scholarly journals Expansion and Functional Divergence of Inositol Polyphosphate 5-Phosphatases in Angiosperms

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 393 ◽  
Author(s):  
Zaibao Zhang ◽  
Yuting Li ◽  
Zhaoyi Luo ◽  
Shuwei Kong ◽  
Yilin Zhao ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Stress Responses ◽  
Functional Divergence ◽  
Purifying Selection ◽  
Ecological Niches ◽  
Evolutionary Analysis ◽  
Inositol Polyphosphate ◽  
Gene Copies ◽  
Group I

Inositol polyphosphate 5-phosphatase (5PTase), a key enzyme that hydrolyzes the 5′ position of the inositol ring, has essential functions in growth, development, and stress responses in plants, yeasts, and animals. However, the evolutionary history and patterns of 5PTases have not been examined systematically. Here, we report a comprehensive molecular evolutionary analysis of the 5PTase gene family and define four groups. These four groups are different from former classifications, which were based on in vitro substrate specificity. Most orthologous groups appear to be conserved as single or low-copy genes in all lineages in Groups II–IV, whereas 5PTase genes in Group I underwent several duplication events in angiosperm, resulting in multiple gene copies. Whole-genome duplication (WGD) was the main mechanism for 5PTase duplications in angiosperm. Plant 5PTases have more members than that of animals, and most plant 5PTase genes appear to have evolved under strong purifying selection. The paralogs have diverged in substrate specificity and expression pattern, showing evidence of selection pressure. Meanwhile, the increase in 5PTases and divergences in sequence, expression, and substrate might have contributed to the divergent functions of 5PTase genes, allowing the angiosperms to successfully adapt to a great number of ecological niches.

scholarly journals Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xin Wang ◽  
Ming-Hua Wu ◽  
Dong Xiao ◽  
Ruo-Lan Huang ◽  
Jie Zhan ◽  
...  
Keyword(s):  
Stress Responses ◽  
Segmental Duplication ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Segmental Duplications ◽  
Evolutionary Analysis ◽  
Gene Pairs ◽  
Al Stress ◽  
Peanut Genome

Abstract Background As an important cash crop, the yield of peanut is influenced by soil acidification and pathogen infection. Receptor-like protein kinases play important roles in plant growth, development and stress responses. However, little is known about the number, location, structure, molecular phylogeny, and expression of RLKs in peanut, and no comprehensive analysis of RLKs in the Al stress response in peanuts have been reported. Results A total of 1311 AhRLKs were identified from the peanut genome. The AhLRR-RLKs and AhLecRLKs were further divided into 24 and 35 subfamilies, respectively. The AhRLKs were randomly distributed across all 20 chromosomes in the peanut. Among these AhRLKs, 9.53% and 61.78% originated from tandem duplications and segmental duplications, respectively. The ka/ks ratios of 96.97% (96/99) of tandem duplication gene pairs and 98.78% (646/654) of segmental duplication gene pairs were less than 1. Among the tested tandem duplication clusters, there were 28 gene conversion events. Moreover, all total of 90 Al-responsive AhRLKs were identified by mining transcriptome data, and they were divided into 7 groups. Most of the Al-responsive AhRLKs that clustered together had similar motifs and evolutionarily conserved structures. The gene expression patterns of these genes in different tissues were further analysed, and tissue-specifically expressed genes, including 14 root-specific Al-responsive AhRLKs were found. In addition, all 90 Al-responsive AhRLKs which were distributed unevenly in the subfamilies of AhRLKs, showed different expression patterns between the two peanut varieties (Al-sensitive and Al-tolerant) under Al stress. Conclusions In this study, we analysed the RLK gene family in the peanut genome. Segmental duplication events were the main driving force for AhRLK evolution, and most AhRLKs subject to purifying selection. A total of 90 genes were identified as Al-responsive AhRLKs, and the classification, conserved motifs, structures, tissue expression patterns and predicted functions of Al-responsive AhRLKs were further analysed and discussed, revealing their putative roles. This study provides a better understanding of the structures and functions of AhRLKs and Al-responsive AhRLKs.

scholarly journals Identification of Histone H3 (HH3) Genes in Gossypium hirsutum Revealed Diverse Expression During Ovule Development and Stress Responses

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 355
Author(s):  
Ghulam Qanmber ◽  
Faiza Ali ◽  
Lili Lu ◽  
Huijuan Mo ◽  
Shuya Ma ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Stress Responses ◽  
Functional Divergence ◽  
Histone H3 ◽  
Purifying Selection ◽  
Histone Variants ◽  
Biological Information ◽  
Amino Acid Residues ◽  
Sequence Logos ◽  
Indole 3 Acetic Acid

