Association between vitamin D status and cardiometabolic risk factors in adults with type 2 diabetes in Shenzhen, China.

Background: Evidence of vitamin D status and cardiometabolic health in adults with type 2 diabetes mellitus (T2DM) is still limited. This study aimed to investigate the association between vitamin D status and cardiometabolic risk factors among adults with T2DM in Shenzhen, China. Methods: This cross-sectional study included 164 adults (aged ≥18 years) with T2DM who were hospitalized at Peking University Shenzhen Hospital from March 1, 2023, to May 31, 2023. Serum 25-hydroxyvitamin D [25(OH)D] concentration, the active marker of vitamin D, and three major cardiometabolic risk factors including blood pressure (BP), glucose metabolism-related indicators, and blood lipid profiles were collected. Vitamin D deficiency (VDD) was defined as 25(OH)D < 20 ng/mL. Correlation, Regression, and Logistic analysis were applied to verify the association among serum 25(OH)D concentration, VDD, and 11 cardiometabolic risk factors. Results: Median 25(OH)D concentration was 21.78 [interquartile range (IQR)=17.51-28.05] ng/mL. The prevalence of VDD was 40.24%. Serum 25(OH)D concentration was significantly negatively correlated with diastolic BP (DBP) and glycated hemoglobin A1c (HbA1c) rather than systolic BP, plasma glucose, plasma C-peptide, and blood lipid profiles among adults with T2DM in both correlation and linear regression analysis. Furthermore, the adjusted odd ratio for poor DBP control (≥90 mmHg) of T2DM patients with VDD was 3.164 (95% confidence interval=1.303, 7.683; P=0.011) compared to those without VDD. Conclusion: In China, VDD was highly prevalent among adults with T2DM and associated with greater cardiovascular risk factors, especially with increased chances of uncontrolled DBP. These findings suggest that vitamin D levels should be monitored in T2DM patients, especially those with high DBP.

Identification of NADPH Oxidase Genes Crucial for Rice Multiple Disease Resistance and Yield Traits.

Reactive oxygen species (ROS) act as a group of signaling molecules in rice functioning in regulation of development and stress responses. Respiratory burst oxidase homologues (Rbohs) are key enzymes in generation of ROS. However, the role of the nine Rboh family members was not fully understood in rice multiple disease resistance and yield traits. In this study, we constructed mutants of each Rboh genes and detected their requirement in rice multiple disease resistance and yield traits. Our results revealed that mutations of five Rboh genes (RbohA, RbohB, RbohE, RbohH, and RbohI) lead to compromised rice blast disease resistance in a disease nursery and lab conditions; mutations of five Rbohs (RbohA, RbohB, RbohC, RbohE, and RbohH) result in suppressed rice sheath blight resistance in a disease nursery and lab conditions; mutations of six Rbohs (RbohA, RbohB, RbohC, RbohE, RbohH and RbohI) lead to decreased rice leaf blight resistance in a paddy yard and ROS production induced by PAMPs and pathogen. Moreover, all Rboh genes participate in the regulation of rice yield traits, for all rboh mutants display one or more compromised yield traits, such as panicle number, grain number per panicle, seed setting rate, and grain weight, resulting in reduced yield per plant except rbohb and rbohf. Our results identified the Rboh family members involved in the regulation of rice resistance against multiple pathogens that caused the most serious diseases worldwide and provide theoretical supporting for breeding application of these Rbohs to coordinate rice disease resistance and yield traits.

Broad-spectrum resistance gene RPW8.1 balances immunity and growth via feedback regulation of WRKYs.

