Comparative Analysis of Fatty Acid Desaturases in Cyanobacterial Genomes

Fatty acid desaturases are enzymes that introduce double bonds into the hydrocarbon chains of fatty acids. The fatty acid desaturases from 37 cyanobacterial genomes were identified and classified based upon their conserved histidine-rich motifs and phylogenetic analysis, which help to determine the amounts and distributions of desaturases in cyanobacterial species. The filamentous or N2-fixing cyanobacteria usually possess more types of fatty acid desaturases than that of unicellular species. The pathway of acyl-lipid desaturation for unicellular marine cyanobacteria Synechococcus and Prochlorococcus differs from that of other cyanobacteria, indicating different phylogenetic histories of the two genera from other cyanobacteria isolated from freshwater, soil, or symbiont. Strain Gloeobacter violaceus PCC 7421 was isolated from calcareous rock and lacks thylakoid membranes. The types and amounts of desaturases of this strain are distinct to those of other cyanobacteria, reflecting the earliest divergence of it from the cyanobacterial line. Three thermophilic unicellular strains, Thermosynechococcus elongatus BP-1 and two Synechococcus Yellowstone species, lack highly unsaturated fatty acids in lipids and contain only one Δ9 desaturase in contrast with mesophilic strains, which is probably due to their thermic habitats. Thus, the amounts and types of fatty acid desaturases are various among different cyanobacterial species, which may result from the adaption to environments in evolution

Genome-Wide Identification, Evolutionary Expansion, and Expression Profile of Homeodomain-Leucine Zipper Gene Family in Poplar (Populus trichocarpa)

BACKGROUND: Homeodomain-leucine zipper (HD-ZIP) proteins are plant-specific transcriptional factors known to play crucial roles in plant development. Although sequence phylogeny analysis of Populus HD-ZIPs was carried out in a previous study, no systematic analysis incorporating genome organization, gene structure, and expression compendium has been conducted in model tree species Populus thus far. PRINCIPAL FINDINGS: In this study, a comprehensive analysis of Populus HD-ZIP gene family was performed. Sixty-three full-length HD-ZIP genes were found in Populus genome. These Populus HD-ZIP genes were phylogenetically clustered into four distinct subfamilies (HD-ZIP I-IV) and predominately distributed across 17 linkage groups (LG). Fifty genes from 25 Populus paralogous pairs were located in the duplicated blocks of Populus genome and then preferentially retained during the sequential evolutionary courses. Genomic organization analyses indicated that purifying selection has played a pivotal role in the retention and maintenance of Populus HD-ZIP gene family. Microarray analysis has shown that 21 Populus paralogous pairs have been differentially expressed across different tissues and under various stresses, with five paralogous pairs showing nearly identical expression patterns, 13 paralogous pairs being partially redundant and three paralogous pairs diversifying significantly. Quantitative real-time RT-PCR (qRT-PCR) analysis performed on 16 selected Populus HD-ZIP genes in different tissues and under both drought and salinity stresses confirms their tissue-specific and stress-inducible expression patterns. CONCLUSIONS: Genomic organizations indicated that segmental duplications contributed significantly to the expansion of Populus HD-ZIP gene family. Exon/intron organization and conserved motif composition of Populus HD-ZIPs are highly conservative in the same subfamily, suggesting the members in the same subfamilies may also have conservative functionalities. Microarray and qRT-PCR analyses showed that 89% (56 out of 63) of Populus HD-ZIPs were duplicate genes that might have been retained by substantial subfunctionalization. Taken together, these observations may lay the foundation for future functional analysis of Populus HD-ZIP genes to unravel their biological roles

Identification and Characterization of microRNAs from Peanut (Arachis hypogaea L.) by High-Throughput Sequencing

BACKGROUND: MicroRNAs (miRNAs) are noncoding RNAs of approximately 21 nt that regulate gene expression in plants post-transcriptionally by endonucleolytic cleavage or translational inhibition. miRNAs play essential roles in numerous developmental and physiological processes and many of them are conserved across species. Extensive studies of miRNAs have been done in a few model plants; however, less is known about the diversity of these regulatory RNAs in peanut (Arachis hypogaea L.), one of the most important oilseed crops cultivated worldwide. RESULTS: A library of small RNA from peanut was constructed for deep sequencing. In addition to 126 known miRNAs from 33 families, 25 novel peanut miRNAs were identified. The miRNA* sequences of four novel miRNAs were discovered, providing additional evidence for the existence of miRNAs. Twenty of the novel miRNAs were considered to be species-specific because no homolog has been found for other plant species. qRT-PCR was used to analyze the expression of seven miRNAs in different tissues and in seed at different developmental stages and some showed tissue- and/or growth stage-specific expression. Furthermore, potential targets of these putative miRNAs were predicted on the basis of the sequence homology search. CONCLUSIONS: We have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library. This study of the identification and characterization of miRNAs in peanut can initiate further study on peanut miRNA regulation mechanisms, and help toward a greater understanding of the important roles of miRNAs in peanut

