Genome-Wide Analysis of the Cyclin Gene Family and Their Expression Profile in Medicago truncatula

Genome-Wide Identification and Evolutionary and Expression Analyses of the Cyclin B Gene Family in Brassica napus

Cyclin B (CYCB) is a regulatory subunit of cyclin-dependent kinase (CDK), the concentration of which fluctuates to regulate cell cycle progression. Extensive studies have been performed on cyclins in numerous species, yet the evolutionary relationships and biological functions of the CYCB family genes in Brassica napus remain unclear. In this study, we identified 299 CYCB genes in 11 B. napus accessions. Phylogenetic analysis suggests that CYCB genes could be divided into three subfamilies in angiosperms and that the CYCB3 subfamily members may be a newer group that evolved in eudicots. The expansion of BnaCYCB genes underwent segmental duplication and purifying selection in genomes, and a number of drought-responsive and light-responsive cis-elements were found in their promoter regions. Additionally, expression analysis revealed that BnaCYCBs were strongly expressed in the developing seed and silique pericarp, as confirmed by the obviously reduced seed size of the mutant cycb3;1 in Arabidopsis thaliana compared with Col-0. This study provides a comprehensive evolutionary analysis of CYCB genes as well as insight into the biological function of CYCB genes in B. napus.

Genome-Wide Identification, Characterization, and Expression Analysis of SPIRAL1 Family Genes in Legume Species

The SPIRAL1 (SPR1) gene family encodes microtubule-associated proteins that are essential for the anisotropic growth of plant cells and abiotic stress resistance. Currently, little is known about the characteristics and roles of the gene family outside of Arabidopsis thaliana. This study intended to investigate the SPR1 gene family in legumes. In contrast to that of A. thaliana, the gene family has undergone shrinking in the model legume species Medicago truncatula and Glycine max. While the orthologues of SPR1 were lost, very few SPR1-Like (SP1L) genes were identified given the genome size of the two species. Specifically, the M. truncatula and G. max genomes only harbor two MtSP1L and eight GmSP1L genes, respectively. Multiple sequence alignment showed that all these members contain conserved N- and C-terminal regions. Phylogenetic analysis clustered the legume SP1L proteins into three clades. The SP1L genes showed similar exon-intron organizations and similar architectures in their conserved motifs. Many essential cis-elements are present in the promoter regions of the MtSP1L and GmSP1L genes associated with growth and development, plant hormones, light, and stress. The expression analysis revealed that clade 1 and clade 2 SP1L genes have relatively high expression in all tested tissues in Medicago and soybean, suggesting their function in plant growth and development. MtSP1L-2, as well as clade 1 and clade 2 GmSP1L genes, display a light-dependent expression pattern. The SP1L genes in clade 2 (MtSP1L-2, GmSP1L-3, and GmSP1L-4) were significantly induced by sodium chloride treatment, suggesting a potential role in the salt-stress response. Our research provides essential information for the functional studies of SP1L genes in legume species in the future.

Genome-Wide Identification, Characterization, and Transcriptomic Analysis of the Cyclin Gene Family in Brassica rapa

Cyclins are involved in cell division and proliferation by activating enzymes required for the cell cycle progression. Our genome-wide analysis identified 76 cyclin genes in Brassica rapa, which were divided into nine different types (A-, B-, C-, D-, H-, L-, P-, T-, and SDS-type). Cyclin genes were unevenly scattered on all chromosomes, with a maximum of 10 on A08 and a minimum of 2 on A04. The gene structure and conserved motif analysis showed that the cyclins which belonged to the same type or subgroup have a comparable intron/exon pattern or motif. A total of 14 collinear gene pairs suggested that the B. rapa cyclin genes experienced a mass of segmental duplication. The Ka/Ks analysis revealed that the Brcyclin gene family has undergone an extensive purifying pressure. By analyzing the cis-elements in the promoters, we identified 11 cis-elements and five of them are related to the hormone response. We observed 48 potential miRNAs targeting 44 Brcyclin genes, which highlighted the involvement of miRNAs in the regulation of cyclin genes. An association analysis between the leaf size and SNPs in mutants and a transcriptome analysis of two Chinese cabbage-cabbage translocation lines also showed that the Brcyclin gene family was involved in the development of the leaves. The functional characterization of the B. rapa cyclin gene family will provide the foundation for future physiological and genetic studies in the regulation of leaf growth.