Arabidopsis RESISTANCE TO POWDERY MILDEW 8.1 (RPW8.1) is an important tool for engineering broad-spectrum disease resistance against multiple pathogens. Ectopic expression of RPW8.1 leads to enhanced disease resistance with cell death at leaves and compromised plant growth, implying a regulatory mechanism balancing RPW8.1-mediated resistance and growth. Here, we show that RPW8.1 constitutively enhances the expression of transcription factor WRKY51 and activates salicylic acid and ethylene signalling pathways; WRKY51 in turn suppresses RPW8.1 expression, forming a feedback regulation loop. RPW8.1 and WRKY51 are both induced by pathogen infection and pathogen-/microbe-associated molecular patterns. In ectopic expression of RPW8.1 background (R1Y4), overexpression of WRKY51 not only rescues the growth suppression and cell death caused by RPW8.1, but also suppresses RPW8.1-mediated broad-spectrum disease resistance and pattern-triggered immunity. Mechanistically, WRKY51 directly binds to and represses RPW8.1 promoter, thus limiting the expression amplitude of RPW8.1. Moreover, WRKY6, WRKY28 and WRKY41 play a role redundant to WRKY51 in the suppression of RPW8.1 expression and are constitutively upregulated in R1Y4 plants with WRKY51 being knocked out (wrky51 R1Y4) plants. Notably, WRKY51 has no significant effects on disease resistance or plant growth in wild type without RPW8.1, indicating a specific role in RPW8.1-mediated disease resistance. Altogether, our results reveal a regulatory circuit controlling the accumulation of RPW8.1 to an appropriate level to precisely balance growth and disease resistance during pathogen invasion.

Safety evaluation of human umbilical cord-mesenchymal stem cells in type 2 diabetes mellitus treatment: A phase 2 clinical trial.

BACKGROUND: Progressive pancreatic ß cell dysfunction is a fundamental aspect of the pathology underlying type 2 diabetes mellitus (T2DM). Recently, mesenchymal stem cell (MSC) transplantation has emerged as a new therapeutic method due to its ability to promote the regeneration of pancreatic ß cells. However, current studies have focused on its efficacy, and there are few clinical studies on its safety. AIM: To evaluate the safety of human umbilical cord (hUC)-MSC infusion in T2DM treatment. METHODS: An open-label and randomized phase 2 clinical trial was designed to evaluate the safety of hUC-MSC transplantation in T2DM in a Class A hospital. Ten patients in the placebo group received acellular saline intravenously once per week for 3 wk. Twenty-four patients in the hUC-MSC group received hUC-MSCs (1 × 106 cells/kg) intravenously once per week for 3 wk. Diabetic clinical symptoms and signs, laboratory findings, and imaging findings were evaluated weekly for the 1st mo and then at weeks 12 and 24 post-treatment. RESULTS: No serious adverse events were observed during the 24-wk follow-up. Four patients (16.7%) in the hUC-MSC group experienced transient fever, which occurred within 24 h after the second or third infusion; this did not occur in any patients in the placebo group. One patient from the hUC-MSC group experienced hypoglycemic attacks within 1 mo after transplantation. Significantly lower lymphocyte levels (weeks 2 and 3) and thrombin coagulation time (week 2) were observed in the hUC-MSC group compared to those in the placebo group (all P < 0.05). Significantly higher platelet levels (week 3), immunoglobulin levels (weeks 1, 2, 3, and 4), fibrinogen levels (weeks 2 and 3), D-dimer levels (weeks 1, 2, 3, 4, 12, and 24), and neutrophil-to-lymphocyte ratios (weeks 2 and 3) were observed in the hUC-MSC group compared to those in the placebo group (all P < 0.05). There were no significant differences between the two groups for tumor markers (alpha-fetoprotein, carcinoembryonic antigen, and carbohydrate antigen 199) or blood fat. No liver damage or other side effects were observed on chest X-ray. CONCLUSION: Our study suggested that hUC-MSC transplantation has good tolerance and high safety in the treatment of T2DM. It can improve human immunity and inhibit lymphocytes. Coagulation function should be monitored vigilantly for abnormalities.

Effectiveness and safety of human umbilical cord-mesenchymal stem cells for treating type 2 diabetes mellitus.

