Molecular evolution of the plant ECERIFERUM1 and ECERIFERUM3 genes involved in aliphatic hydrocarbon production

The Arabidopsis ECERIFERUM1 (CER1) protein is a decarbonylase that converts fatty acid metabolites into alkanes. Alkanes are components of waxes in the plant cuticle, a waterproof barrier serving to protect land plants from both biotic and abiotic stimuli. CER1 enzymes can be used to produce alternative and sustainable hydrocarbons in eukaryotic systems. In this report we identified 193 CER1 and 128 CER3 sequences from 56 land plants respectively. CER1 and CER3 proteins have high amino acid similarity and both are involved in alkane synthesis in Arabidopsis. The common homologues of CER1 and CER3 genes were identified in three species of chlorophytes, which may be one of the earliest plant taxa that possess CER1 and CER3 genes. To facilitate potential applications, the 3-dimensional structure and conserved motifs of CER1 proteins were also characterized. CER1 and CER3 proteins are structurally similar, but CER1 proteins have more conserved histidine-containing motifs common to fatty acid hydroxylases and stearoyl-CoA desaturases. There was no significant loss or gain of protein motifs after ancient and recent duplications, suggesting that varied properties of CER1 proteins may be associated with less-conserved regions. Among 56 land plants, the codon-based assessments of selection modes revealed that neither entire proteins nor individual amino acids of CER1 proteins were significantly subjected to positive selection, indicating that CER1 proteins are highly conserved throughout evolution.     

Genome-wide analysis of magnesium transporter genes in Solanum lycopersicum

Magnesium (Mg) is an important micronutrient for various physiological processes in plants. In this study, putative Magnesium Transporter (MGT) genes have been identified in Solanum lycopersicum, Solanum tuberosum, Brachypodium distachyon, Fagaria vesca, Brassica juncea and were classified into 5 distinct groups based on their sequence homology. MGT genes are very diverse and possess very low sequence identity within its family. However, the Gly-Met-Asn (GMN) signature motif is present in most of the genes which are believed to be essential for Mg²⁺ recognition. In S. lycopersicum, different physiological root growth pattern was observed in both Mg excess and deficient conditions. Quantitative RT-PCR gene expression study shows that most of the SlMGT genes were upregulated in response to Mg deficient condition.     

Molecular phylogenetic study and expression analysis of ATP-binding cassette transporter gene family in Oryza sativa in response to salt stress

ATP-binding cassette (ABC) transporter is a large gene superfamily that utilizes the energy released from ATP hydrolysis for transporting myriad of substrates across the biological membranes. Although many investigations have been done on the structural and functional analysis of the ABC transporters in Oryza sativa, much less is known about molecular phylogenetic and global expression pattern of the complete ABC family in rice. In this study, we have carried out a comprehensive phylogenetic analysis constructing neighbor-joining and maximum-likelihood trees based on various statistical methods of different ABC protein subfamily of five plant lineages including Chlamydomonas reinhardtii (green algae), Physcomitrella patens (moss), Selaginella moellendorffii (lycophyte), Arabidopsis thaliana (dicot) and O. sativa (monocot) to explore the origin and evolutionary patterns of these ABC genes. We have identified several conserved motifs in nucleotide binding domain (NBD) of ABC proteins among all plant lineages during evolution. Amongst the different ABC protein subfamilies, ‘ABCE’ has not yet been identified in lower plant genomes (algae, moss and lycophytes). The result indicated that gene duplication and diversification process acted upon these genes as a major operative force creating new groups and subgroups and functional divergence during evolution. We have demonstrated that rice ABCI subfamily consists of only half size transporters that represented highly dynamic members showing maximum sequence variations among the other rice ABC subfamilies. The evolutionary and the expression analysis contribute to a deep insight into the evolution and diversity of rice ABC proteins and their roles in response to salt stress that facilitate our further understanding on rice ABC transporters.     

