Airway Remodeling ◽

Periodic Acid ◽

Expression Patterns ◽

Allergic Inflammation ◽

Rrna Gene ◽

Chronic Asthma ◽

Functional Prediction ◽

Dynamic Changes ◽

Cytokine Levels ◽

Respiratory Microbiota

BackgroundThe dysbiosis of respiratory microbiota plays an important role in asthma development. However, there is limited information on the changes in the respiratory microbiota and how these affect the host during the progression from acute allergic inflammation to airway remodeling in asthma.ObjectiveAn ovalbumin (OVA)-induced mouse model of chronic asthma was established to explore the dynamic changes in the respiratory microbiota in the different stages of asthma and their association with chronic asthma progression.MethodsHematoxylin and eosin (H&E), periodic acid-schiff (PAS), and Masson staining were performed to observe the pathological changes in the lung tissues of asthmatic mice. The respiratory microbiota was analyzed using 16S rRNA gene sequencing followed by taxonomical analysis. The cytokine levels in bronchoalveolar lavage fluid (BALF) specimens were measured. The matrix metallopeptidase 9 (MMP-9) and vascular endothelial growth factor (VEGF-A) expression levels in lung tissues were measured to detect airway remodeling in OVA-challenged mice.ResultsAcute allergic inflammation was the major manifestation at weeks 1 and 2 after OVA atomization stimulation, whereas at week 6 after the stimulation, airway remodeling was the most prominent observation. In the acute inflammatory stage, Pseudomonas was more abundant, whereas Staphylococcus and Cupriavidus were more abundant at the airway remodeling stage. The microbial compositions of the upper and lower respiratory tracts were similar. However, the dominant respiratory microbiota in the acute inflammatory and airway remodeling phases were different. Metagenomic functional prediction showed that the pathways significantly upregulated in the acute inflammatory phase and airway remodeling phase were different. The cytokine levels in BALF and the expression patterns of proteins associated with airway remodeling in the lung tissue were consistent with the metagenomic function results.ConclusionThe dynamic changes in respiratory microbiota are closely associated with the progression of chronic asthma. Metagenomic functional prediction indicated the changes associated with acute allergic inflammation and airway remodeling.

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On the regulatory evolution of new genes throughout their life history

10.1101/276667 ◽

2018 ◽

Author(s):

Jia-yu Zhang ◽

Qi Zhou

Keyword(s):

Life History ◽

Expression Patterns ◽

Housekeeping Genes ◽

Regulatory Elements ◽

Basic Question ◽

Regulatory Evolution ◽

New Genes ◽

Age Dependent ◽

Gain Loss ◽

Evolution Trajectory

AbstractEvery gene has a birthplace and an age, i.e., a cis-regulatory environment and an evolution lifespan since its origination, yet how gene’s evolution trajectory is shaped by the two remains unclear. Here we address this basic question by comparing phylogenetically dated new genes of different ages among Drosophila and vertebrate species. For both, we find a clear ‘out of testis’ transition from the testis-specific young genes to the broadly expressed old housekeeping genes. Particularly, many new genes have evolved specific activation at maternal-zygotic transition, or distinctive spatiotemporal embryonic expression patterns from the parental genes. We uncover an age-dependent gain/loss of active/repressive histone modifications and cis-regulatory elements, with variations between species and between somatic/germline tissues, which together underpin the stepwise acquisition of novel and important function by new genes. These results illuminate the general evolution trajectory and the underlying regulatory mechanisms of genes throughout their life history.

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The DUB family in Populus: identification, characterization, evolution and expression patterns

BMC Genomics ◽

10.1186/s12864-021-07844-3 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Wenqing Zheng ◽

Liang Du

Keyword(s):

Abiotic Stress ◽

Stress Response ◽

Gene Structure ◽

Expression Profiles ◽

Populus Trichocarpa ◽

Expression Patterns ◽

Foliar Spray ◽

Regulatory Elements ◽

Limited Information ◽

Abiotic Stress Response

Abstract Background The deubiquitinase (DUB) family constitutes a group of proteases that regulate the stability or reverse the ubiquitination of many proteins in the cell. These enzymes participate in cell-cycle regulation, cell division and differentiation, diverse physiological activities such as DNA damage repair, growth and development, and response to stress. However, limited information is available on this family of genes in woody plants. Results In the present study, 88 DUB family genes were identified in the woody model plant Populus trichocarpa, comprising 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM genes with similar domains. According to phylogenetic analysis, the PtrUBP genes were classified into 16 groups, the PtrUCH genes into two, the PtrOTU genes into eight, the PtrMJD genes into two, and the PtrJAMM genes into seven. Members of same subfamily had similar gene structure and motif distribution characteristics. Synteny analysis of the DUB family genes from P. thrchocarpa and four other plant species provided insight into the evolutionary traits of DUB genes. Expression profiles derived from previously published transcriptome data revealed distinct expression patterns of DUB genes in various tissues. On the basis of the results of analysis of promoter cis-regulatory elements, we selected 16 representative PtrUBP genes to treatment with abscisic acid, methyl jasmonate, or salicylic acid applied as a foliar spray. The majority of PtrUBP genes were upregulated in response to the phytohormone treatments, which implied that the genes play potential roles in abiotic stress response in Populus. Conclusions The results of this study broaden our understanding of the DUB family in plants. Analysis of the gene structure, conserved elements, and expression patterns of the DUB family provides a solid foundation for exploration of their specific functions in Populus and to elucidate the potential role of PtrUBP gene in abiotic stress response.