BACKGROUND: Progressive pancreatic ß-cell dysfunction is a fundamental part of the pathology of type 2 diabetes mellitus (T2DM). Cellular therapies offer novel opportunities for the treatment of T2DM to improve the function of islet ß-cells. AIM: To evaluate the effectiveness and safety of human umbilical cord-mesenchymal stem cell (hUC-MSC) infusion in T2DM treatment. METHODS: Sixteen patients were enrolled and received 1 × 106 cells/kg per week for 3 wk as intravenous hUC-MSC infusion. The effectiveness was evaluated by assessing fasting blood glucose, C-peptide, normal glycosylated hemoglobin A1c (HbA1c), insulin resistance index (homeostatic model assessment for insulin resistance), and islet ß-cell function (homeostasis model assessment of ß-cell function). The dosage of hypoglycemic agents and safety were evaluated by monitoring the occurrence of any adverse events (AEs). RESULTS: During the entire intervention period, the fasting plasma glucose level was significantly reduced [baseline: 9.3400 (8.3575, 11.7725), day 14 ± 3: 6.5200 (5.2200, 8.6900); P < 0.01]. The HbA1c level was significantly reduced on day 84 ± 3 [baseline: 7.8000 (7.5250, 8.6750), day 84 ± 3: 7.150 (6.600, 7.925); P < 0.01]. The patients' islet ß-cell function was significantly improved on day 28 ± 3 of intervention [baseline: 29.90 (16.43, 37.40), day 28 ± 3: 40.97 (19.27, 56.36); P < 0.01]. The dosage of hypoglycemic agents was reduced in all patients, of whom 6 (50%) had a decrement of more than 50% and 1 (6.25%) discontinued the hypoglycemic agents. Four patients had transient fever, which occurred within 24 h after the second or third infusion. One patient (2.08%) had asymptomatic nocturnal hypoglycemia after infusion on day 28 ± 3. No liver damage or other side effects were reported. CONCLUSION: The results of this study suggest that hUC-MSC infusion can improve glycemia, restore islet ß-cell function, and reduce the dosage of hypoglycemic agents without serious AEs. Thus, hUC-MSC infusion may be a novel option for the treatment of T2DM.

Efficacy and Safety of Gegen Qinlian Decoction for Pediatric Diarrhea: A Systematic Review and Meta-Analysis.

Objective: To evaluate the clinical efficacy and safety of Gegen Qinlian decoction in the treatment of pediatric diarrhea. Methods: A search for relevant RCTs was performed from which a systematic review and meta-analysis was conducted. This meta-analysis was registered at INPLASY (reference number ID: INPLASY202180105). Results: (1) Eleven trials involving 1126 patients were included in the meta-analysis. (2) Two trials recorded the adverse events. (3) The meta-analysis showed that compared with the control group, the experimental group has a significantly shorter duration of diarrhea in children (MD = -18.64, 95% CI (-23.76, -13.52), P < 0.00001), duration of fever (MD = -19.43, 95% CI (-25.76, -13.11), P < 0.00001), duration of vomiting [MD = -22.51, 95% CI (-29.92, -15.09), P < 0.00001], duration of correcting dehydration (MD = -23.35, 95% CI (-35.48, -11.22), P=0.0002), and the effective rate (OR = 4.64, 95% CI (3.12, 6.90), P < 0.00001). Conclusion: There were significant differences in the clinical efficacy in the treatment of pediatric diarrhea between the experimental and control groups. Thus, Gegen Qinlian decoction may have certain advantages in the treatment of pediatric diarrhea. In addition, we conclude the following: (1) the application of Gegen Qinlian decoction to treat this disease is recommended for >5 days. (2) We recommend conducting multicenter RCTs to avoid the impact of regional differences on the results. (3) We recommend using the unmodified Gegen Qinlian decoction, which may have better efficacy.

The Larix kaempferi genome reveals new insights into wood properties.

Here, through single-molecule real-time sequencing, we present a high-quality genome sequence of the Japanese larch (Larix kaempferi), a conifer species with great value for wood production and ecological afforestation. The assembled genome is 10.97 Gb in size, harboring 45,828 protein-coding genes. Of the genome, 66.8% consists of repeat sequences, of which long terminal repeat retrotransposons are dominant and make up 69.86%. We find that tandem duplications have been responsible for the expansion of genes involved in transcriptional regulation and stress responses, unveiling their crucial roles in adaptive evolution. Population transcriptome analysis reveals that lignin content in L. kaempferi is mainly determined by the process of monolignol polymerization. The expression values of six genes (LkCOMT7, LkCOMT8, LkLAC23, LkLAC102, LkPRX148, and LkPRX166) have significantly positive correlations with lignin content. These results indicated that the increased expression of these six genes might be responsible for the high lignin content of the larches' wood. Overall, this study provides new genome resources for investigating the evolution and biological function of conifer trees, and also offers new insights into wood properties of larches.

Detection of Two Copies of a bla NDM-1-Encoding Plasmid in Escherichia coli Isolates from a Pediatric Patient with Diarrhea.

