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Innovations in biocatalysts provide great prospects for intolerant environments or novel reactions. Due to the limited catalytic capacity and the long-term and labor-intensive characteristics of mining enzymes with the desired functions, de novo enzyme design was developed to obtain industrial application candidates in a rapid and convenient way. Here, based on the catalytic mechanisms and the known structures of proteins, we proposed a computational protein design strategy combining de novo enzyme design and laboratory-directed evolution. Starting with the theozyme constructed using a quantum-mechanical approach, the theoretical enzyme-skeleton combinations were assembled and optimized via the Rosetta “inside-out” protocol. A small number of designed sequences were experimentally screened using SDS-PAGE, mass spectrometry and a qualitative activity assay in which the designed enzyme 1a8uD1 exhibited a measurable hydrolysis activity of 24.25 ± 0.57 U/g towards p-nitrophenyl octanoate. To improve the activity of the designed enzyme, molecular dynamics simulations and the RosettaDesign application were utilized to further optimize the substrate binding mode and amino acid sequence, thus keeping the residues of theozyme intact. The redesigned lipase 1a8uD1–M8 displayed enhanced hydrolysis activity towards p-nitrophenyl octanoate—3.34 times higher than that of 1a8uD1. Meanwhile, the natural skeleton protein (PDB entry 1a8u) did not display any hydrolysis activity, confirming that the hydrolysis abilities of the designed 1a8uD1 and the redesigned 1a8uD1–M8 were devised from scratch. More importantly, the designed 1a8uD1–M8 was also able to hydrolyze the natural middle-chained substrate (glycerol trioctanoate), for which the activity was 27.67 ± 0.69 U/g. This study indicates that the strategy employed here has great potential to generate novel enzymes exhibiting the desired reactions.

Here, we combined PacBio long reads, Hi-C, and Illumina short reads to assembleWe generated a 957.1 Mb genome with a contig N50 of 1.2 Mb and scaffold N50 of 77.0 Mb. The repetitive sequences constituted 55.63% of the genome, among which long terminal repeats were the majority and accounted for 23.07% of the genome.The assembled and annotated high-quality

We analyzed the genetic diversity and population genetic structure of Neillia incisa (Thunb.) Zabel using EST-SSR markers. Neillia incisa (Thunb.) Zabel is an undomesticated plant species which is distributed along the coastal areas of East Asia. N. incisa has rarely been planted in cities despite its potential usefulness in removing particulate air pollution. Our study utilized EST-SSR markers to investigate the genetic diversity of 122 wild N. incisa individuals from five populations, including Anshan (AS), Zhuanghe (ZH), Changhai (CH), Kunyu (KU) and Laoshan (LS). All indexes measured indicated moderate polymorphism. The CH population was found to have the highest genetic diversity, while the AS population was observed to have the lowest. The average genetic differentiation coefficient (Fst) of the five N. incisa populations was found to be 0.2075. Analysis of molecular variance revealed that the genetic variation observed among various populations was only 16.99% of the total variation, while the genetic variation within populations accounted for 83.01% of the total variation. Principal coordinate analysis, unweighted pair group with arithmetic mean clustering and genetic structure analysis revealed that the five N. incisa populations could be differentiated into three groups. ZH was found to group with CH, LS grouped with KU and AS formed its own cluster. The results of this study provide a preliminary genetic basis for the use and conservation of N. incisa.

There is a pressing need today to mechanistically interpret sets of genomic variants associated with diseases. Here we present a tool called ‘VarSAn’ that uses a network analysis algorithm to identify pathways relevant to a given set of variants. VarSAn analyzes a configurable network whose nodes represent variants, genes and pathways, using a Random Walk with Restarts algorithm to rank pathways for relevance to the given variants, and reports P-values for pathway relevance. It treats non-coding and coding variants differently, properly accounts for the number of pathways impacted by each variant and identifies relevant pathways even if many variants do not directly impact genes of the pathway. We use VarSAn to identify pathways relevant to variants related to cancer and several other diseases, as well as drug response variation. We find VarSAn's pathway ranking to be complementary to the standard approach of enrichment tests on genes related to the query set. We adopt a novel benchmarking strategy to quantify its advantage over this baseline approach. Finally, we use VarSAn to discover key pathways, including the VEGFA-VEGFR2 pathway, related to de novo variants in patients of Hypoplastic Left Heart Syndrome, a rare and severe congenital heart defect.

