The mitochondrial genome of Ophiostoma himal-ulmi and comparison with other Dutch elm disease causing fungi.

The mitochondrial genome of Ophiostoma himal-ulmi, a species endemic to the Western Himalayas and a member of the Dutch elm disease-causing fungi, has been sequenced and characterized. The mitochondrial genome was compared with other available genomes for members of the Ophiostomatales, including other agents of Dutch elm disease (Ophiostoma ulmi, Ophiostoma novo-ulmi subspecies novo-ulmi and Ophiostoma novo-ulmi subspecies americana) and it was noted that gene synteny is highly conserved and variability among members of the Dutch-elm disease-causing fungi is primarily due to the number of intron insertions. Among the Dutch elm disease-causing fungi examined, O. himal-ulmi has the largest mitochondrial genomes ranging from 94 934 bp to 111 712 bp due to the expansion of the number of introns.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

Programmable Genome Editing Tools and their Regulation for Efficient Genome Engineering

Targeted genome editing has become a powerful genetic tool for studying gene function or for modifying genomes by correcting defective genes or introducing genes. A variety of reagents have been developed in recent years that can generate targeted double-stranded DNA cuts which can be repaired by the error-prone, non-homologous end joining repair system or via the homologous recombination-based double-strand break repair pathway provided a suitable template is available. These genome editing reagents require components for recognizing a specific DNA target site and for DNA-cleavage that generates the double-stranded break. In order to reduce potential toxic effects of genome editing reagents, it might be desirable to control the in vitro or in vivo activity of these reagents by incorporating regulatory switches that can reduce off-target activities and/or allow for these reagents to be turned on or off. This review will outline the various genome editing tools that are currently available and describe the strategies that have so far been employed for regulating these editing reagents. In addition, this review will examine potential regulatory switches/strategies that can be employed in the future in order to provide temporal control for these reagents. Keywords: Meganuclease, TALEN, Zinc finger nuclease, CRISPR/Cas9, Regulatory switch, Hammerhead ribozym

The complete mitochondrial genome of the Dutch elm disease fungus Ophiostoma novo-ulmi subspecies novo-ulmi.

Ophiostoma novo-ulmi, a member of the Ophiostomatales (Ascomycota) is the causal agents of the current Dutch elm disease pandemic in Europe and North America. The complete mitochondrial genome (mtDNA) of Ophiostoma novo-ulmi subsp. novo-ulmi, the European component of O. novo-ulmi, has been sequenced and annotated. Gene order (synteny) among the currently available members of the Ophiostomatales was examined and appears to be conserved and mtDNA size variability among the Ophiostomatales in part is due the presence of introns and their encoded open reading frames. Phylogenetic analysis of concatenated mitochondrial protein-coding genes yielded phylogenetic estimates for various members of the Ophiostomatales with strong statistical support showing that mtDNA analysis may provide valuable insights into the evolution of the Ophiostomatales.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

Physiological, Structural, and Functional Analysis of the Paralogous Cation–Proton Antiporters of NhaP Type from <i>Vibrio cholerae</i>

The transmembrane K+/H+ antiporters of NhaP type of Vibrio cholerae (Vc-NhaP1, 2, and 3) are critical for maintenance of K+ homeostasis in the cytoplasm. The entire functional NhaP group is indispensable for the survival of V. cholerae at low pHs suggesting their possible role in the acid tolerance response (ATR) of V. cholerae. Our findings suggest that the Vc-NhaP123 group, and especially its major component, Vc-NhaP2, might be a promising target for the development of novel antimicrobials by narrowly targeting V. cholerae and other NhaP-expressing pathogens. On the basis of Vc-NhaP2 in silico structure modeling, Molecular Dynamics Simulations, and extensive mutagenesis studies, we suggest that the ion-motive module of Vc-NhaP2 is comprised of two functional regions: (i) a putative cation-binding pocket that is formed by antiparallel unfolded regions of two transmembrane segments (TMSs V/XII) crossing each other in the middle of the membrane, known as the NhaA fold; and (ii) a cluster of amino acids determining the ion selectivity