A comparative multivariate analysis of nitrilase enzymes: An ensemble based computational approach

Nitrilases, member of nitrilase superfamily catalyse the hydrolysis of different nitriles to corresponding amides and acids. In this article, we demonstrate two-fold computational comparative analysis on coding gene sequences, amino acid sequences, three-dimensional structure of the nitrilases from different species and discovered conserved motifs linked with related species. A large ensemble-based dataset was utilized from bacteria, fungi, plants and animals. Here, we used comparative genomics, motif analyses and Bayesian phylogenetic analyses in combination with structural analyses [molecular dynamics simulation, principal component analysis (PCA), dynamic cross correlation (DCCM), root mean squared inner product (RMSIP), free energy surface (FES)] to investigate the evolution, ecological relationship and structure-function association of nitrilase family. The inferred evolutionary tree displayed nitrilase gene clusters to be shared among bacteria, fungi and plants. Structural analysis revealed that the folding of catalytic sites is similar among species; however, the loop region varies. We provide evidence based on PCA that the nitrilases are clustered into different clades due to variation in side chains. Numerous of significant correlations were found between sequence clades and the structural discriminating properties of nitrilases originating from different species. The results are consistent with the hypothesis that bacterial nitrilases are in ecological and evolutionary relationships with fungi and plants during plant-pathogen interaction to large extent. This compact and detail results also open new dimensions for further studying and improvement of industrially important nitrilase enzymes.     

Siderophore as a Potential Plant Growth-Promoting Agent Produced by Pseudomonas aeruginosa JAS-25

Siderophores scavenges Fe⁺³ from the vicinity of the roots of plants, and thus limit the amount of iron required for the growth of pathogens such as Fusarium oxysporum, Pythium ultimum, and Fusarium udum, which cause wilt and root rot disease in crops. The ability of Pseudomonas to grow and to produce siderophore depends upon the iron content, pH, and temperature. Maximum yield of siderophore of 130 μM was observed at pH 7.0?±?0.2 and temperature of 30 °C at 30 h. The threshold level of iron was 50 μM, which increases up to 150 μM, favoring growth but drastically affecting the production of siderophore by Pseudomonas aeruginosa JAS-25. The seeds of agricultural crops like Cicer arietinum (chick pea), Cajanus cajan (pigeon pea), and Arachis hypogaea (ground nut) were treated with P. aeruginosa JAS-25, which enhanced the seed germination, root length, shoot length, and dry weight of chick pea, pigeon pea, and ground nut plants under pot studies. The efficient growth of the plants was not only due to the biocontrol activity of the siderophore produced by P. aeruginosa JAS-25 but also may be by the production of indole acetic acid (IAA), which influences the growth of the plants as phytohormones.     

Comparative and evolutionary studies of mammalian arylsulfatase and sterylsulfatase genes and proteins encoded on the X-chromosome

At least 19 sulfatase genes have been reported on the human genome, including four arylsulfatase (ARS) genes (ARSD; ARSE; ARSF; ARSH) and a sterylsulfatase (STS) gene located together on the X-chromosome. Bioinformatic analyses of mammalian genomes were undertaken using known human STS and ARS amino acid sequences to study the evolution of these genes and proteins encoded on eutherian and marsupial genomes. Several domain regions and key residues were conserved including signal peptides, active site residues, metal (Ca²⁺) and substrate binding sequences, transmembranes and N-glycosylation sites. Phylogenetic analyses describe the relationships and potential origins of these genes during mammalian evolution. Primate ARSH enzymes lacked signal peptide sequences which may influence their biological functions. CpG117 and CpG92 were detected within the 5′ region of the human STS and ARSD genes, respectively, and miR-205 within the 3′-UTR for the human STS gene, using bioinformatic methods A proposal is described for a primordial invertebrate STS-like gene serving as an ancestor for unequal cross over events generating the gene complex on the eutherian mammalian X-chromosome.     

The characteristic IR spectra of heterothiometallic cluster compounds

This article summarizes and presents the obtainable characteristic IR spectra of the existing heterothiometallic cluster compounds containing the [MXS₃]²⁻ (X=O, S; M=V, Mo, W, Re) moiety. The MS stretching vibration modes are classified into four categories including ν(MS_t), ν(Mμ₂-S), ν(Mμ₃-S) and ν(Mμ₄-S) according to the different conjunction ways between the transition metal and sulfur atoms. The structures of the heterothiometallic cluster compounds could be inferred from their characteristic IR spectra, the core structure's symmetry of the heterothiometallic clusters and the M/M′ ratio.     