The search for and characterization of new lipases with excellent properties has always been urgent and is of great importance to meet industrial needs. In this study, a new lipase, lipB, from Pseudomonas fluorescens SBW25, belonging to the lipase subfamily I.3, was cloned and expressed in Bacillus subtilis WB800N. Enzymatic properties studies of recombinant LipB found that it exhibited the highest activity towards p-nitrophenyl caprylate at 40 °C and pH 8.0, retaining 73% of its original activity after incubation at 70 °C for 6 h. In addition, Ca2+, Mg2+, and Ba2+ strongly enhanced the activity of LipB, while Cu2+, Zn2+, Mn2+, and CTAB showed an inhibiting effect. The LipB also displayed noticeable tolerance to organic solvents, especially acetonitrile, isopropanol, acetone, and DMSO. Moreover, LipB was applied to the enrichment of polyunsaturated fatty acids from fish oil. After hydrolyzing for 24 h, it could increase the contents of polyunsaturated fatty acids from 43.16% to 72.18%, consisting of 5.75% eicosapentaenoic acid, 19.57% docosapentaenoic acid, and 46.86% docosahexaenoic acid, respectively. The properties of LipB render it great potential in industrial applications, especially in health food production.

The traditional mining processes of rare earth elements (REEs) are accompanied by the production of a large number of acid mine drainage rich in REEs. A wide-adaptive, low-cost and environmentally friendly biosorbent is an attractive technology to enrich and recycle REEs from the liquid wastes. To construct a broad-spectrum and efficient biosorbent, a novel REEs-binding protein Lanmodulin (LanM) is successfully displayed on the cell surface of a fungus, Yarrowia lipolytica, for the first time, and the adsorption capacities for various REEs are studied. The LanM-displayed Y. lipolytica shows significantly enhanced adsorption capacities for multiple REEs, achieving the highest reported values of 49.83 ± 2.87 mg Yb /g DCW, 50.38 ± 1.46 mg Tm /g DCW, 49.94 ± 3.61 mg Er /g DCW and 48.72 ± 3.09 mg Tb/g DCW, respectively. Moreover, the LanM-displayed Y. lipolytica possesses a high selectivity for REEs over other common metal cations and excellent suitability under acidic conditions. The kinetics and equilibrium analysis of biosorption processes agree well with the pseudo-first kinetic and Langmuir isotherm model. Based on the FTIR and SEM-EDS analysis, the chelation with phosphate/carboxylate groups dominates the Yb binding in LanM-displayed cells, and LanM enhances the adsorption performances by introducing more binding sites with high selectivity towards a wide range of REEs. Thus, the LanM-displayed Y. lipolytica investigated in this study exhibits prosperous potential for the enriching/removal of REEs from acid mine drainage.

Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.

Recent epidemiological studies have found that diisononyl phthalate (DINP) is associated with an increase in blood pressure. However, this correlation had not been clarified, nor has the underlying mechanism been characterized. In this study, C57/BL6 mice were exposed to DINP doses of 0.15 mg/kg/day, 1.5 mg/kg/day or 15 mg/kg/day for 6 weeks. Dexamethasone (DEXA) was used to build the hypertension model. After DINP exposure and 1 mg/kg/day DEXA treatment, the levels of systolic blood pressure (SBP), diastolic blood pressure (DBP), mean blood pressure (MBP) and heart rate (HR) were determined, and any histopathological changes in hypertension targeted organs of the mice were investigated. The results suggest that DINP exposure and DEXA treatment induced marked increases in SBP, DBP, and MBP, and that 15 mg/kg/day DINP exposure could also increase the HR level. Along with the blood pressure increase, DINP exposure induced pathological changes to the heart, aorta, and kidney. To explore the underlying mechanism, we measured the expression of angiotensin converting enzyme (ACE), angiotensin-II type 1 receptor (AT1R) and endothelial nitric oxide synthase (eNOS) in the aorta, as well as the nitric oxide (NO) concentration in serum. The data suggest that DINP exposure and DEXA treatment enhance the expression of ACE and AT1R, and inhibit eNOS expression and NO production. Interestingly, treatment with 5 mg/kg/day ACE inhibitor (ACEI) alleviated the increase in blood pressure induced by DINP exposure and DEXA treatment. These findings expand our understanding of how DINP exposure impacts the development of hypertension, and elucidates the underlying mechanisms.