Genome-Wide Identification, Expression Profiling, and Characterization of Cyclin-like Genes Reveal Their Role in the Fertility of the Diamondback Moth

Simple Summary

Cyclin genes are known as cell cycle regulators and play a significant role in the fertility of different organisms, including mice and insects. Until now, no study has been performed on the complete identification of the cyclin genes in insects. Here, we identified 21 cyclin genes in the diamondback moth (DBM) genome through a comprehensive genome-wide analysis and evaluated the gene structure, genomic location, and evolutionary relationship. Cis-regulatory elements and potential miRNA targeting the cyclin genes were also assessed. By analyzing the transcriptomic and RT-qPCR based expression profiling at different stages and tissues, we found that the majority of the cyclin genes were significantly expressed in the reproductive tissues. Moreover, RNAi-mediated characterization of PxCyc B1 showed its role in female fertility. The current study provides a basis for further evaluation of the cyclin genes, which may be used as a potential target for pest management programs.

Abstract

Cyclin-like genes are primarily considered as cell cycle regulators and have shown to be crucial for insect growth, development, reproduction, and fertility. However, no research has been performed on the cyclin-like genes in the diamondback moth (Plutella xylostella). Here, we identified the 21 cyclin genes in the genome of P. xylostella and clustered them into four groups. Most cyclin genes showed a well-maintained gene structure and motif distribution within the same group. The putative promoter regions of cyclin genes contained several transcription binding factors related to reproduction, along with growth and development. Furthermore, 16 miRNAs were identified targeting the 13 cyclin genes. Transcriptome and quantitative real-time PCR (qRT-PCR)-based expression profiling of cyclin-like genes at different stages and tissues were evaluated, revealing that 16 out of 21 cyclin genes were highly expressed in reproductive tissues of adult females and males. The Cyclin B1 gene (PxCyc B1) was only expressed in the ovary of the adult female and selected for the subsequent analysis. RNAi-mediated suppression of PxCyc B1 interrupted the external genitalia and length of the ovariole of female adults. Furthermore, the egg-laying capacity and hatching rate were also significantly decreased by suppressing the PxCyc B1, indicating the importance of cyclin genes in the reproduction and fertility of P. xylostella. The current study explained the detailed genome-wide analysis of cyclin-like genes in P. xylostella, which provided a basis for subsequent research to assess the roles of cyclin genes in reproduction, and the cyclin gene may be considered an effective target site to control this pest.

A dual legume-rhizobium transcriptome of symbiotic nodule senescence reveals coordinated plant and bacterial responses

Senescence determines plant organ lifespan depending on aging and environmental cues. During the endosymbiotic interaction with rhizobia, legume plants develop a specific organ, the root nodule, which houses nitrogen (N)-fixing bacteria. Unlike earlier processes of the legume-rhizobium interaction (nodule formation, N fixation), mechanisms controlling nodule senescence remain poorly understood. To identify nodule senescence-associated genes, we performed a dual plant-bacteria RNA sequencing approach on Medicago truncatula-Sinorhizobium meliloti nodules having initiated senescence either naturally (aging) or following an environmental trigger (nitrate treatment or salt stress). The resulting data allowed the identification of hundreds of plant and bacterial genes differentially regulated during nodule senescence, thus providing an unprecedented comprehensive resource of new candidate genes associated with this process. Remarkably, several plant and bacterial genes related to the cell cycle and stress responses were regulated in senescent nodules, including the rhizobial RpoE2-dependent general stress response. Analysis of selected core nodule senescence plant genes allowed showing that MtNAC969 and MtS40, both homologous to leaf senescence-associated genes, negatively regulate the transition between N fixation and senescence. In contrast, overexpression of a gene involved in the biosynthesis of cytokinins, well-known negative regulators of leaf senescence, may promote the transition from N fixation to senescence in nodules.

Diabetes complications and extracellular vesicle therapy

Diabetes is a chronic disorder characterized by dysregulated glycemic conditions. Diabetic complications include microvascular and macrovascular abnormalities and account for high morbidity and mortality rates in patients. Current clinical approaches for diabetic complications are limited to symptomatic treatments and tight control of blood sugar levels. Extracellular vesicles (EVs) released by somatic and stem cells have recently emerged as a new class of potent cell-free therapeutic delivery packets with a great potential to treat diabetic complications. EVs contain a mixture of bioactive molecules and can affect underlying pathological processes in favor of tissue healing. In addition, EVs have low immunogenicity and high storage capacity while maintaining nearly the same regenerative and immunomodulatory effects compared to current cell-based therapies. Therefore, EVs have received increasing attention for diabetes-related complications in recent years. In this review, we provide an outlook on diabetic complications and summarizes new knowledge and advances in EV applications. Moreover, we highlight recommendations for future EV-related research.