Genome-wide identification,functional and evolutionary analysis of terpene synthases in pineapple

Terpene synthases (TPSs) are vital for the biosynthesis of active terpenoids, which have important physiological, ecological and medicinal value. Although terpenoids have been reported in pineapple (Ananas comosus), genome-wide investigations of the TPS genes responsible for pineapple terpenoid synthesis are still lacking. By integrating pineapple genome and proteome data, twenty-one putative terpene synthase genes were found in pineapple and divided into five subfamilies. Tandem duplication is the cause of TPS gene family duplication. Furthermore, functional differentiation between each TPS subfamily may have occurred for several reasons. Sixty-two key amino acid sites were identified as being type-II functionally divergence between TPS-a and TPS-c subfamily. Finally, coevolution analysis indicated that multiple amino acid residues are involved in coevolutionary processes. In addition, the enzyme activity of two TPSs were tested. This genome-wide identification, functional and evolutionary analysis of pineapple TPS genes provide a new insight into understanding the roles of TPS family and lay the basis for further characterizing the function and evolution of TPS gene family.     

Sequencing and characterisation of complete mitogenome DNA for Rasbora sarawakensis (Cypriniformes: Cyprinidae: Rasbora) with phylogenetic consideration

The Blueline Rasbora (Rasbora sarawakensis) is a small ray-finned fish categorized under the genus Rasbora in the Cyprinidae family. In this study, the complete mitogenome sequence of R. sarawakensis was sequenced using four primers targeting overlapping regions. The mitogenome is 16,709 bp in size, accommodating 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organisation was detected between this species and other genus counterparts. The heavy strand houses 28 genes while the light strand stores the other nine genes. Most protein-coding genes employ ATG as start codon, excluding COI gene, which utilizes GTG instead. The central conserved sequence blocks (CSB-F, CSB-E and CSB-D), variable sequence blocks (CSB-3, CSB-2 and CSB-1) as well as the terminal associated sequence (TAS) are conserved in the control region. The maximum likelihood phylogenetic tree revealed the divergence of R. sarawakensis from the basal region of the Rasbora clade, where its evolutionary relationships with R. maculatus and R. pauciperforata are poorly resolved as indicated by the low bootstrap values. This work acts as steppingstone towards further molecular evolution and population genetics studies of Rasbora genus in future.     

Three-dimensional acentric coordination polymers formed from the linkage of cobalt and nickel malonate quadratic layers through a kinked organodiimine: Synthesis,structure, thermal properties and magnetochemistry

Hydrothermal synthesis has afforded a pair of isostructural acentric three-dimensional coordination polymers {[M₂(malonate)₂(dpa)(H₂O)₂] · 2H₂O}_n (M = Co, 1; M = Ni, 2; dpa = 4,4′-dipyridylamine), which were structurally characterized via single-crystal X-ray diffraction and spectroscopically and thermally analyzed. Both materials exhibit exotridentate malonate ligands conjoining metal atoms into grid-like [M(malonate)(H₂O)]_n layers; in turn, these are connected into 3-D sqp lattices (4⁴6⁶ topology) through tethering dpa ligands. The central kink and inter-ring torsion within the dpa ligands enforces the acentric Aba2 space group of crystals of 1 and 2. Antiferromagnetic coupling (g = 2.08(2), J = –1.05(8) cm⁻³) was observed within the malonate-bridged layer motifs within the cobalt derivative 1. In contrast, the nickel congener 2 exhibited ferromagnetic coupling (g = 2.201(1), J = 0.289(1) cm⁻³).     