PURPOSE: To elucidate the contribution of a transferable plasmid harboring the bla NDM-1 gene in an Escherichia coli clinical isolate to the spread of resistance determinants. METHODS: Nine extended-spectrum ß-lactamase-producing E. coli were collected from diarrhea samples from a pediatric patient and genetic linkage was investigated through enterobacteriaceae repetitive intragenic consensus polymerase chain reaction (PCR). Bacterial species were identified by 16s rRNA sequencing, susceptibility testing with the use of a BD PhoenixTM-100 Automated Microbiology System, and assessment of virulence genes by PCR. The transferability of bla NDM-1 in E. coli strain TCM3e1 was confirmed by conjugation experiments. Complete sequencing of E. coli strain TCM3e1 was determined with the PacBio and Illumina NovaSeq platforms and the characteristics were analyzed with bioinformatics software. RESULTS: The results showed that all nine E. coli strains were the same clone. E. coli strain TCM3e1 was resistant to 12 antimicrobial agents and carried the virulence gene EAST-1. Conjugation transfer analysis showed that bla NDM-1 was carried on a self-transmissible plasmid. Two copies of the bla NDM-1 gene were present on an IncC plasmid and some resistance genes with two or three copies were located downstream of the bla NDM-1 gene and formed a tandem repeat fragment (bla DNM-1-bleo-sul1- aadA17- dfrA12). CONCLUSION: A transmissible plasmid harboring two copies of the bla NDM-1 gene, including clonal dispersions of the bla NDM-1 gene, was identified in clinical isolates. These findings emphasized the necessity of surveillance of the plasmid-borne bla NDM-1 to prevent dissemination.

Divergence of active site motifs among different classes of Populus glutaredoxins results in substrate switches.

Enzymes are essential components of all biological systems. The key characteristics of proteins functioning as enzymes are their substrate specificities and catalytic efficiencies. In plants, most genes encoding enzymes are members of large gene families. Within such families, the contributions of active site motifs to the functional divergence of duplicate genes have not been well elucidated. In this study, we identified 41 glutaredoxin (GRX) genes in the Populus trichocarpa genome. GRXs are ubiquitous enzymes in plants that play important roles in developmental and stress tolerance processes. In poplar, GRX genes were divided into four classes based on clear differences in gene structure and expression pattern, subcellular localization, enzymatic activity, and substrate specificity of the encoded proteins. Using site-directed mutagenesis, this study revealed that the divergence of the active site motif among different classes of GRX proteins resulted in substrate switches and thus provided new insights into the molecular evolution of these important plant enzymes.

Ectopic expression of Populus MYB10 promotes secondary cell wall thickening and inhibits anthocyanin accumulation.

Secondary cell wall (SCW) formation is regulated by a multilevel transcriptional regulatory network, in which MYB transcription factors (TFs) play key roles. In woody plants, hundreds of MYB TFs have been identified, most of which have unknown functions in wood SCW biosynthesis. Here, we characterized the function of a Populus MYB gene, PtoMYB10. PtoMYB10 was found to encode an R2R3-MYB TF and exhibit dominant expression in xylem tissues. PtoMYB10 was determined to be located in the nucleus with the ability to activate transcription. Overexpression of PtoMYB10 in Populus resulted in a drastic increase in SCW thickening in xylem fiber cells as well as ectopic deposition of lignin in cortex cells. The expression of genes associated with lignin biosynthesis was induced in PtoMYB10 overexpressing plants, whereas repressed gene expression was found with the anthocyanin biosynthesis pathway. Lignin and anthocyanin are both produced from metabolites of the phenylpropanoid pathway. Accordingly, the anthocyanin content of Populus overexpressing PtoMYB10 decreased by more than 68%. These results indicate that PtoMYB10 can positively regulate xylary fiber SCW thickening, accompanied by the reprogramming of phenylpropanoid metabolism, which redirects metabolic flux from anthocyanin biosynthesis to monolignol biosynthesis.

Effects of Zhishi Daozhi Decoction on the intestinal flora of nonalcoholic fatty liver disease mice induced by a high-fat diet.