Histone acts as the core for nucleosomes and is a key protein component of chromatin. Among different histone variants, histone H3 (HH3) variants have been reported to play vital roles in plant development. However, biological information and evolutionary relationships of HH3 genes in cotton remain to be elucidated. The current study identified 34 HH3 genes in Gossypium hirsutum. Phylogenetic analysis classified HH3 genes of 19 plant species into eight distinct clades. Sequence logos analysis among Arabidopsis, rice, and G. hirsutum amino acid residues showed higher conservation in amino acids. Using collinearity analysis, we identified 81 orthologous/paralogous gene pairs among the four genomes (A, D, At, and Dt) of cotton. Further, orthologous/paralogous and the Ka/Ks ratio demonstrated that cotton HH3 genes experienced strong purifying selection pressure with restricted functional divergence resulting from segmental and whole genome duplication. Expression pattern analysis indicated that GhHH3 genes were preferentially expressed in cotton ovule tissues. Additionally, GhHH3 gene expression can be regulated by abiotic stresses (cold, heat, sodium chloride (NaCl), and polyethylene glycol (PEG)) and phytohormonal (brassinolide (BL), gibberellic acid (GA), indole-3-acetic acid (IAA), salicylic acid (SA), and methyl jasmonate (MeJA)) treatments, suggesting that GhHH3 genes might play roles in abiotic and hormone stress resistance. Taken together, this work provides important information to decipher complete molecular and physiological functions of HH3 genes in cotton.

scholarly journals Recent Duplications Dominate VQ and WRKY Gene Expansions in Six Prunus Species

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Yan Zhong ◽  
Ping Wang ◽  
Xiaohui Zhang ◽  
Zong-Ming Cheng
Keyword(s):  
Stress Responses ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Gene Families ◽  
Wrky Gene ◽  
Prunus Species ◽  
Gene Copies ◽  
Genes Encoding ◽  
Tree Topologies ◽  
The Common

Genes encoding VQ motif-containing (VQ) transcriptional regulators and WRKY transcription factors can participate separately or jointly in plant growth, development, and abiotic and biotic stress responses. In this study, 222 VQ and 645 WRKY genes were identified in six Prunus species. Based on phylogenetic tree topologies, the VQ and WRKY genes were classified into 13 and 32 clades, respectively. Therefore, at least 13 VQ gene copies and 32 WRKY gene copies were present in the genome of the common ancestor of the six Prunus species. Similar small Ks value peaks for the VQ and WRKY genes suggest that the two gene families underwent recent duplications in the six studied species. The majority of the Ka/Ks ratios were less than 1, implying that most of the VQ and WRKY genes had undergone purifying selection. Pi values were significantly higher in the VQ genes than in the WRKY genes, and the VQ genes therefore exhibited greater nucleotide diversity in the six species. Forty-one of the Prunus VQ genes were predicted to interact with 44 of the WRKY genes, and the expression levels of some predicted VQ-WRKY interacting pairs were significantly correlated. Differential expression patterns of the VQ and WRKY genes suggested that some might be involved in regulating aphid resistance in P. persica and fruit development in P. avium.

scholarly journals Comparative analysis of MAPK and MKK gene families reveals differential evolutionary patterns in Brachypodium distachyon inbred lines

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11238
Author(s):  
Min Jiang ◽  
Peng Li ◽  
Wei Wang
Keyword(s):  
Differential Evolution ◽  
Stress Responses ◽  
Brachypodium Distachyon ◽  
Functional Divergence ◽  
Gene Families ◽  
Inbred Lines ◽  
Mitogen Activated Protein Kinase ◽  
Evolutionary Analysis ◽  
Biotic And Abiotic Stress ◽  
Evolutionary Patterns