Comparative analysis of plant lycopene cyclases

Carotenoids are essential isoprenoid pigments produced by plants, algae, fungi and bacteria. Lycopene cyclase (LYC) commonly cyclize carotenoids, which is an important branching step in the carotenogenesis, at one or both end of the backbone. Plants have two types of LYC (β-LCY and ϵ-LCY). In this study, plant LYCs were analyzed. Based on domain analysis, all LYCs accommodate lycopene cyclase domain (Pf05834). Furthermore, motif analysis indicated that motifs were conserved among the plants. On the basis of phylogenetic analysis, β-LCYs and ϵ-LCYs were classified in β and ϵ groups. Monocot and dicot plants separated from each other in the phylogenetic tree. Subsequently, Oryza sativa Japonica Group and Zea mays of LYCs as monocot plants and Vitis vinifera and Solanum lycopersicum of LYCs as dicot plants were analyzed. According to nucleotide diversity analysis of β-LCY and ϵ-LCY genes, nucleotide diversities were found to be π: 0.30 and π: 0.25, respectively. The result highlighted β-LCY genes showed higher nucleotide diversity than ϵ-LCY genes. LYCs interacting genes and their co-expression partners were also predicted using String server. The obtained data suggested the importance of LYCs in carotenoid metabolism. 3D modeling revealed that depicted structures were similar in O. sativa, Z mays, S. lycopersicum, and V. vinifera β-LCYs and ϵ-LCYs. Likewise, the predicted binding sites were highly similar between O. sativa, Z mays, S. lycopersicum, and V. vinifera LCYs. Most importantly, analysis elucidated the V/IXGXGXXGXXXA motif for both type of LYC (β-LCY and ϵ-LCY). This motif related to Rossmann fold domain and probably provides a flat platform for binding of FAD in O. sativa, Z mays, S. lycopersicum, and V. vinifera β-LCYs and ϵ-LCYs with conserved structure. In addition to lycopene cyclase domain, the V/IXGXGXXGXXXA motif can be used for exploring LYCs proteins and to annotate the function of unknown proteins containing lycopene cyclase domain. Overall results indicated that a high degree of conserved signature were observed in plant LYCs.     

Distribution and accumulation of antimony in plants in the super-large Sb deposit areas, China

Antimony (Sb) distribution and accumulation in plants in Xikuangshan Sb deposit area, the only one super-large Sb deposit in the world, Hunan, China were investigated. Results show that soils were severely polluted with the average Sb concentrations up to 5949.20 mg kg^− 1. Sb widely occurred in 34 plants with various concentrations ranging from 3.92 mg kg⁻¹ to 143.69 mg kg^− 1, Equisetaceae family has the highest concentration (98.23 mg kg^− 1) while Dryopteridacea family has the lowest one (6.43 mg kg^− 1). H. ramosissima species of Equisetaceae family had the highest Sb average concentration of 98.23 mg kg^− 1 and P. vittata species of Pteridaceae family showed advantage of accumulating Sb from the contaminated environment (Biological Accumulation Coefficient, BAC = 0.08). Almost all species enriched Sb in their upground part such as shoot, leaf and flower (Biological Transfer Coefficient, BTC > 1), which may attribute to the high acropetal coefficient and Sb transformation from the atmosphere to the plants. P. phaseoloides and D. indicum showed predominantly accumulation of Sb in the upground part with BTC of 6.65 and 5.47, respectively.From the low bioavailable fraction in soils and weak relationship between total soil concentrations in soils and plants, it seems that the Sb bioavailability was limited and varied with different soil sites as well as plant species. Those observations would be significant to the phytoaccumulation and phytoremediation of plants and ecological and environmental risk assessment in Sb contaminated areas.     

The Biological Activity of Monarda didyma L. Essential Oil and Its Effect as a Diet Supplement in Mice and Broiler Chicken

The use of growth-promoting antibiotics in livestock faces increasing scrutiny and opposition due to concerns about the increased occurrence of antibiotic-resistant bacteria. Alternative solutions are being sought, and plants of Lamiaceae may provide an alternative to synthetic antibiotics in animal nutrition. In this study, we extracted essential oil from Monarda didyma, a member of the Lamiaceae family. We examined the chemical composition of the essential oil and then evaluated the antibacterial, antioxidant, and anti-inflammatory activities of M. didyma essential oil and its main compounds in vitro. We then evaluated the effectiveness of M. didyma essential oil in regard to growth performance, feed efficiency, and mortality in both mice and broilers. Carvacrol (49.03%) was the dominant compound in the essential oil extracts. M. didyma essential oil demonstrated antibacterial properties against Escherichia coli (MIC = 87 µg·mL⁻¹), Staphylococcus aureus (MIC = 47 µg·mL⁻¹), and Clostridium perfringens (MIC = 35 µg·mL⁻¹). Supplementing the diet of mice with essential oil at a concentration of 0.1% significantly increased body weight (+5.4%) and feed efficiency (+18.85%). In broilers, M. didyma essential oil significantly improved body weight gain (2.64%). Our results suggest that adding M. didyma essential oil to the diet of broilers offers a potential substitute for antibiotic growth promoters.