The B-Type Cyclin CYCB1-1 Regulates Embryonic Development and Seed Size in Maize

Progress through the cell cycle is a critical process during plant embryo and seed development and its progression is regulated by cyclins. Despite extensive study of cyclins in other systems, their role in embryo and seed development of maize is unclear. In this study, we demonstrate that ZmCYCB1-1 overexpression significantly accelerated embryo growth and increased seed size. In situ hybridization and toluidine blue staining indicated that ZmCYCB1-1 was highly expressed in the plumule of embryos, and the cells of the plumule were smaller, denser, and more regularly arranged in ZmCYCB1-1 overexpression plants. Overexpression of ZmCYCB1-1 in maize also resulted in an increased ear length and enhanced kernel weight by increasing kernel width. Transcriptome analysis indicated that the overexpression of ZmCYCB1-1 affected several different metabolic pathways, including photosynthesis in embryos and leaves, and lipid metabolism in leaves. Conversely, knocking out ZmCYCB1-1 resulted in plants with slow growth. Our results suggest that ZmCYCB1-1 regulates embryo growth and seed size, making it an ideal target for efforts aimed at maize yield improvement.

Effects of different short-chain fatty acids (SCFA) on gene expression of proteins involved in barrier function in IPEC-J2

Background

Gut microbial anaerobic fermentation produces short-chain fatty acids (SCFA), which are important substrates for energy metabolism and anabolic processes in mammals. SCFA can regulate the inflammatory response and increase the intestinal barrier integrity by enhancing the tight junction protein (TJp) functions, which prevent the passage of antigens through the paracellular space. The aim of this study was to evaluate the effect of in vitro supplementation with SCFA (acetate, propionate, butyrate, and lactate) at different concentrations on viability, nitric oxide (NO) release (oxidative stress parameter) in cell culture supernatants, and gene expression of TJp (occludin, zonula occludens-1, and claudin-4) and pro-inflammatory pathway-related mediators (β-defensin 1, TNF-α, and NF-κB) in intestinal porcine epithelial cell line J2 (IPEC-J2).

Results

The SCFA tested showed significant effects on IPEC-J2, which proved to be dependent on the type and specific concentration of the fatty acid. Acetate stimulated cell viability and NO production in a dose-dependent manner (P < 0.05), and specifically, 5 mM acetate activated the barrier response through claudin-4, and immunity through β-defensin 1 (P < 0.05). The same effect on these parameters was shown by propionate supplementation, especially at 1 mM (P < 0.05). Contrarily, lactate and butyrate showed different effects compared to acetate and propionate, as they did not stimulate an increase of cell viability and regulated barrier integrity through zonula occludens-1 and occludin, especially at 30 mM and 0.5 mM, respectively (P < 0.05). Upon supplementation with SCFA, the increase of NO release at low levels proved not to have detrimental effects on IPEC-J2 proliferation/survival, and in the case of acetate and propionate, such levels were associated with beneficial effects. Furthermore, the results showed that SCFA supplementation induced β-defensin 1 (P < 0.05) that, in turn, may have been involved in the inhibition of TNF-α and NF-κB gene expression (P < 0.05).

Conclusions

The present study demonstrates that the supplementation with specific SCFA in IPEC-J2 can significantly modulate the process of barrier protection, and that particularly acetate and propionate sustain cell viability, low oxidative stress activity and intestinal barrier function.

Exogenous 6-Benzyladenine Improves Waterlogging Tolerance in Maize Seedlings by Mitigating Oxidative Stress and Upregulating the Ascorbate-Glutathione Cycle

The synthetic cytokinin 6-benzyladenine (6-BA) regulates plant growth and prevents the negative consequences of various forms of abiotic stress, including waterlogging in crop plants. The present study aimed to investigate the effects of exogenous 6-BA on the growth, oxidative stress, and ascorbate-glutathione (AsA-GSH) cycle system in the inbred SY-MY13 (waterlogging-resistant) and SY-XT1 (waterlogging-sensitive) seedlings of waxy corn in conditions of waterlogging stress. The results demonstrated that waterlogging stress causes chlorosis and necrosis in waxy corn leaves, inhibiting growth and leading to the accumulation of reactive oxygen species (ROS), which induces oxidative stress and, in turn, reduces membrane lipid peroxidation and the disruption of membrane homeostasis. This is specifically manifested in the increased concentrations of superoxide anion radicals ( O 2 - ), hydrogen peroxide (H₂O₂), and malondialdehyde (MDA), in addition to increased relative electrical conductivity (REC%) values. The SY-MY13 strain exhibited growth superior to that of SY-XT1 when waterlogged due to its excellent waterlogging resistance. Thus, exogenous 6-BA was found to be effective in enhancing the growth of plants stressed by waterlogging in terms of the weight of the shoots and roots, shoot height, and leaf area. In addition to this, exogenous 6-BA also reduced the accumulation of O 2 - , H₂O₂, and MDA, increased ascorbate peroxidase (APX), glutathione reductase (GR), dehydroascorbate reductase (DHAR), and monodehydroascorbate reductase (MDHAR) activity, and enhanced ascorbic acid (AsA), and reduced glutathione (GSH) concentration through the regulation of the efficiency of the AsA-GSH cycle system in maize plants. Hence, the application of exogenous 6-BA can alleviate waterlogging-induced damage and improve waterlogging tolerance in waxy corn via the activation of the AsA-GSH cycle system and the elimination of ROS.