Background and aims: Nonalcoholic fatty liver disease (NAFLD) is the most common type of chronic liver disease with a high incidence, and the situation is not optimistic. Intestinal flora imbalance is strongly correlated with NAFLD pathogenesis. Zhishi Daozhi Decoction (ZDD) is a water decoction of the herbs used in the classical Chinese medicine prescription Zhishi Daozhi Pills. Zhishi Daozhi Pills has shown promising hepatoprotective and hypolipidemic properties, but its specific mechanism remains unclear. Methods: Mice were fed on a high fat-rich diet (HFD) for ten weeks, and then the animals were administrated ZDD through oral gavage for four weeks. The serum liver function and blood lipid indexes of the mice were then tested using an automatic biochemical analyzer. H&E and Oil Red O staining were used to observe the pathological conditions of mice liver tissue, and 16S rRNA sequencing technology was used to analyze the changes in intestinal flora of mice. The concentration of short-chain fatty acids (SCFAs) in the gut of mice was analyzed by gas chromatography-mass spectrometry (GC-MS). The expression of tight junction (TJ) proteins between ileal mucosal epithelial cells was analyzed using the immunofluorescence technique. Results: ZDD was found to reduce the bodyweight of NAFLD mice, reduce serum TG, CHO, ALT, and AST levels, reduce fat accumulation in liver tissue, make the structure of intestinal flora comparable to the control group, and increase the concentration of intestinal SCFAs. It was also found to increase the expression of TJ proteins such as occludin and ZO-1, making them comparable to the control group. Conclusions: ZDD has a therapeutic effect on NAFLD mice induced by HFD, which may act by optimizing the intestinal flora structure.

Frequent ploidy changes in Salicaceae indicates widespread sharing of the salicoid whole genome duplication by the relatives of Populus L. and Salix L.

BACKGROUNDS: Populus and Salix belong to Salicaceae and are used as models to investigate woody plant physiology. The variation of karyotype and nuclear DNA content can partly reflect the evolutionary history of the whole genome, and can provide critical information for understanding, predicting, and potentially ameliorating the woody plant traits. Therefore, it is essential to study the chromosome number (CN) and genome size in detail to provide information for revealing the evolutionary process of Salicaceae. RESULTS: In this study, we report the somatic CNs of seventeen species from eight genera in Salicaceae. Of these, CNs for twelve species and for five genera are reported for the first time. Among the three subfamilies of Salicaceae, the available data indicate CN in Samydoideae is n = 21, 22, 42. The only two genera, Dianyuea and Scyphostegia, in Scyphostegioideae respectively have n = 9 and 18. In Salicoideae, Populus, Salix and five genera closely related to them (Bennettiodendron, Idesia, Carrierea, Poliothyrsis, Itoa) are based on relatively high CNs from n = 19, 20, 21, 22 to n = 95 in Salix. However, the other genera of Salicoideae are mainly based on relatively low CNs of n = 9, 10, 11. The genome sizes of 35 taxa belonging to 14 genera of Salicaceae were estimated. Of these, the genome sizes of 12 genera and all taxa except Populus euphratica are first reported. Except for Dianyuea, Idesia and Bennettiodendron, all examined species have relatively small genome sizes of less than 1 pg, although polyploidization exists. CONCLUSIONS: The variation of CN and genome size across Salicaceae indicates frequent ploidy changes and a widespread sharing of the salicoid whole genome duplication (WGD) by the relatives of Populus and Salix. The shrinkage of genome size after WGD indicates massive loss of genomic components. The phylogenetic asymmetry in clade of Populus, Salix, and their close relatives suggests that there is a lag-time for the subsequent radiations after the salicoid WGD event. Our results provide useful data for studying the evolutionary events of Salicaceae.

Efficacy and mechanism of traditional Chinese medicine in relieving antibiotic-resistant bacterial diarrhea in children: study protocol for a randomized controlled trial.

BACKGROUND: Bacterial infection is an important cause of diarrhea in children, potentially leading to malnutrition, growth and development disorders, and even death. Antibiotic abuse and resistance are widespread problems worldwide, especially in China. We therefore designed a study to evaluate the clinical efficacy and mechanism of traditional Chinese medicine in alleviating the effects of antibiotic resistance in childhood bacterial diarrhea and enhancing the sensitivity of pathogenic bacteria to antibiotics. METHODS: This randomized, double-blind, placebo-controlled clinical trial has completed ChiCTR registration. The trial will randomly divide 120 children who meet the inclusion criteria into three groups: experimental group 1 (basic treatment + Gegen Qinlian decoction granules + Erbai drink placebo), experimental group 2 (basic treatment + Erbai drink granules + Gegen Qinlian decoction placebo), and control group (basic treatment + Gegen Qinlian decoction placebo + Erbai drink placebo). The main efficacy indicators will be antibiotic use rate and clinical cure rate, and the secondary efficacy indicators will be time to antibiotic intervention, effective rate, and course of treatment determined after 5 days. The following physical and chemical indicators will be measured: routine blood parameters, procalcitonin, C-reactive protein, electrocardiogram, liver and kidney function, electrolytes, routine urinalysis, routine stool analysis, and stool culture (including drug sensitivity). DISCUSSION: The results of this study may provide an objective clinical basis for the use of traditional Chinese medicine in managing antibiotic-resistant bacterial diarrhea in children, formulating relevant guidelines, and demonstrating the use of traditional Chinese medicine for reducing the use of antibiotics. TRIAL REGISTRATION: Chinese Clinical Trial Registry ChiCTR1900027915 . Last refreshed on December 4, 2019.