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Global gene expression patterns in response to white patch syndrome: Disentangling symbiont loss from the thermal stress response in reef-building coral

10.1101/2019.12.13.875989 ◽

2019 ◽

Author(s):

Carly D. Kenkel ◽

Veronique J.L. Mocellin ◽

Line K. Bay

Keyword(s):

Gene Expression ◽

Abiotic Stress ◽

Thermal Stress ◽

Stress Response ◽

Meta Analysis ◽

Expression Patterns ◽

Global Gene Expression ◽

Host Protein ◽

Gene Expression Patterns ◽

White Patch

AbstractThe mechanisms resulting in the breakdown of the coral symbiosis once the process of bleaching has been initiated remain unclear. Distinguishing symbiont loss from the abiotic stress response may shed light on the cellular and molecular pathways involved in each process. This study examined physiological changes and global gene expression patterns associated with white patch syndrome (WPS) in P. lobata, which manifests in localized bleaching independent of thermal stress. In addition, a meta-analysis of global gene expression studies in other corals and anemones was used to contrast differential regulation as a result of abiotic stress from expression patterns correlated with symbiotic state. Symbiont density, chlorophyll a content, holobiont productivity, instant calcification rate, and total host protein content were uniformly reduced in WPS relative to healthy tissue. While expression patterns associated with WPS were secondary to fixed effects of source colony, specific functional enrichments suggest that the viral infection putatively giving rise to this condition affects symbiont rather than host cells. The meta-analysis revealed that expression patterns in WPS-affected tissues were significantly correlated with prior studies examining short-term thermal stress responses. This correlation was independent of symbiotic state, as the strongest correlations were found between WPS adults and both symbiotic adult and aposymbiotic coral larvae experiencing thermal stress, suggesting that the majority of expression changes reflect a non-specific stress response. Across studies, the magnitude and direction of expression change among particular functional enrichments suggests unique responses to stressor duration, and highlights unique responses to bleaching in an anemone model which engages in a non-obligate symbiosis.

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Interactions between stress response, carbohydrate metabolism, and defense pathways modulate rootstock root-dependent fire blight susceptibility in apple (Malus × domestica)

10.21203/rs.2.10413/v1 ◽

2019 ◽

Author(s):

Jugpreet Singh ◽

Jack Fabrizio ◽

Elsa Desnoues ◽

Julliany Pereira Silva ◽

Wolfgang Busch ◽

...

Keyword(s):

Stress Response ◽

Carbohydrate Metabolism ◽

Fire Blight ◽

Expression Patterns ◽

Root Traits ◽

Root Surface ◽

Root Surface Area ◽

Protein Kinase Activity ◽

Root Mass ◽

Molecular Relationships

Abstract Background Although it is known that resistant rootstocks facilitate management of fire blight disease, incited by Erwinia amylovora (Burr.) Winslow et al., of apple scion cultivars, the role of rootstock root traits in providing systemic defense against E. amylovora is unclear. In this study, the hypothesis that rootstocks of higher root mass provide higher tolerance to fire blight infection in apples is tested. Several apple scion cultivars grafted onto a single rootstock genotype and non-grafted ‘M.7’ rootstocks of varying root mass are used to assess phenotypic and molecular relationships between root traits of rootstocks and fire blight susceptibility of apple scion cultivars. Results It is observed that different root traits display significant (p < 0.05) negative correlations with fire blight susceptibility. In fact, root surface area partially dictates differential levels of fire blight susceptibility of ‘M.7’ rootstocks. Furthermore, contrasting changes in gene expression patterns of diverse molecular pathways accompany observed differences in levels of root-driven fire blight susceptibility. It is noted that a singular co-expression gene network consisting of genes from defense, carbohydrate metabolism, protein kinase activity, oxidation-reduction, and stress response pathways modulates root-dependent fire blight susceptibility in apple. In particular, WRKY75 and UDP-glycotransferase are singled-out as hub genes deserving of further detailed analysis. Conclusions It is proposed that low root mass may incite resource-limiting conditions to activate carbohydrate metabolic pathways, which reciprocally interact with plant immune system genes to elicit differential levels of fire blight susceptibility.

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