Epidemiological studies and animal experiments have suggested that exposure to Di-(2-ethylhexyl) phthalate (DEHP) is strongly associated with an increase in blood pressure. However, the mechanisms that result in the detrimental effects of DEHP exposure on blood pressure are unclear. In our study, mice were orally exposed to DEHP dosages of 0.1, 1, 10 mg/kg/day for 6 weeks. The results showed that DEHP could induce a significant increase in systolic blood pressure (SBP) and heart rate, and a significant thickening of the ventricular wall. To explore the underlying mechanism, we measured the level of: angiotensin converting enzyme (ACE); bradykinin B2 receptor (BK2R); endothelial nitric oxide synthase (eNOS); bradykinin and Ca2+ in cardiac cytoplasm as well as in serum nitric oxide (NO). The results suggested that DEHP could induce an increase in ACE levels, and a decrease in bradykinin levels. Moreover, BK2R, Ca2+, eNOS and NO decreased when mice were exposed to 10 mg/kg/day DEHP. Interestingly, 5 mg/kg/day angiotensin converting enzyme inhibitor (ACEI) treatment inhibited the increase in blood pressure, and inhibited the decrease in the levels of BK2R, Ca2+, eNOS, and NO, that were induced by DEHP exposure. Our results suggest that DEHP might increase blood pressure by activating ACE expression, and inhibiting the bradykinin-NO pathway.

Conventional mining processes of rare earth elements (REEs) usually produce REEs-rich industrial waterwastes, which leads to a significant waste of REEs resources and causes serious environmental pollution. Biosorption using engineered microorganisms is an attractive technology for the recovery of REEs from aqueous solution. To regulate the REEs’ adsorption and recovery by sensing extraneous REEs, an engineered cascaded induction system, pmrCAB operon containing a lanthanide-binding tag (LBT) for sensing REEs, was incorporated into E. coli in conjunction with a silica-binding protein (Si-tag) and dLBT anchored onto the cell membrane. The sensing and adsorption capacities for Terbium (Tb), a typical study subject of REEs, were enhanced by screening an effective LBT and increasing the dLBT copy number. The adsorption capacity for Tb reached the highest reported value of 41.9 mg g−1 dry cell weight (DCW). After adhering the engineered cells onto the silica column surface through overexpressed Si-tag, a high recovering efficiency (> 90%) of Tb desorption could be obtained with 3 bed volumes of citrate solution. In addition, the engineered cells also possessed fairly good adsorption capacity of other tested REEs. Our findings showed that the recovery of REEs with high efficiency, selectivity and controllability from aqueous solution can be well achieved via specifically bio-engineered strains.

Cyanobacteria are considered potential photosynthetic microbial cell factories for biofuel and biochemical production. Ethylene, one of the most important organic chemicals, has been successfully synthesized in cyanobacteria by introducing an exogenous ethylene-forming enzyme (Efe). However, it remains challenging to significantly improve the biosynthetic efficiency of cyanobacterial ethylene. Genetic modification of transcription factors is a powerful strategy for reprogramming cellular metabolism toward target products. In cyanobacteria, nitrogen control A (NtcA), an important global transcription regulator of primary carbon/nitrogen metabolism, is expected to play a crucial role in ethylene biosynthesis. The partial deletion of ntcA (MH021) enhanced ethylene production by 23%, while ntcA overexpression (MH023) in a single-copy efe recombinant Synechocystis (XX76) reduced ethylene production by 26%. Compared to XX76, the Efe protein content increased 1.5-fold in MH021. This result may be due to the release of the negative regulation of NtcA on promoter P cpcB , which controls efe expression. Glycogen content showed a 23% reduction in MH021, and the ratio of intracellular succinate to 2-oxoglutarate (2-OG) increased 4.8-fold. In a four-copy efe recombinant strain with partially deleted ntcA and a modified tricarboxylic acid (TCA) cycle (MH043), a peak specific ethylene production rate of 2463 ± 219 μL L−1 h−1 OD 730 −1 was achieved, which is higher than previously reported. The effects of global transcription factor NtcA on ethylene synthesis in genetically engineered Synechocystis sp. PCC 6803 were evaluated, and the partial deletion of ntcA enhanced ethylene production in both single-copy and multi-copy efe recombinant Synechocystis strains. Increased Efe expression, accelerated TCA cycling, and redirected carbon flux from glycogen probably account for this improvement. The results show great potential for improving ethylene synthetic efficiency in cyanobacteria by modulating global regulation factors.

