Advances in the Bioinformatics Knowledge of mRNA Polyadenylation in Baculovirus Genes

Baculoviruses are a group of insect viruses with large circular dsDNA genomes exploited in numerous biotechnological applications, such as the biological control of agricultural pests, the expression of recombinant proteins or the gene delivery of therapeutic sequences in mammals, among others. Their genomes encode between 80 and 200 proteins, of which 38 are shared by all reported species. Thanks to multi-omic studies, there is remarkable information about the baculoviral proteome and the temporality in the virus gene expression. This allows some functional elements of the genome to be very well described, such as promoters and open reading frames. However, less information is available about the transcription termination signals and, consequently, there are still imprecisions about what are the limits of the transcriptional units present in the baculovirus genomes and how is the processing of the 3′ end of viral mRNA. Regarding to this, in this review we provide an update about the characteristics of DNA signals involved in this process and we contribute to their correct prediction through an exhaustive analysis that involves bibliography information, data mining, RNA structure and a comprehensive study of the core gene 3′ ends from 180 baculovirus genomes.

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Cloning and Characterization of a Gene Cluster Involved in Cyclopentanol Metabolism in Comamonas sp. Strain NCIMB 9872 and Biotransformations Effected by Escherichia coli-Expressed Cyclopentanone 1,2-Monooxygenase

Applied and Environmental Microbiology ◽

10.1128/aem.68.11.5671-5684.2002 ◽

2002 ◽

Vol 68 (11) ◽

pp. 5671-5684 ◽

Cited By ~ 87

Author(s):

Hiroaki Iwaki ◽

Yoshie Hasegawa ◽

Shaozhao Wang ◽

Margaret M. Kayser ◽

Peter C. K. Lau

Keyword(s):

Escherichia Coli ◽

Regulatory Gene ◽

Regulatory Elements ◽

Open Reading Frames ◽

Chromosomal Locus ◽

New Genes ◽

Transcriptional Units ◽

Acid Catalyzed ◽

Reading Frames

ABSTRACT Cyclopentanone 1,2-monooxygenase, a flavoprotein produced by Pseudomonas sp. strain NCIMB 9872 upon induction by cyclopentanol or cyclopentanone (M. Griffin and P. W. Trudgill, Biochem. J. 129:595-603, 1972), has been utilized as a biocatalyst in Baeyer-Villiger oxidations. To further explore this biocatalytic potential and to discover new genes, we have cloned and sequenced a 16-kb chromosomal locus of strain 9872 that is herein reclassified as belonging to the genus Comamonas. Sequence analysis revealed a cluster of genes and six potential open reading frames designated and grouped in at least four possible transcriptional units as (orf11-orf10-orf9)-(cpnE-cpnD-orf6-cpnC)-(cpnR-cpnB-cpnA)-(orf3-orf4 [partial 3′ end]). The cpnABCDE genes encode enzymes for the five-step conversion of cyclopentanol to glutaric acid catalyzed by cyclopentanol dehydrogenase, cyclopentanone 1,2-monooxygenase, a ring-opening 5-valerolactone hydrolase, 5-hydroxyvalerate dehydrogenase, and 5-oxovalerate dehydrogenase, respectively. Inactivation of cpnB by using a lacZ-Kmr cassette resulted in a strain that was not capable of growth on cyclopentanol or cyclopentanone as a sole carbon and energy source. The presence of σ54-dependent regulatory elements in front of the divergently transcribed cpnB and cpnC genes supports the notion that cpnR is a regulatory gene of the NtrC type. Knowledge of the nucleotide sequence of the cpn genes was used to construct isopropyl-β-thio-d-galactoside-inducible clones of Escherichia coli cells that overproduce the five enzymes of the cpn pathway. The substrate specificities of CpnA and CpnB were studied in particular to evaluate the potential of these enzymes and establish the latter recombinant strain as a bioreagent for Baeyer-Villiger oxidations. Although frequently nonenantioselective, cyclopentanone 1,2-monooxygenase was found to exhibit a broader substrate range than the related cyclohexanone 1,2-monooxygenase from Acinetobacter sp. strain NCIMB 9871. However, in a few cases opposite enantioselectivity was observed between the two biocatalysts.