Background Mitogen-activated protein kinase (MAPK) cascades are involved with signal transduction in almost every aspect of plant growth and development, as well as biotic and abiotic stress responses. The evolutionary analysis of MAPKs and MKKs in individual or entire plant species has been reported, but the evolutionary patterns in the diverse inbred lines of Brachypodium distachyon are still unclear. Results We conducted the systematical molecular evolutionary analysis of B. distachyon. A total of 799 MAPKs and 618 MKKs were identified from 53 B. distachyon inbred lines. Remarkably, only three inbred lines had 16 MPKs and most of those inbred lines lacked MPK7-2 members, whereas 12 MKKs existed in almost all B. distachyon inbred lines. Phylogenetic analysis indicated that MAPKs and MKKs were divided into four groups as previously reported, grouping them in the same branch as corresponding members. MPK21-2 was the exception and fell into two groups, which may be due to their exon-intron patterns, especially the untranslated regions (UTRs). We also found that differential evolution patterns of MKK10 paralogues from ancient tandem duplicates may have undergone functional divergence. Expression analyses suggested that MAPKs and MKKs likely played different roles in different genetic contexts within various tissues and with abiotic stresses. Conclusion Our study revealed that UTRs affected the structure and evolution of MPK21-2 genes and the differential evolution of MKK10 paralogues with ancient tandem duplication might have functional divergences. Our findings provide new insights into the functional evolution of genes in closely inbred lines.

scholarly journals The evolutionary analysis of PEBP Gene Family among Rosaceae tree species

2019 ◽  
Author(s):  
Man Zhang ◽  
Ping Li ◽  
Xiaolan Yan ◽  
Jia Wang ◽  
Tangren Cheng ◽  
...  
Keyword(s):  
Gene Family ◽  
Flowering Time ◽  
Tree Species ◽  
Floral Induction ◽  
Functional Divergence ◽  
Purifying Selection ◽  
Gene Family Evolution ◽  
Evolutionary Analysis ◽  
Functional Roles ◽  
Rosaceae Species

Abstract Phosphatidylethanolamine-binding proteins (PEBPs) are a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, as well as seed and bud dormancy. PEBP proteins can be divided into three major clades: FLOWERING LOCUS T-like (FT-like), TERMINAL FLOWER1-like (TFL1-like), and MOTHER OF FT AND TFL1-like (MFT-like). Though PEBP family genes have been well studied in Arabidopsis and other model species, their functional role in perennial trees is not fully understood. To characterize the evolution of PEBP genes and their role in flowering control among Rosaceae species, we identified a total of 46 PEBP members in seven Rosaceae species. Sequence and gene structure analysis revealed highly conserved intron/exon distributions and featured motifs among Rosaceae PEBP proteins. Analysis of synonymous/nonsysnonymous substitution rates showed purifying selection constraining divergence within most lineages, while positive selection appears to have driven divergence of FT-like and TFL-like genes from the MFT clade. The expression of PEBP genes varied among different tissues indicating their functional divergence during gene family evolution. Furthermore, by employing a weighted gene co-expression network approach, we inferred a putative FT regulatory module essential for dormancy release and floral induction in P. mume. Our study sheds new light on the evolution of PEBP genes and their functional roles in controlling flowering time among Rosaceae tree species.

Effects of Rest and Exercise on Cardiac Blood Volume Determinations

1997 ◽  
Vol 36 (08) ◽  
pp. 259-264
Author(s):  
N. Topuzović
Keyword(s):  
Radionuclide Ventriculography ◽  
Left Ventricular ◽  
Peak Exercise ◽  
Volume Determination ◽  
Group I ◽  
Lv Volumes ◽  
Group Ii ◽  
Lv Volume

Summary Aim: The purpose of this study was to investigate the changes in blood activity during rest, exercise and recovery, and to assess its influence on left ventricular (LV) volume determination using the count-based method requiring blood sampling. Methods: Forty-four patients underwent rest-stress radionuclide ventriculography; Tc-99m-human serum albumin was used in 13 patients (Group I), red blood cells was labeled using Tc-99m in 17 patients (Group II) in vivo, and in 14 patients (Group III) by modified in vivo/in vitro method. LV volumes were determined by a count-based method using corrected count rate in blood samples obtained during rest, peak exercise and after recovery. Results: In group I at stress, the blood activity decreased by 12.6 ± 5.4%, p <0.05, as compared to the rest level, and increased by 25.1 ± 6.4%, p <0.001, and 12.8 ± 4.5%, p <0.05, above the resting level in group II and III, respectively. This had profound effects on LV volume determinations if only one rest blood aliquot was used: during exercise, the LV volumes significantly decreased by 22.1 ± 9.6%, p <0.05, in group I, whereas in groups II and III it was significantly overestimated by 32.1 ± 10.3%, p <0.001, and 10.7 ± 6.4%, p <0.05, respectively. The changes in blood activity between stress and recovery were not significantly different for any of the groups. Conclusion: The use of only a single blood sample as volume aliquot at rest in rest-stress studies leads to erroneous estimation of cardiac volumes due to significant changes in blood radioactivity during exercise and recovery.