Sophora japonica var. violacea is an important ornamental plant, but its wild populations are now in danger, and need urgent conservation. In the present study, we sequenced the complete chloroplast genome of S. japonica var. violacea and used these data to assess genomic resources. The S. japonica var. violacea chloroplast genome is 158,837 bp in length, and includes a pair of inverted repeats of 25,398 bp that are separated by small and large single copy regions of 19,058 and 88,983 bp, respectively. The chloroplast genome of S. japonica var. violacea encodes 112 different genes, including 78 protein-coding genes, 30 transfer RNAs (tRNA) and 4 ribosomal RNAs (rRNA). We identified a total of 171 simple sequence repeat markers in the chloroplast genome. A phylogenetic tree constructed based on 78 protein-coding genes of 42 angiosperms showed that the position of S. japonica var. violacea is on the base of Papilionoideae. Overall, the results of this study will contribute to better support of the evolution, molecular biology and genetic improvement of S. japonica var. violacea.

What factors and underlying mechanisms influence the occurrence of the atopic march remain unclear. Recent studies suggest that exposure to diisononyl phthalate (DINP) might be associated with the occurrence of atopic dermatitis (AD) and asthma. However, little is known about the role of DINP exposure in the atopic march. In this study, we investigated the effect of DINP exposure on the progression from AD to asthma, and explored the potential mechanisms. We built an atopic march mouse model from AD to asthma, by exposure to DINP and sensitization with OVA. Pyrrolidine dithiocarbamate and SB203580 were used to block NF-κB and p38 MAPK respectively, to explore the possible molecular mechanisms. The data showed that DINP aggravated airway remodeling and airway hyperresponsiveness (AhR) in the progression from AD to asthma, induced a sharp increase in IL-33, IgE, Th2 and Th17 cytokines, and resulted in an increase in the expression of thymic stromal lymphopoietin (TSLP) and in the number of inflammatory cells. Blocking NF-κB inhibited AD-like lesions, and the production of IL-33 and TSLP in the progression of AD, while alleviating airway remodeling, AhR, and the expression of Th2 and Th17 cytokines in both the progression of AD and the asthmatic phenotype. Blocking p38 MAPK in the progression of asthma, inhibited airway remodeling, AhR, and the expression of Th2 and Th17 cytokines. The results demonstrated that exposure to DINP enhanced the immune response to memory CD4+ T helper cells through the NF-κB and p38 MAPK signaling pathways, leading to an aggravation of the atopic march.

Background Identification of functional non-coding variants and their mechanistic interpretation is a major challenge of modern genomics, especially for precision medicine. Transcription factor (TF) binding profiles and epigenomic landscapes in reference samples allow functional annotation of the genome, but do not provide ready answers regarding the effects of non-coding variants on phenotypes. A promising computational approach is to build models that predict TF-DNA binding from sequence, and use such models to score a variant’s impact on TF binding strength. Here, we asked if this mechanistic approach to variant interpretation can be combined with information on genotype-phenotype associations to discover transcription factors regulating phenotypic variation among individuals. Results We developed a statistical approach that integrates phenotype, genotype, gene expression, TF ChIP-seq, and Hi-C chromatin interaction data to answer this question. Using drug sensitivity of lymphoblastoid cell lines as the phenotype of interest, we tested if non-coding variants statistically linked to the phenotype are enriched for strong predicted impact on DNA binding strength of a TF and thus identified TFs regulating individual differences in the phenotype. Our approach relies on a new method for predicting variant impact on TF-DNA binding that uses a combination of biophysical modeling and machine learning. We report statistical and literature-based support for many of the TFs discovered here as regulators of drug response variation. We show that the use of mechanistically driven variant impact predictors can identify TF-drug associations that would otherwise be missed. We examined in depth one reported association—that of the transcription factor ELF1 with the drug doxorubicin—and identified several genes that may mediate this regulatory relationship. Conclusion Our work represents initial steps in utilizing predictions of variant impact on TF binding sites for discovery of regulatory mechanisms underlying phenotypic variation. Future advances on this topic will be greatly beneficial to the reconstruction of phenotype-associated gene regulatory networks. Electronic supplementary material The online version of this article (10.1186/s12915-019-0679-8) contains supplementary material, which is available to authorized users.

