Long Noncoding Region Research Articles

Characterization of the complete mitogenome of brown-spotted locust, Cyrtacanthacris tatarica (Orthoptera: Acrididae: Cyrtacanthacridinae)

The complete mitochondrial genome of Cyrtacanthacris tatarica was firstly sequenced and analyzed. The circular mitogenome was 15,679 bp long, showing a bias of AT rich on the majority strand (42.34% of A, 29.99% of T, 11.19% of G, and 16.18% of C). It consisted of the typical 37 genes (13 protein-coding genes, two ribosomal RNA genes, and 22 transfer tRNA genes) and one longest non-coding region (called as control region). All PCGs used standard ATN initiation codons, and most PCGs were terminated with complete codons (TAA/TAG), apart from cox1 and nad5. Phylogenetic analyses based on the concatenated nucleotide sequences of PCGs supported that Cyrtacanthacridinae was monophyletic, and the sister group relationship between C. tatarica and Schistocerca gregaria gregaria was determined. Our results may provide molecular information for the genetic evolution and taxonomy of the acridid species.

Population Variability Generated during Rescue Process and Passaging of Recombinant Mumps Viruses.

Recombinant mumps viruses (MuVs) based on established vaccine strains represent attractive vector candidates as they have known track records for high efficacy and the viral genome does not integrate in the host cells. We developed a rescue system based on the consensus sequence of the L-Zagreb vaccine and generated seven different recombinant MuVs by (a) insertion of one or two additional transcription units (ATUs), (b) lengthening of a noncoding region to the extent that the longest noncoding region in MuV genome is created, or (c) replacement of original L-Zagreb sequences with sequences rich in CG and AT dinucleotides. All viruses were successfully rescued and faithfully matched sequences of input plasmids. In primary rescued stocks, low percentages of heterogeneous positions were found (maximum 0.12%) and substitutions were predominantly obtained in minor variants, with maximally four substitutions seen in consensus. ATUs did not accumulate more mutations than the natural MuV genes. Six substitutions characteristic for recombinant viruses generated in our system were defined, as they repetitively occurred during rescue processes. In subsequent passaging of primary rescue stocks in Vero cells, different inconsistencies within quasispecies structures were observed. In order to assure that unwanted mutations did not emerge and accumulate, sub-consensus variability should be closely monitored. As we show for Pro408Leu mutation in L gene and a stop codon in one of ATUs, positively selected variants can rise to frequencies over 85% in only few passages.

The first mitochondrial genome of Tetraclita kuroshioensis (Crustacea: Sessilia) from China: insight into the phylogeny within Cirripedia

We determined the first mitochondrial genome of Tetraclita kuroshioensis from China. The mitochondrial genome of T. kuroshioensis was found to be 15,175 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs. The longest non-coding region was 425 bp in length. Phylogenetic analysis showed that T. kuroshioensis clustered with T. serrata and then clustered with T. squamosa squamosa with high bootstrap value (BP = 100). In the future, sequencing of additional mitochondrial genomes should provide additional insights into the deep phylogeny of Cirripedia.

The complete mitochondrial genome of Tetrancistrum nebulosi (Monogenea: Ancyrocephalidae)

The first complete mitochondrial (mt) genome of Ancyrocephalidae is reported herein. The mt genome of Tetrancistrum nebulosi was 13,392 bp in length containing 12 protein-coding genes (lacking atp8), 22 tRNA genes and 2 rRNA genes. The longest non-coding region was located between nad5 and trnG, and the A + T content was 72.4%. All tRNAs had the typical clover-leaf secondary structure except for trnS1(AGN), trnR, trnF and trnQ. The rrnL and rrnS subunits were separated by trnC, as documented in the monopisthocotylean groups (Benedenia and Gyrodactylus species), while they were adjacent to each other in the polyopisthocotylean species (Microcotyle sebastis, Polylabris halichoeres and Pseudochauhanea macrorchis).

The complete mitochondrial genome of Orientobilharzia turkestanicum supports its affinity with African Schistosoma spp.

Orientobilharzia turkestanicum is a blood fluke of many mammals and causes orientobilharziasis that is also a neglected parasitic zoonosis because the cercaria of O. turkestanicum can infect humans and cause cercarial dermatitis. The present study determined the complete sequence of mt genome of O. turkestanicum and revised its phylogenetic position based on mt gene content and arrangement. The complete mtDNA sequence of O. turkestanicum was 14,755bp in length, which is slightly larger than the mtDNA genomes of three species of the blood flukes, Schistosoma mekongi (14,072bp), Schistosoma japonicum (14,085bp) and Schistosoma mansoni (14,415bp), but smaller than Schistosoma haematobium (15,003bp) and Schistosoma spindale (16,901bp). The mt genome of O. turkestanicum contains 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes, but lacks an atp8 gene, consistent with that of Schistosoma species. The mt genome arrangement of O. turkestanicum contains an AT-rich region and two non-coding regions (NCRs), including long non-coding region (LNR) and short non-coding region (SNR). Phylogenetic analysis based on amino acids sequences showed that O. turkestanicum belonged to the genus Schistosoma, and is phylogenetically closer to the African schistosome group (S. haematobium, S. spindale and S. mansoni) than to the Asian group (S. mekongi and S. japonicum). But the arrangement of mtDNA protein-coding genes for O. turkestanicum is the same as Asian group, and distinct from the African species. Combining content and arrangement of mtDNA for O. turkestanicum, we conclude that O. turkestanicum should be considered a member of the Schistosoma genus, which shares a closer affinity to the African schistosomes than the Asian species, and gene order of mt genome in O. turkestanicum would be considered sympleisiomorphic (perhaps retained from the ancestor).

