Tomato golden mosaic virus (TGMV) belongs to the geminivirus subgroup that is characterized by a split genome consisting of two single-stranded circular DNAs. The TGMV A genome component encodes the virus coat protein as well as all of the functions necessary for viral DNA replication. Analysis of the nucleotide sequence indicates that the TGMV A component has, in addition to the coat protein e...

was recently demonstrated that the expression of numerous E. coli proteins is greatly enhanced in an hns deletion background compared with their levels in wild-type cells (8). H-NS thus appears to function as a global DNA-binding transcriptional regulator (7). In a previous study, we purified a subset of proteins whose expression is affected by H-NS and cloned the genes coding for some of these...

MOTIVATION Dozens of studies in recent years have demonstrated that codon usage encodes various aspects related to all stages of gene expression regulation. When relevant high-quality large-scale gene expression data are available, it is possible to statistically infer and model these signals, enabling analysing and engineering gene expression. However, when these data are not available, it is ...

The 3374 nucleotide sequence of RNA2 from the British PEBV strain SP5 has been determined. The RNA includes three open reading frames flanked by 5' and 3' noncoding regions of 509 and 480 nucleotides. The open reading frames specify coat protein, a 29.6K product homologous to the 29.1K product of TRV(TCM) RNA2 and a 23K product not homologous to any previously described protein. The homology de...

Mobile group I introns are hypothesized to have arisen after invasion by endonuclease-encoding open reading frames (ORFs), which mediate their mobility. Consistent with an endonuclease-ORF invasion event, we report similarity between exon junction sequences (the recognition site for the mobility endonuclease) and intron sequences flanking the endonuclease ORF in the sunY gene of phage T4. Furth...

A 1.7-kb DNA fragment cloned from Zymomonas mobilis genomic DNA complemented the inability to grow on sucrose of a Suc- mutant of Z. mobilis that was deficient in the production of both extracellular levansucrase and invertase. Analysis of the nucleotide sequence of the fragment found two open reading frames (ORFs), both of which did not correspond to the structural gene for the levansucrase or...

Genomic segment S12 of rice dwarf virus and segment S9 of wound tumor virus, both members of the genus Phytoreovirus, have small out-of-phase overlapping open reading frames (ORFs). Western blot (immunoblot) analysis revealed that rice dwarf virus S12 mRNA specified translation products from the large ORF and two overlapping small ORFs both in rice plant hosts and in Spodoptera frugiperda insec...

We have cloned, sequenced, and characterized the complete genome of a novel human papillomavirus (HPV), candHPV62. During cloning, 2 candHPV62 viral isolates were recovered from a single cervical sample; 1 had all anticipated HPV open-reading frames (ORFs) intact, whereas the other exhibited an E1 frame-shift mutation. Further experiments indicated that the 2 strains were equivalent in abundanc...

The nucleotide sequence of the genomic RNA of narcissus mosaic virus (NMV) was deduced from a set of cDNA clones and by direct sequencing of RNA. The genome, with a length of 6955 nucleotides [excluding the 3'poly(A) tail], contains six open reading frames (ORFs) with the capacity to code for polypeptides of more than 10K, with Mr values of 186284, 25845, 13998, 11059, 26097 and 10519. The firs...