Identification of functional non-coding variants (polymorphisms) and their mechanistic interpretation is a major challenge of modern genomics, especially for precision medicine. Transcription factor (TF) binding profiles and epigenomic landscapes in reference samples can help us functionally annotate the genome, but do not provide ready answers regarding the effects of non-coding variants. A promising computational approach is to build models that predict TF-DNA binding from sequence, and use such models to score a variant’s impact on TF binding strength. Here, we asked if this mechanistic approach to variant interpretation can be combined with information on genotype-phenotype associations to discover important transcription factors regulating phenotypic variation among individuals. We developed a statistical approach that integrates phenotype, genotype, gene expression, TF ChIP-seq and Hi-C chromatin interaction data to answer this question. Using drug sensitivity measured in lymphoblastoid cell lines as the phenotype of interest, we tested if the non-coding variants statistically linked to the phenotype are enriched for strong predicted impact on DNA-binding strength of a TF, and used this test to identify TFs regulating individual differences in the phenotype. Our method relies on a new method for predicting variant impact on TF-DNA binding, that uses a combination of biophysical modelling and machine learning. We report statistical and literature-based support for many of the TFs discovered here as regulators of drug response variation. We show that the use of mechanistically driven variant impact predictors can identify TF-drug associations that would otherwise be missed. We examined in depth the evidence underlying one reported association – that of the transcription factor ELF1 with the drug doxorubicin – and identified several genes that may mediate this regulatory relationship.

Pyrus hopeiensis is endangered and was listed in the category of “the wild plants with tiny population” in China because of its limited distribution and population decline. In this study, we reported the complete chloroplast genome of Pyrus hopeiensis by Illumina pair-end sequencing. The entire chloroplast genome map was a circular molecule of 159,996 bp built with a quadripartite organization: two inverted repeats of 26,386 bp separated by a large single copy sequence of 88,023 bp and a small single copy sequence of 19,201 bp. The chloroplast genome contained the conservative structure present in most Rosaceae chloroplasts composing of 78 protein-coding genes, 30 tRNAs and 4 rRNAs. Among these genes, 15 harbored a single intron, and two contained a couple of introns. A total of 99 perfect microsatellites were analyzed in the P. hopeiensis. We identified four mutation hotspot regions for genome divergence that could be utilized as potential markers for plant identification in this genus by compared with Pyrus pyrifolia and Pyrus pashia. There were only 107 substitutions and 100 indels among the three genomes.

Actinidia arguta, known as hardy kiwi or bower vine, is a cold-hardy species native to East-Asia. Wild populations of hardy kiwi are now in danger which need urgent conservation. In this study, we sequenced the complete chloroplast genome of A. arguta and used these data to assess its genomic resources. The chloroplast genome size of A. arguta is 156,809 bp with a typical quadripartite structure consisting of a pair of inverted repeats of 23,918 bp separated by small and large single copy regions of 20,475 and 88,497 bp. There were 113 unique representative genes, and 50 simple sequences repeats were discovered. Phylogenetic analyses based on whole chloroplast genome showed that the position of A. arguta was on the base of Actinidia. Thus, the complete A. arguta chloroplast genome provides interesting insights and valuable genomic resources that can be used to reconstruct its phylogeny, evaluate genetic variations, and develop conservation strategy of this specie.

Microplastics (MP) are receiving increased attention as a harmful environmental pollutant, however information on the reproduction toxicity of MP in terrestrial animals, especially mammals, is limited. In this experiment, we investigated the impact of polystyrene microplastics (micro-PS) on the reproductive system of male mice. Healthy Balb/c mice were exposed to saline or to different doses of micro-PS for 6 weeks. The results showed that micro-PS exposure resulted in a significant decrease in the number and motility of sperm, and a significant increase in sperm deformity rate. We also detected a decrease in the activity of the sperm metabolism-related enzymes, succinate dehydrogenase (SDH) and lactate dehydrogenase (LDH), and a decrease in the serum testosterone content in the micro-PS exposure group. We found that micro-PS exposure caused oxidative stress and activated JNK and p38 MAPK. In addition, we found that when N-acetylcysteine (NAC) scavenges ROS, and when the p38 MAPK-specific inhibitor SB203580 inhibits p38MAPK, the micro-PS-induced sperm damage is alleviated and testosterone secretion improves. In conclusion, our findings suggest that micro-PS induces reproductive toxicity in mice through oxidative stress and activation of the p38 MAPK signaling pathways.