Physiological and transcriptomic analysis provide novel insight into cobalt stress responses in willow.

Cobalt (Co) is an essential component of several enzymes and coenzymes in living organisms. Excess Co is highly toxic to plants. The knowledge of molecular response mechanisms to cobalt stress in plants is still limited, especially in woody plants. The responses of weeping willow (Salix babylonica) seedlings to Co stress were studied using morphological and physiochemical measurements and RNA-seq analysis. The physiological and biochemical indexes such as growth rate, the content of chlorophyll and soluble sugar, photosynthesis and peroxidase activity were all changed in willow seedlings under Co stress. The metal ion concentrations in willow including Cu, Zn and Mg were disturbed due to excess Co. Of 2002 differentially expressed genes (DEGs), 1165 were root-specific DEGs and 837 were stem and leaf-specific DEGs. Further analysis of DEGs showed there were multiple complex cascades in the response network at the transcriptome level under Co stress. Detailed elucidation of responses to oxidative stress, phytohormone signaling-related genes and transcription factors (TFs), and detoxification of excess cellular Co ion indicated the various defense mechanisms in plants respond to cobalt stress. Our findings provide new and comprehensive insights into the plant tolerance to excess Co stress.

NRAMP1 promotes iron uptake at the late stage of iron deficiency in poplars.

Iron (Fe) is an essential micronutrient for plant survival and proliferation. Plants have evolved complex mechanisms to maintain Fe homeostasis in response to Fe deficiency. In this study, we evaluated the physiological, biochemical and transcriptomic differences between poplars grown under Fe-sufficient and Fe-deficient conditions to elucidate the mechanistic responses of poplars to Fe deficiency. Our results revealed that chlorophyll synthesis and photosynthesis were inhibited under Fe-deficient conditions. The inhibition of these pathways caused chlorosis and reduced shoot growth. Although both photosynthetic systems (PSI and PSII) were inhibited under Fe limitation, PSI was affected more severely and earlier than PSII. Fe deficiency also promoted root growth and increased the accumulation of divalent metal ions in roots. IRT1 and NRAMP1 are both Fe2+ transporters for iron uptake in Arabidopsis. In this study, however, only NRAMP1 was induced to promote Fe2+ uptake in roots at the late stage of Fe deficiency response. It indicated that NRAMP1, rather than the more well-known IRT1, might be a major Fe2+ transporter at the late stage of Fe-deficiency in poplars.

De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China.

The white poplar (Populus alba) is widely distributed in Central Asia and Europe. There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China. In this study, we sequenced the genome of P. alba by single-molecule real-time technology. De novo assembly of P. alba had a genome size of 415.99 Mb with a contig N50 of 1.18 Mb. A total of 32,963 protein-coding genes were identified. 45.16% of the genome was annotated as repetitive elements. Genome evolution analysis revealed that divergence between P. alba and Populus trichocarpa (black cottonwood) occurred ~5.0 Mya (3.0, 7.1). Fourfold synonymous third-codon transversion (4DTV) and synonymous substitution rate (ks) distributions supported the occurrence of the salicoid WGD event (~ 65 Mya). Twelve natural populations of P. alba in the Irtysh River basin in China were sequenced to explore the genetic diversity. Average pooled heterozygosity value of P. alba populations was 0.170±0.014, which was lower than that in Italy (0.271±0.051) and Hungary (0.264±0.054). Tajima's D values showed a negative distribution, which might signify an excess of low frequency polymorphisms and a bottleneck with later expansion of P. alba populations examined.

Genome-wide analysis of superoxide dismutase genes in Larix kaempferi.