Anamnestic factors that shape reproductive health of women with repeated unsuccessful popygamy in vitro fertilization

2016 ◽  
pp. 140-143
Author(s):  
N.V. Cotsabin ◽  
◽  
O.M. Makarchuk ◽  
Keyword(s):  
High Risk ◽  
Risk Group ◽  
Polycystic Ovary ◽  
High Risk Group ◽  
Stress Factors ◽  
Control Group ◽  
Fertilization In Vitro ◽  
Infertile Women ◽  
Group I

The proportion of patients with multiple unsuccessful attempts of assisted reproductive technology (ART) is about 30% of all patients treated with the use of ART. Women with history of unsuccessful ART attempts - a special category of patients who require emergency attention and a thorough examination at the stage of preparation for superovulation stimulation,the selection of embryos and endometrium preparation for embryo transfer. The objective: to distinguish high-risk group of unsuccessful attempts based on a detailed analysis of anamnestic and clinical data of infertile women with repeated unsuccessful ART attempts that requires more in-depth study of hormonal features, ovarian reserve and condition of the endometrium. Materials and methods. For better understanding of the problem of repeated unsuccessful ART attempts and сreation of efficient infertility treatment algorithms for these couples we conducted a thorough analysis of anamnestic data of three groups of infertile women (105 patients), which were distributed by age: group I – younger than 35, the II group – from 35 to 40, the III group - over 40 years. These groups of patients were compared with each other and with the control group of healthy women (30 persons). Results. Leading stress factors in the percentage three times prevailed in the group of infertile women and had a direct connection with the fact of procedure «fertilization in vitro» and chronic stressors caused by prolonged infertility. Primary infertility was observed significantly more frequent in patients younger than 35 years (p <0.05), secondary infertility - mostly in the second and third experimental groups (p <0.05). Noteworthy significant percentage of wellknown causes of infertility and idiopathic factor in all groups, and the prevalence of tubal-peritoneal factor in the second and third experimental groups, and endocrine dysfunction in the I experimental group. The most common disorder among this category of woman was polycystic ovary syndrome. Frequency of usual miscarriage among patients of I ana II groups was two times higher than in the third group (p <0.05). Among the experimental groups the leading place belongs urinary tract infection, respiratory tract diseases, pathologies of the cardiovascular system. Data of the stratified analysis show an increase likelihood of repeated unsuccessful ART attempts under the influence of constant chronic stress (odds ratio OR=2.06; 95% CI: 0.95–3.17; p<0.05). Conclusions. Among infertile patients with repeated unsuccessful ART attempts must be separated a high risk group of failures. The identity depends on the duration of infertility, female age and leading combination of factors. Key words: repeated unsuccessful ART attempts, anamnesis, infertility, high risk.

scholarly journals InsP7is a small-molecule regulator of NUDT3-mediated mRNA decapping and processing-body dynamics

2020 ◽  
Vol 117 (32) ◽  
pp. 19245-19253 ◽  
Author(s):  
Soumyadip Sahu ◽  
Zhenzhen Wang ◽  
Xinfu Jiao ◽  
Chunfang Gu ◽  
Nikolaus Jork ◽  
...  
Keyword(s):  
Stress Responses ◽  
Messenger Rna ◽  
Control Process ◽  
Stem Cell Differentiation ◽  
Wild Type ◽  
Inositol Pyrophosphate ◽  
Body Dynamics ◽  
Processing Body ◽  
The Stability