Some studies have indicated that formaldehyde, a ubiquitous environmental pollutant, can induce or aggravate allergic asthma. Epidemiological studies have also shown that the relative humidity indoors may be an independent and a key factor associated with the aggravation of allergic asthma. However, the synergy of humidity and formaldehyde on allergic asthma and the mechanism underlying this effect remain largely unknown. In this study, we aim to determine the effect of high relative humidity and/or formaldehyde exposure on allergic asthma and explore the underlying mechanisms. Male Balb/c mice were modeled with ovalbumin (OVA) and exposure to 0.5 mg/m3 formaldehyde and/or different relative humidity (60%/75%/90%). Histopathological changes, pulmonary function, Th1/Th2 balance, the status of mucus hypersecretion and the levels of inflammatory factors were detected to assess the exacerbation of allergic asthma. The levels of the transient receptor potential vanilloid 4 (TRPV4), calcium ion and the activation of p38 mitogen-activated protein kinases (p38 MAPK) were detected to explore the underlying mechanisms. The results showed that exposure to high relative humidity or to 0.5 mg/m3 formaldehyde alone had a slight, but not significant, affect on allergic asthma. However, the pathological response and airway hyperresponsiveness (AHR) were greatly aggravated by simultaneous exposure to 0.5 mg/m3 formaldehyde and 90% relative humidity. Blocking TRPV4or p38 MAPK using HC-067047 and SB203580 respectively, effectively alleviated the exacerbation of allergic asthma induced by this simultaneous exposure to formaldehyde and high relative humidity. The results show that when formaldehyde and high relative humidity are present this can enhance the activation of the TRPV4 ion channel in the lung leading to the aggravation of the p38 MAPK activation, resulting in the exacerbation of inflammation and hypersecretion of mucus in the airways.

Epidemiological studies have shown that high molecular weight phthalates (HMW) such as diethylhexyl phthalate (DEHP), are associated with hypertension in humans, while low molecular weight phthalates (LMW) such as dibutyl phthalate (DBP), have hardly any impact on the elevation of blood pressure. However, the molecular mechanisms responsible for this difference are not completely understood. In this experiment, mice were exposed to 0.1/1/10 mg/kg/day DEHP and 0.1/1/10 mg/kg/day DBP for 6 weeks, and their blood pressure was monitored using the tail pressure method. The results showed that exposure to DEHP dosages of 1 or 10 mg/kg/day resulted in a sharp increase in blood pressure, while exposure to DBP did not induce any significant changes in blood pressure. Investigating the renin-angiotensin-aldosterone system (RAAS) and NO pathway in mice exposed to DEHP, we found that levels of angiotensin-converting enzyme (ACE) and angiotensin II (AngII) increased with increasing exposure to DEHP, and the expression of nitric oxide synthase (eNOS) and the level of NO decreased. Treatment with ACE inhibitor (ACEI) to block the ACE pathway inhibited the enhancement of RAAS expression, inhibited the increase in blood pressure, and inhibited the decrease in NO levels induced by DEHP. However, the expression of ACE, AngII, AT1R, and eNOS in the DBP treatment groups showed no significant changes. When examining estradiol in vivo, we found that exposure to DBP resulted in a significant increase in the level of estradiol, while exposure to DEHP did not lead to a significant change. When ICI182780 was used to block the estradiol receptors, any increase in the level of NO induced by DBP exposure, was inhibited. These results indicate that exposure to DEHP induces an increase in mouse blood pressure through RAAS, and the different effects of DEHP and DBP on blood pressure are partly due to the different estradiol levels induced by DEHP and DBP.