A Numerical Study on the Water Entry of Cylindrical Trans-Media Vehicles

In recent years, more attention has been paid to vehicles that can travel between air and water, known as trans-media vehicles. They are often designed as cylindrical bodies in order to reduce the impact load during water entry. In this paper, the water-entry processes of small-sized cylindrical trans-media vehicles, with a characteristic length of 1 m, were investigated numerically by solving the unsteady Reynolds-averaged Navier–Stokes equations using the volume-of-fluid method, the dynamic grid method and the six degrees of freedom solver. The numerical methods were first validated by comparing the numerical results with the existing experimental data. Then, the effects of the body mass, the diameter-to-length ratio, the water-entry angle and the head shape on the water-entry process were investigated. The results show that the peak impact load, measured by the peak force exerted by water on the body, can be significantly reduced by decreasing the body mass, decreasing the diameter, entering the water at an optimum water-entry angle or installing an ellipsoidal head. In particular, the peak impact load was found to be approximately proportional to the square of the body mass or the cube of the cylinder diameter. Furthermore, installing an ellipsoidal head can reduce about 94% of the peak impact load experienced by a cylindrical body

Comparison of Envelope-Related Genes in Unicellular and Filamentous Cyanobacteria

To elucidate the evolution of cyanobacterial envelopes and the relation between gene content and environmental adaptation, cell envelope structures and components of unicellular and filamentous cyanobacteria were analyzed in comparative genomics. Hundreds of envelope biogenesis genes were divided into 5 major groups and annotated according to their conserved domains and phylogenetic profiles. Compared to unicellular species, the gene numbers of filamentous cyanobacteria expanded due to genome enlargement effect, but only few gene families amplified disproportionately, such as those encoding waaG and glycosyl transferase 2. Comparison of envelope genes among various species suggested that the significant variance of certain cyanobacterial envelope biogenesis genes should be the response to their environmental adaptation, which might be also related to the emergence of filamentous shapes with some new functions

Combinational biosynthesis and characterization of a fluorescent 82 beta-phycocyanin of Spirulina platensis

To biosynthesize fluorescent Spirulina platensis (Sp) beta-phycocyanin (PC) in Escherichia coli, a BLASTP search for homologs of the cpeS gene, a chromophore lyase, was performed against the Synechocystis sp. PCC 6803 (S6) proteome. A highly homologous gene, slr2049, was obtained from the S6 genome. Sites 82 and 153 in beta-phycocyanin of Sp were modified by site-directed mutagenesis. Two recombinant expression vectors were constructed and transformed into E. coli BL21: (i) pCDF-cpcB (C153A)-slr2049-sll0583-ho1-pcyA; and (ii) pCDF-cpcB (C82I)-slr2049-sll0583-ho1-pcyA. Lyases encoded by the genes slr2049 and sll0583 catalyzed the linking of Sp 82 beta-PC to phycocyanobilin (PCB), and fluorescent CpcB (C153A)-PCB was generated. We present a strategy for the co-expression of multiple genes in a single expression vector to identify the function of an unknown gene. Recombinant phycobiliproteins produced on a large scale are promising fluorescent tags for diagnostics and pharmacology.To biosynthesize fluorescent Spirulina platensis (Sp) beta-phycocyanin (PC) in Escherichia coli, a BLASTP search for homologs of the cpeS gene, a chromophore lyase, was performed against the Synechocystis sp. PCC 6803 (S6) proteome. A highly homologous gene, slr2049, was obtained from the S6 genome. Sites 82 and 153 in beta-phycocyanin of Sp were modified by site-directed mutagenesis. Two recombinant expression vectors were constructed and transformed into E. coli BL21: (i) pCDF-cpcB (C153A)-slr2049-sll0583-ho1-pcyA; and (ii) pCDF-cpcB (C82I)-slr2049-sll0583-ho1-pcyA. Lyases encoded by the genes slr2049 and sll0583 catalyzed the linking of Sp 82 beta-PC to phycocyanobilin (PCB), and fluorescent CpcB (C153A)-PCB was generated. We present a strategy for the co-expression of multiple genes in a single expression vector to identify the function of an unknown gene. Recombinant phycobiliproteins produced on a large scale are promising fluorescent tags for diagnostics and pharmacology

Diversity and arsenic-tolerance potential of bacterial communities from soil and sediments along a gold tailing contamination gradient

Gold tailings often lead to the release of arsenic (As) contaminants into the surrounding environment. Microorganisms play an important role in the As cycle, whereas the effects of As on bacterial communities remain unclear. To reveal the effects of As on diversity and variation of bacterial communities and their As-tolerance potential, farmland soil and river sediment samples were collected according to distance from tailings in Dandong area of northeastern China. The bacterial communities were analyzed using high-throughput sequencing of 16S rRNA genes. The membrane transport proteins ArsB or ACR3 pump As(III) out of the cell to resist As toxicity. We studied the abundance and phylogeny of ArsB and ACR3 by using PCR-based clone libraries and Quantitative PCR. The bacterial community was divided into 10 phyla and 59 genera. It was indicated that the transformation from As (V) to As(III) process was predominant, which was coupled with denitrification. Both of ArsB and ACR3 likely evolved from different orders of Proteobacteria. The arsB gene seems to be more stable in bestowing the capability of bacteria to respond to the As concentration. Moreover, As with iron, manganese and total organic carbon also influenced the clustering relationships of samples and bacterial distribution.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author