Regulation of enzymatic 5′ decapping of messenger RNA (mRNA), which normally commits transcripts to their destruction, has the capacity to dynamically reshape the transcriptome. For example, protection from 5′ decapping promotes accumulation of mRNAs into processing (P) bodies—membraneless, biomolecular condensates. Such compartmentalization of mRNAs temporarily removes them from the translatable pool; these repressed transcripts are stabilized and stored until P-body dissolution permits transcript reentry into the cytosol. Here, we describe regulation of mRNA stability and P-body dynamics by the inositol pyrophosphate signaling molecule 5-InsP7(5-diphosphoinositol pentakisphosphate). First, we demonstrate 5-InsP7inhibits decapping by recombinant NUDT3 (Nudix [nucleoside diphosphate linked moiety X]-type hydrolase 3) in vitro. Next, in intact HEK293 and HCT116 cells, we monitored the stability of a cadre of NUDT3 mRNA substrates following CRISPR-Cas9 knockout ofPPIP5Ks(diphosphoinositol pentakisphosphate 5-kinases type 1 and 2, i.e.,PPIP5KKO), which elevates cellular 5-InsP7levels by two- to threefold (i.e., within the physiological rheostatic range). ThePPIP5KKO cells exhibited elevated levels of NUDT3 mRNA substrates and increased P-body abundance. Pharmacological and genetic attenuation of 5-InsP7synthesis in the KO background reverted both NUDT3 mRNA substrate levels and P-body counts to those of wild-type cells. Furthermore, liposomal delivery of a metabolically resistant 5-InsP7analog into wild-type cells elevated levels of NUDT3 mRNA substrates and raised P-body abundance. In the context that cellular 5-InsP7levels normally fluctuate in response to changes in the bioenergetic environment, regulation of mRNA structure by this inositol pyrophosphate represents an epitranscriptomic control process. The associated impact on P-body dynamics has relevance to regulation of stem cell differentiation, stress responses, and, potentially, amelioration of neurodegenerative diseases and aging.

scholarly journals Analysis of Sequence Divergence in Mammalian ABCGs Predicts a Structural Network of Residues That Underlies Functional Divergence

2021 ◽  
Vol 22 (6) ◽  
pp. 3012
Author(s):  
James I. Mitchell-White ◽  
Thomas Stockner ◽  
Nicholas Holliday ◽  
Stephen J. Briddon ◽  
Ian D. Kerr
Keyword(s):  
Substrate Specificity ◽  
Functional Divergence ◽  
3D Structure ◽  
Sequence Divergence ◽  
Conformational Flexibility ◽  
Substrate Selectivity ◽  
Multiple Sequence ◽  
Atp Binding Cassette Transporters ◽  
Structural Network ◽  
Wide Substrate Specificity

The five members of the mammalian G subfamily of ATP-binding cassette transporters differ greatly in their substrate specificity. Four members of the subfamily are important in lipid transport and the wide substrate specificity of one of the members, ABCG2, is of significance due to its role in multidrug resistance. To explore the origin of substrate selectivity in members 1, 2, 4, 5 and 8 of this subfamily, we have analysed the differences in conservation between members in a multiple sequence alignment of ABCG sequences from mammals. Mapping sets of residues with similar patterns of conservation onto the resolved 3D structure of ABCG2 reveals possible explanations for differences in function, via a connected network of residues from the cytoplasmic to transmembrane domains. In ABCG2, this network of residues may confer extra conformational flexibility, enabling it to transport a wider array of substrates.

scholarly journals Comparative Evaluation of Fracture Resistance of Endodontically Treated Teeth Restored with Resin Fiber Post and Stainless Steel Post: An In Vitro Study

2015 ◽  
Vol 03 (02) ◽  
pp. 080-084
Author(s):  
Vijay Singh ◽  
Poonam Bogra ◽  
Saurabh Gupta ◽  
Navneet Kukreja ◽  
Neha Gupta
Keyword(s):  
Stainless Steel ◽  
Fracture Resistance ◽  
Testing Machine ◽  
Compressive Force ◽  
Control Group ◽  
Fiber Post ◽  
Endodontically Treated Teeth ◽  
Group I ◽  
Significant Difference

AbstractFracture resistance of endodontically treated teeth restored with post. Aims: This study aims to compare the fracture resistance of endodontically treated teeth restored with resin fiber and stainless steel post. Commercially available prefabricated resin fiber post(Dentsply Maillefer Easy Post), prefabricated stainless steel post(Coltene/Whaledent Parapost) were used. Methods and Material: Forty five maxillary central incisors were obturated and divided into 3 groups: Control Group (Group I) without any post (n = 15), Resin Fiber Post Group (Group II) (n = 15) and Stainless Steel Post Group (Group III) (n = 15). In all Groups except control group, post space was prepared; a post was cemented, and a core build-up was provided. All the specimens were subjected to compressive force under a universal testing machine until fracture. Statistical analysis used: The results were analyzed using the variable analysis test (ANOVA). Results: One-way analysis of variance revealed significant difference among test groups. The control group demonstrated highest fracture resistance (925.2183 N), followed by the resin fiber post group (486.7265 N) and stainless steel post group (423.539N). Conclusions: Teeth restored with resin fiber post showed higher fracture resistance values than prefabricated stainless steel post.

Sign in / Sign up

Export Citation Format

Share Document