Superoxide dismutase is a key enzyme that scavenges superoxide anion and plays vital roles in plant antioxidant system. This study identified six SOD genes from the deciduous conifer Larix kaempferi, which is widely distributed across the cooler regions of the northern hemisphere. These six SOD genes were classified into three types: Cu/Zn-SOD (LkSOD1, 2, 3 and 4), Fe-SOD (LkSOD5) and Mn-SODs (LkSOD6). Three Cu/Zn-SOD proteins (LkSOD1, 3 and 4) were cytosolic-localized, while the other three proteins (LkSOD2, 5 and 6) were chloroplast-localized. Larix SOD proteins displayed catalytic activities toward superoxide anion, and retained >55% of its maximum enzymatic activity between 10 °C and 40 °C. Over expressions of three Larix SOD genes (LkSOD2, 4 and 6) in Arabidopsis thaliana, respectively, showed increased germination rates and root lengths during salt stress. LkSOD5 gene could rescue pale green and dwarf phenotype of Arabidopsis atfsd2-2 mutant. Taken together, this study provided comprehensive insight into the gymnosperm SOD gene family.

Functional and structural profiles of GST gene family from three Populus species reveal the sequence-function decoupling of orthologous genes.

A common assumption in comparative genomics is that orthologous genes are functionally more similar than paralogous genes. However, the validity of this assumption needs to be assessed using robust experimental data. We conducted tissue-specific gene expression and protein function analyses of orthologous groups within the glutathione S-transferase (GST) gene family in three closely related Populus species: Populus trichocarpa, Populus euphratica and Populus yatungensis. This study identified 21 GST orthologous groups in the three Populus species. Although the sequences of the GST orthologous groups were highly conserved, the divergence in enzymatic functions was prevalent. Through site-directed mutagenesis of orthologous proteins, this study revealed that nonsynonymous substitutions at key amino acid sites played an important role in the divergence of enzymatic functions. In particular, a single amino acid mutation (Arg39→Trp39) contributed to P. euphratica PeGSTU30 possessing high enzymatic activity via increasing the hydrophobicity of the active cavity. This study provided experimental evidence showing that orthologues belonging to the gene family have functional divergences. The nonsynonymous substitutions at a few amino acid sites resulted in functional divergence of the orthologous genes. Our findings provide new insights into the evolution of orthologous genes in closely related species.

Genome-wide profiling of expression and biochemical functions of the Medicago glutathione S-transferase gene family.

Glutathione S-transferases are ubiquitous enzyme in plants, playing vital roles in several physiological and developmental processes. In this study we identified 73 GST genes from the genome of Medicago truncatula. The Medicago GSTs were divided to eight classes with tau and phi being the most numerous. Six clusters were found on four Medicago chromosomes. The local gene duplication mainly contributed to the expansion of this large gene family. Functional divergence was found in their gene structures, gene expression patterns, and enzyme properties. A genomic comparative analysis revealed lineage-specific loss/gain events between Medicago and Glycine. This study offered new insights into the evolution of gene family between closely related species.

Evolution and Function of the Populus SABATH Family Reveal That a Single Amino Acid Change Results in a Substrate Switch.

Evolutionary mechanisms of substrate specificities of enzyme families remain poorly understood. Plant SABATH methyltransferases catalyze methylation of the carboxyl group of various low molecular weight metabolites. Investigation of the functional diversification of the SABATH family in plants could shed light on the evolution of substrate specificities in this enzyme family. Previous studies identified 28 SABATH genes from the Populus trichocarpa genome. In this study, we re-annotated the Populus SABATH gene family, and performed molecular evolution, gene expression and biochemical analyses of this large gene family. Twenty-eight Populus SABATH genes were divided into three classes with distinct divergences in their gene structure, expression responses to abiotic stressors and enzymatic properties of encoded proteins. Populus class I SABATH proteins converted IAA to methyl-IAA, class II SABATH proteins converted benzoic acid (BA) and salicylic acid (SA) to methyl-BA and methyl-SA, while class III SABATH proteins converted farnesoic acid (FA) to methyl-FA. For Populus class II SABATH proteins, both forward and reverse mutagenesis studies showed that a single amino acid switch between PtSABATH4 and PtSABATH24 resulted in substrate switch. Our findings provide new insights into the evolution of substrate specificities of enzyme families.