Three new active members of the I-OnuI family of homing endonucleases

In vitro characterization of three LAGLIDADG-type homing endonucleases (I-CcaI, I-CcaII and I-AstI) that belong to the I-OnuI family showed that they are functional homing endonucleases that cleave their respective cognate target sites. These endonucleases are encoded within group ID introns and appear to be orthologs that have inserted into three different mitochondrial genes, rns, rnl and cox3, respectively. The endonuclease activity of I-CcaI was tested using various substrates and its minimum DNA recognition sequence was estimated to be 26 nt. This set of homing endonucleases may provide some insight on how these types of mobile elements can migrate into new locations. This study provides additional endonucleases that can be added to the catalog of currently available HEs that may have various biotechnology applications.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

Predicting human RNA quadruplex helicases through comparative sequence approaches and helicase mRNA interactome analyses

RNA quadruplexes are non-canonical nucleic acid structures involved in several human disease states and are regulated by a specific subset of RNA helicases. Given the difficulty in identifying RNA quadruplex helicases due to the multifunctionality of these enzymes, we sought to provide a comprehensive in silico analysis of features found in validated RNA quadruplex helicases to predict novel human RNA quadruplex helicases. Using the 64 human RNA helicases, we correlated their amino acid compositions with subsets of RNA quadruplex helicases categorized by varying level of evidence of RNA quadruplex interaction. Utilizing phylogenetic and synonymous/non-synonymous substitution analyses, we identified an evolutionarily conserved pattern involving predicted intrinsic disorder and a previously identified motif. We analyzed available next generation sequencing data to determine which RNA helicases were directly interacting with predicted RNA quadruplex regions intracellularly and elucidated a relationship with miRNA binding sites adjacent to RNA quadruplexes. Finally, we employed a phylogenetic analysis of all 64 human RNA helicases to establish how RNA quadruplex detection and unwinding activity may be conserved among helicase subfamilies. This work furthers understanding of commonalities between RNA quadruplex helicases and provides support for the future validation of several human RNA helicases.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

The intron landscape of the mtDNA <i>cytb</i> gene among the Ascomycota: introns and intron-encoded open reading frames

<p>Fungal mitochondrial genes are frequently noted for the presence of introns. These introns are self-splicing and can be assigned to either group I or II introns and they can encode open reading frames (ORFs). This study examines the introns present within the cytochrome b (<i>cytb</i>) gene of ascomycetes fungi. Cytochrome b gene sequences were sampled from GenBank and supplemented with our own data for species of <i>Leptographium</i> and <i>Ophiostoma</i>. Group I introns were encountered most frequently, many encoding either LAGLIDADG or GIY-YIG homing endonucleases (HEs). Numerous examples of different intron/ORF arrangements were observed including nested ORFs, multiple ORFs within a single intron and intron ORFs at various stages of erosion due to the accumulation of mutations. In addition, we noted one example of a nested intron and one complex group II intron that could potentially allow for alternative splicing. Documenting the distribution of introns within the same gene across a range of species allows for a better understanding of the evolution of introns and intronic ORFs. Intron landscapes also are a resource that can help in annotating genes and in bioprospecting for potentially active HEs, which are rare-cutting DNA endonucleases with applications in biotechnology.</p

Syntenic view of two chromosomes of <i>S. reilianum</i> that merged as one in <i>S. scitamineum</i>.

<p>Links represents alignment length of more than 1 kbp obtained by BLASTn (e-value < 1 x 10^-5). The first outer circle represents the chromosome and scale is coordinates in base pairs. The second indicates the GC content followed by predicted coding regions of the plus and minus strands. Bars display the % of identity to orthologous in <i>S. reilianum</i>. The most inner circle represents the RNAseq coverage of each chromosome region. Red lines are RNAseq data of <i>S. scitamineum</i> growing in planta and blue lines growing <i>in vitro</i>. Circle images of all chromosomes are available in the Supporting Information <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129318#pone.0129318.s003" target="_blank">S3 File</a>.</p

Comparative analysis of orthology among four smut fungi obtained by OrthoMCL.

<p>Comparative analysis of orthology among four smut fungi obtained by OrthoMCL.</p