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ATUCG — AN AGENT–BASED ENVIRONMENT FOR AUTOMATIC ANNOTATION OF GENOMES

International Journal of Cooperative Information Systems ◽

10.1142/s0218843003000735 ◽

2003 ◽

Vol 12 (02) ◽

pp. 241-273 ◽

Cited By ~ 5

Author(s):

ANA L. C. BAZZAN ◽

ROGÉRIO DUARTE ◽

ABNER N. PITINGA ◽

LUCIANA F. SCHROEDER ◽

FARLON DE A. SOUTO ◽

...

Keyword(s):

Machine Learning ◽

Mycoplasma Hyopneumoniae ◽

Machine Learning Algorithms ◽

Open Reading Frames ◽

Automatic Annotation ◽

Agent Based ◽

The Core ◽

Layer I ◽

Using Data ◽

Reading Frames

This work reports on the ATUCG environment (Agent-based environmenT for aUtomatiC annotation of Genomes). It consists of three layers, each having several agents in charge of performing repetitive and time-consuming tasks. Layer I aims at automating the tasks behind the process of finding ORFs (Open Reading Frames). Layer II (the core of our approach) is associated with three main tasks: extraction and formatting of data, automatic annotation of data regarding profiles or families of proteins, and generation and validation of rules to automatically annotate the Keywords field in the SWISS-PROT database. Layer III permits the user to check the correctness of the automatic annotation. This environment is being designed having the sequencing of the Mycoplasma hyopneumoniae in mind. Thus examples are presented using data of organisms of the Mycoplasmataceae family. We have concentrated the developments in layer II because this is the most general one and because it focusses on machine learning algorithms, a characteristic which is not usual in annotation systems. Results regarding this layer show that with learning (individual or colaborative), agents are able to generate rules for annotation which achieve better results than those reported in the literature.

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The carboxyl-terminal part of the putative Berne virus polymerase is expressed by ribosomal frameshifting and contains sequence motifs which indicate that toro- and coronaviruses are evolutionary related

Nucleic Acids Research ◽

10.1093/nar/18.15.4535 ◽

1990 ◽

Vol 18 (15) ◽

pp. 4535-4542 ◽

Cited By ~ 69

Author(s):

Eric J. Snijder ◽

Johan A.den Boon ◽

Peter J. Bredenbeek ◽

Marian C. Horzinek ◽

Rene Rijnbrand ◽

...

Keyword(s):

Rna Structure ◽

Complete Sequence ◽

Open Reading Frames ◽

Sequence Motifs ◽

Polymerase Gene ◽

Terminal Part ◽

Ribosomal Frameshifting ◽

Polymerase Domain ◽

Carboxyl Terminal ◽

Reading Frames

Abstract Sequence analysis of the 3′ part (8 kb) of the polymerase gene of the torovirus prototype Berne virus (BEV) revealed that this area contains at least two open reading frames (provisionally designated ORF1a and ORF1b) which overlap by 12 nucleotides. The complete sequence of ORF1b (6873 nucleotides) was determined. Like the coronaviruses, BEV was shown to express its ORF1 b by ribosomal frameshifting during translation of the genomic RN A. The predicted tertiary RNA structure (a pseudoknot) in the toro- and coronaviral frameshift-directing region is similar. Analysis of the amino acid sequence of the predicted BEV ORF1b translation product revealed homology with the ORF1b product of coronaviruses. Four conserved domains were identified: the putative polymerase domain, an area containing conserved cysteine and histidine residues, a putative helicase motif, and a domain which seems to be unique for toroand coronaviruses. The data on the 3′ part of the polymerase gene of BEV supplement previously observed similarities between toro- and coronaviruses at the level of genome organization and expression. The two virus families are more closely related to each other than to other families of positive-stranded RNA viruses.

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