Figure S1. NJ trees of Diospyros taxa based on each of the ten chloroplast barcodes, showing the resolutions of each different locus for revealing the phylogeny. The figures above the lines are the bootstrap support values for the clades. (PDF 506Â kb)

Figure S1. PCR products using genomic DNA as template. (PDF 73 kb)

Ethylene is widely used in the petrochemical industry and has traditionally been produced via the steam cracking of petroleum-based feedstock. The exploration of sustainable and carbon-neutral methods of producing ethylene from the renewable feedstock seems promising. The direct photosynthetic production of ethylene after the recycling of carbon dioxide shows great potential. In this study, continuous and stable ethylene production was achieved in Synechocystis sp. PCC 6803 by introducing a codon-optimized ethylene-forming enzyme (EFE) from Pseudomonas syringae pv. sesami and using 2-oxoglutarate (2-OG) as the substrate. Based on diverse promoter screening, PcpcB was proved to be a highly efficient promoter for ethylene production in cyanobacteria. The genes encoding 2-OG decarboxylase (OGDC) and succinic semialdehyde dehydrogenase (SSADH) in the tricarboxylic acid (TCA) cycle in Synechocystis sp. PCC 6803 were identified, and the TCA cycle was genetically modified by blocking these two enzymes with the simultaneous overexpression of EFE. Meanwhile, a gene encoding 2-OG permease (KgtP) from E. coli was introduced into the phaAB loci to increase the 2-OG supply. A peak volumetric production rate of 9.7 mL L−1 h−1 for ethylene was eventually achieved in the Synechocystis recombinant (XX110), with the genetic modification of the TCA cycle and heterologous expression of 2-oxoglutarate permease by the modified semi-continuous cultivation.

Background The sulfate-reducing bacterium Desulfatiglans anilini can grow with phenol as sole source of carbon and energy under strictly anaerobic, sulfate-reducing conditions. In the nitrate-reducing bacterium Thauera aromatica, the enzymes involved in phenol degradation have been well elucidated, whereas the anaerobic phenol degradation pathway by D. anilini was not studied in detail yet. Results The pathway of anaerobic phenol degradation by the sulfate-reducing bacterium Desulfatiglans anilini was studied by identification of genes coding for phenylphosphate synthase (encoded by pps genes) and phenylphosphate carboxylase (encoded by ppc genes) in the genome of D. anilini, by analysis of the transcription and translation of pps-ppc genes, and by measurement of phenylphosphate synthase activity in cell-free extracts of phenol-grown cells. The majority of genes involved in phenol degradation were found to be organized in one gene cluster. The gene cluster contained genes ppsα (phenylphosphate synthase alpha subunit), ppsβ (phenylphosphate synthase beta subunit), ppcβ (phenylphosphate carboxylase beta subunit), as well as 4-hydroxybenzoyl-CoA ligase and 4-hydroxylbenzoyl-CoA reductase-encoding genes. The genes ppsγ (phenylphosphate synthase gamma subunit), ppcα (phenylphosphate carboxylase alpha subunit) and ppcδ (phenylphosphate carboxylase delta subunit) were located elsewhere in the genome of D. anilini, and no obvious homologue of ppcγ (phenylphosphate carboxylase gamma subunit) was found in the genome. Induction of genes pps and ppc during growth on phenol was confirmed by reverse transcription polymerase chain reaction. Total proteome analysis revealed that the abundance of enzymes encoded by the gene cluster under study was much higher in phenol-grown cells than that in benzoate-grown cells. In in-vitro enzyme assays with cell-free extracts of phenol-grown cells, phenylphosphate was formed from phenol in the presence of ATP, Mg2+, Mn2+, K+ as co-factors. Conclusions The genes coding for enzymes involved in the anaerobic phenol degradation pathway were identified in the sulfate-reducing bacterium D. anilini. The results indicate that the first steps of anaerobic phenol degradation in D. anilini are phosphorylation of phenol to phenylphosphate by phenylphosphate synthase and carboxylation of phenylphosphate by phenylphosphate carboxylase. Electronic supplementary material The online version of this article (10.1186/s12866-018-1238-0) contains supplementary material, which is available to authorized users.