Plant CDKs-Driving the Cell Cycle through Climate Change

In a growing population, producing enough food has become a challenge in the face of the dramatic increase in climate change. Plants, during their evolution as sessile organisms, developed countless mechanisms to better adapt to the environment and its fluctuations. One important way is through the plasticity of their body and their forms, which are modulated during plant growth by accurate control of cell divisions. A family of serine/threonine kinases called cyclin-dependent kinases (CDK) is a key regulator of cell divisions by controlling cell cycle progression. In this review, we compile information on the primary response of plants in the regulation of the cell cycle in response to environmental stresses and show how the cell cycle proteins (mainly the cyclin-dependent kinases) involved in this regulation can act as components of environmental response signaling cascades, triggering adaptive responses to drive the cycle through climate fluctuations. Understanding the roles of CDKs and their regulators in the face of adversity may be crucial to meeting the challenge of increasing agricultural productivity in a new climate.

OPT gene family analysis of potato (Solanum tuberosum) responding to heavy metal stress: Comparative omics and co-expression networks revealed the underlying core templates and specific response patterns

Oligopeptides transporter (OPT) can maintain intracellular metal homeostat, however, their evolutionary characteristics, as well as their expression patterns in heavy metal exposure, remain unclear. Compared with previous OPT family identification, we identified 94 OPT genes (including 21 in potato) in potato and 4 other plants by HMMER program based on OPT domain (PF03169) for the first time. Secondly, conserved and special OPTs were found through comprehensive analysis. Thirdly, spatio-temporal tissue specific expression patterns and co-expression frameworks of potato OPT genes under different heavy metal stress were constructed. These data can provide excellent gene resources for food security and soil remediation.

Overexpression Populus d-Type Cyclin Gene PsnCYCD1;1 Influences Cell Division and Produces Curved Leaf in Arabidopsis thaliana

d-type cyclins (CYCDs) are a special class of cyclins and play extremely important roles in plant growth and development. In the plant kingdom, most of the existing studies on CYCDs have been done on herbaceous plants, with few on perennial woody plants. Here, we identified a Populus&nbsp;d-type cyclin gene, PsnCYCD1;1, which is mainly transcribed in leaf buds and stems. The promoter of PsnCYCD1;1 activated GUS gene expression and transgenic Arabidopsis lines were strongly GUS stained in whole seedlings and mature anthers. Moreover, subcellular localization analysis showed the fluorescence signal of PsnCYCD1;1-GFP fusion protein is present in the nucleus. Furthermore, overexpression of the PsnCYCD1;1 gene in Arabidopsis can promote cell division and lead to small cell generation and cytokinin response, resulting in curved leaves and twisted inflorescence stems. Moreover, the transcriptional levels of endogenous genes, such as ASs, KNATs, EXP10, and PHB, were upregulated by PsnCYCD1;1. Together, our results indicated that PsnCYCD1;1 participates in cell division by cytokinin response, providing new information on controlling plant architecture in woody plants.

Physiological effects of nutrients on insulin release by pancreatic beta cells

Obesity and type 2 diabetes (T2D) are growing health problems associated with a loss of insulin sensitivity. Both conditions arise from a long-term energy imbalance, and frequently, lifestyle measures can be useful in its prevention, including physical activity and a healthy diet. Pancreatic β-cells are determinant nutrient sensors that participate in energetic homeostasis needs. However, when pancreatic β-cells are incapable of secreting enough insulin to counteract the reduced sensitivity, the pathology evolves to an insulin resistance condition. The primary nutrient that stimulates insulin secretion is glucose, but also, there are multiple dietary and hormonal factors influencing that response. Many studies of the physiology of β-cells have highlighted the importance of glucose, fructose, amino acids, and free fatty acids on insulin secretion. The present review summarizes recent research on how β-cells respond to the most abundant nutrients that influence insulin secretion. Taken together, understand the subjacent mechanisms of each nutrient on β-cells can help to unravel the effects of mixed variables and complexity in the context of β-cell pathology.