Determination of the complete mitochondrial DNA sequence of Octopus minor

In this study, we have determined the complete nucleotide sequence of the mitochondrial genome of Octopus minor. It is 15,974 nucleotide pairs and encodes 13 proteins, two ribosomal RNAs and 22 tRNAs of the mitochondrion's own protein synthesizing system. Seven of thirteen proteins are encoded by the H-strand, while the other six proteins, as well as the two ribosomal RNAs are encoded by the L-strand. The nucleotide composition of the proteins showed a nucleotide bias against G encoded by the H-strand, while they showed a nucleotide bias against A and C encoded by the L-strand. Two of the 13 protein coding genes of O. minor began with the unorthodox translation initiation codon ATA and all others use the standard ATG. In addition, six of thirteen mt proteins of O. minor have unambiguous termination codons. There are four cases where tRNA genes appear to overlap. The long noncoding region (LNCR) of O. minor was 930 nucleotides and no repeated sequences were found in this LNCR. The gene arrangements of O. minor showed remarkable similarity to that of O. ocellatus and O. vulgaris. Phylogenetic analysis demonstrated that O. minor appears as sister taxan to the monophyletic group combined by O. ocellatus and O. vulgaris, suggesting a relative distant genetic relationship between O. minor and the other two octopus species.

The 5' external transcribed spacer in mouse ribosomal RNA contains two cleavage sites.

The 5' external transcribed spacer (5'ETS) is critical for 18S rRNA formation and is the longest noncoding region in a ribosomal RNA transcript. Here we show that processing in mouse 5'ETS involves two cleavage events. Processing at site A' corresponds to the previously described "primary cleavage," which precedes other processing steps. Processing at the novel site A0 occurs 1 kb downstream from A' yielding two new rRNA precursors: 43S and 29S. The excised 5'-A' and A'-A0 fragments are rapidly degraded under normal conditions. Depletion of the exosome component EXOSC10/PM-Scl100 (ortholog of yeast Rrp6p) results in a strong accumulation of the A'-A0 spacer fragment in mouse cells. We discuss the finding of a second processing site in mammalian 5'ETS in relation to the involvement of the U3 snoRNA in pre-rRNA processing and present a revised map of the mouse 18S rRNA processing pathway.

NUCLEOTIDE-SEQUENCE OF A CANINE ORAL PAPILLOMAVIRUS CONTAINING A LONG NONCODING REGION

The DNA genome of a canine oral papillomavirus (COPV) was completely sequenced and found to consist of 8607 base pairs, which were the longest of all known papillomaviruses (PVs). Its organization was similar to that of other PVs except that it lacked early gene 5 (E5) and possessed a unique long noncoding region (L-NCR) between the end of the early genes and the beginning of the late genes. COPV also possessed a short noncoding region (S-NCR) which contained a putative upper regulatory region (URR), which is commonly found in PVs. The L-NCR did not show any similarity to known PV DNAs nor other DNA sequences in the GenBank database. Nucleotide sequence analysis of COPV showed that it was closely related to human papillomavirus type 1 (HPV 1) and animal PVs associated with cutaneous lesions in rabbit, European elk, deer and cow as we reported previously.

Nucleotide sequence from the genetic left end of bacteriophage T7 DNA to the beginning of gene 4

The nucleotide sequence running from the genetic left end of bacteriophage T7 DNA to within the coding sequence of gene 4 is given, except for the internal coding sequence for the gene 1 protein, which has been determined elsewhere. The sequence presented contains nucleotides 1 to 3342 and 5654 to 12,100 of the approximately 40,000 base-pairs of T7 DNA. This sequence includes: the three strong early promoters and the termination site for Escherichia coli RNA polymerase: eight promoter sites for T7 RNA polymerase; six RNAase III cleavage sites; the primary origin of replication of T7 DNA; the complete coding sequences for 13 previously known T7 proteins, including the anti-restriction protein, protein kinase, DNA ligase, the gene 2 inhibitor of E. coli RNA polymerase, single-strand DNA binding protein, the gene 3 endonuclease, and lysozyme (which is actually an N-acetylmuramyl- l-alanine amidase); the complete coding sequences for eight potential new T7-coded proteins; and two apparently independent initiation sites that produce overlapping polypeptide chains of gene 4 primase. More than 86% of the first 12,100 base-pairs of T7 DNA appear to be devoted to specifying amino acid sequences for T7 proteins, and the arrangement of coding sequences and other genetic elements is very efficient. There is little overlap between coding sequences for different proteins, but junctions between adjacent coding sequences are typically close, the termination codon for one protein often overlapping the initiation codon for the next. For almost half of the potential T7 proteins, the sequence in the messenger RNA that can interact with 16 S ribosomal RNA in initiation of protein synthesis is part of the coding sequence for the preceding protein. The longest non-coding region, about 900 base-pairs, is at the left end of the DNA. The right half of this region contains the strong early promoters for E. coli RNA polymerase and the first RNAase III cleavage site. The left end contains the terminal repetition (nucleotides 1 to 160), followed by a striking array of repeated sequences (nucleotides 175 to 340) that might have some role in packaging the DNA into phage particles, and an A · T-rich region (nucleotides 356 to 492) that contains a promoter for T7 RNA polymerase, and which might function as a replication origin.