Background Fruits of persimmon plants are traditional healthy food in China, Korea and Japan. However, due to the shortage of morphological and DNA markers, the development of persimmon industry has been heavily inhibited. Results Chloroplast genomes of Diospyros cathayensis, D. virginiana, D. rhombifolia and D. deyangensis were newly sequenced. Comparative analyses of ten chloroplast genomes including six previously published chloroplast genomes of Diospyros provided new insights into the genome sequence diversity and genomic resources of the genus. Eight hyper-variable regions, trnH-psbA, rps16-trnQ, rpoB-trnC, rps4-trnT-trnL, ndhF, ndhF-rpl32-trnL, ycf1a, and ycf1b, were discovered and can be used as chloroplast DNA markers at/above species levels. The complete chloroplast genome sequences provided the best resolution at inter-specific level in comparison with different chloroplast DNA sequence datasets. Conclusion Diospyros oleifera, D. deyangensis, D. virginiana, D. glaucifolia, D. lotus and D. jinzaoshi are important wild species closely related to the cultivated persimmon D. kaki. The hyper-variable regions can be used as DNA markers for global genetic diversity detection of Diospyros. Deeper study on these taxa would be helpful for elucidating the origin of D. kaki. Electronic supplementary material The online version of this article (10.1186/s12870-018-1421-3) contains supplementary material, which is available to authorized users.

Crape myrtles are economically important tree species of the genus Lagerstroemia L. (Lythraceae), with a distribution from tropical to northern temperate zones. They are positioned phylogenetically to a large subclade of rosids (in the eudicots) which contain more than 25% of all the angiosperms. Lagerstroemia plants are important ornamental trees which produce big and showy panicles of gorgeous flowers. They commonly bloom from summer till fall and are of significant value in of city landscape and environmental protection. Morphological traits are shared inter-specifically among plants of Lagerstroemia to certain extent and are also influenced by environmental conditions and different developmental stages. Thus, classification of plants in Lagerstroemia at species and cultivar levels is still a challenging task. Chloroplast (cp) genome sequences have been proven to be an informative and valuable source of cp DNA markers for genetic diversity evaluation. In this study, the complete cp genomes of three Lagerstroemia species were newly sequenced, and three other published cp genome sequences of Lagerstroemia were retrieved for comparative analyses in order to obtain an upgraded understanding of the application value of genetic information from the cp genomes. The six cp genomes ranged from 152,049 bp (L. subcostata) to 152,526 bp (L. speciosa) in length. Their organization, gene order and GC content, were similar to the typical cp genome structure of other higher plants. We analyzed nucleotide substitutions, insertions/deletions, and simple sequence repeats in the cp genomes, and discovered 12 relatively highly variable regions that will potentially provide plastid markers for further taxonomic, phylogenetic and population genetics studies in Lagerstroemia. The phylogenetic relationships of the Lagerstroemia taxa inferred from the cp genomes obtained high support, indicating that cp genome data may be useful in resolving relationships in this genus.

Additional file 2: Table S1. Putative NtcA binding sites upstream of the cpcB gene from different cyanobacteria.

Desulfatiglans anilini is a sulfate-reducing bacterium (SRB) capable of oxidizing aniline, although growth and aniline turnover rates are slow, making it difficult to analyze the metabolism of the strain. Therefore, this study was designed to investigate the effect of sulfide on growth of D. anilini cultures, in order to improve its growth and aniline turnover rates, and study the biochemical mechanisms of sulfide inhibition. Hydrogen sulfide was found to inhibit growth of D. anilini, regardless of whether the strain was grown with aniline or phenol, and complete inhibition was observed at 20mM hydrogen sulfide. For improving the growth of D. anilini with aniline, the sulfide-consuming phototrophic bacterium Thiocapsa roseopersicina was co-cultured in a synthetic microbial community with D. anilini using a co-cultivation device that continuously removed hydrogen sulfide from the culture. The doubling time of D. anilini with aniline was 15 days in the co-cultivation device, compared to 26 days in the absence of a sulfide-oxidizing partner. Moreover, the aniline degradation rate was significantly increased by a factor of 2.66 during co-cultivation of D. anilini with T. roseopersicina. The initial carboxylation reaction during aniline degradation was measured in cell-free extracts of D. anilini with carbon dioxide (CO2) as a co-substrate in the presence of aniline and ATP. The effects of hydrogen sulfide on this aniline carboxylating system and on phenylphosphate synthase activity for phenol activation were studied, and it was concluded that hydrogen sulfide severely inhibited these enzyme activities.