scholarly journals Isolation of Neurospora crassa A mating type mutants by repeat induced point (RIP) mutation.

Genetics ◽  
1992 ◽  
Vol 132 (1) ◽  
pp. 125-133 ◽  
Author(s):  
N L Glass ◽  
L Lee
Keyword(s):  
Neurospora Crassa ◽  
Mating Type ◽  
Single Copy ◽  
Open Reading Frame ◽  
Sexual Cycle ◽  
Reading Frame ◽  
Heterokaryon Incompatibility ◽  
Functional Regions ◽  
A Genome ◽  
Ascospore Formation

Abstract In the filamentous fungus, Neurospora crassa, mating type is regulated by a single locus with alternate alleles, termed A and a. The mating type alleles control entry into the sexual cycle, but during vegetative growth they function to elicit heterokaryon incompatibility, such that fusion of A and a hypha results in death of cells along the fusion point. Previous studies have shown that the A allele consists of 5301 bp and has no similarity to the a allele; it is found as a single copy and only within the A genome. The a allele is 3235 bp in length and it, too, is found as a single copy within the a genome. Within the A sequence, a single open reading frame (ORF) of 288 amino acids (mt A-1) is thought to confer fertility and heterokaryon incompatibility. In this study, we have used repeat induced point (RIP) mutation to identify functional regions of the A idiomorph. RIP mutations in mt A-1 resulted in the isolation of sterile, heterokaryon-compatible mutants, while RIP mutations generated in a region outside of mt A-1 resulted in the isolation of mutants capable of mating, but deficient in ascospore formation.

scholarly journals Sequence and structure of mtr, an amino acid transport gene of Neurospora crassa

Genome ◽  
1991 ◽  
Vol 34 (4) ◽  
pp. 644-651 ◽  
Author(s):  
Kenneth Koo ◽  
W. Dorsey Stuart
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Neurospora Crassa ◽  
Rna Binding ◽  
Signal Sequence ◽  
Average Length ◽  
Open Reading Frame ◽  
Mrna Transcript ◽  
S1 Nuclease ◽  
Reading Frame

The gene product of the mtr locus of Neurospora crassa is required for the transport of neutral aliphatic and aromatic amino acids via the N system. We have previously cloned three cosmids containing Neurospora DNA that complement the mtr-6(r) mutant allele. The cloned DNAs were tightly linked to restriction fragment length polymorphisms that flank the mtr locus. A 2.9-kbp fragment from one cosmid was subcloned and found to complement the mtr-6(r) allele. Here we report the sequence of the fragment that hybridized to a poly(A)+ mRNA transcript of about 2300 nucleotides. We have identified an 845-bp open reading frame (ORF) having a 59-bp intron as the potential mtr ORF. S1 nuclease analysis of the transcript confirmed the transcript size and the presence of the intron. A second open reading frame was found upstream in the same reading frame as the mtr ORF and appears to be present in the mRNA transcript. The mtr ORF is predicted to encode a 261 amino acid polypeptide with a molecular mass of 28 613 Da. The proposed polypeptide exhibits six potential α-helical transmembrane domains with an average length of 23 amino acids, does not have a signal sequence, and contains amino acid sequence homologous to an RNA binding motif.Key words: sequence, membranes, ribonucleoprotein.

Retroviral insertions in the murine His-1 locus activate the expression of a novel RNA that lacks an extensive open reading frame

1994 ◽  
Vol 14 (3) ◽  
pp. 1743-1751
Author(s):  
D S Askew ◽  
J Li ◽  
J N Ihle
Keyword(s):  
Cell Lines ◽  
Wild Mouse ◽  
Myeloid Cell ◽  
Single Copy ◽  
Open Reading Frame ◽  
Chromosome 2 ◽  
Coding Region ◽  
Reading Frame ◽  
Novel Gene ◽  
Myeloid Leukemias

The His-1 locus is a common site of viral insertion in murine myeloid leukemias induced by the wild mouse ecotropic retrovirus, CasBrM. In this report, we describe the cloning of a novel gene at the His-1 locus and show that His-1 expression is associated with the transformed phenotype. Northern (RNA) blot analysis identified His-1 transcripts in four transformed myeloid cell lines but in no normal tissues examined. Two of these cell lines were derived from retrovirus-induced myeloid leukemias that harbor integrated proviruses which drive His-1 gene expression by promoter insertion. The two other cell lines expressed a discrete 3-kb His-1 RNA that is derived from a novel gene consisting of three exons that span 6 kb on mouse chromosome 2. The His-1 gene is conserved as a single-copy sequence in multiple vertebrate species and is expressed as a spliced and polyadenylated RNA. A protein-coding region is not evident from analysis of the His-1 sequence because of the presence of multiple small open reading frames, none of which are greater than 219 bp. This lack of an extensive open reading frame is an unusual feature that is shared by other RNA molecules believed to function in the absence of translation.

scholarly journals Design of in vitro Transcribed mRNA Vectors for Research and Therapy

2019 ◽  
Vol 73 (5) ◽  
pp. 391-394
Author(s):  
Marina Tusup ◽  
Lars E. French ◽  
Mara De Matos ◽  
David Gatfield ◽  
Thomas Kundig ◽  
...  
Keyword(s):  
Gene Therapy ◽  
Messenger Rna ◽  
Untranslated Region ◽  
Open Reading Frame ◽  
Purification Method ◽  
Reading Frame ◽  
Mrna Purification ◽  
Functional Regions ◽  
In Cells

The use of in vitro transcribed messenger RNA (ivt mRNA) for vaccination, gene therapy and cell reprograming has become increasingly popular in research and medicine. This method can be used in vitro (transfected in cells) or administered naked or formulated (lipoplexes, polyplexes, and lipopolyplexes that deliver the RNA to specific organs, such as immune structures, the lung or liver) and is designed to be an immunostimulatory or immunosilent agent. This vector contains several functional regions (Cap, 5' untranslated region, open reading frame, 3' untranslated region and poly-A tail) that can all be optimised to generate a highly efficacious ivt mRNA. In this study, we review these aspects and report on the effect of the ivt mRNA purification method on the functionality of this synthetic transient genetic vector.

scholarly journals Efficient Homologous RNA Recombination and Requirement for an Open Reading Frame during Replication of Equine Arteritis Virus Defective Interfering RNAs

2000 ◽  
Vol 74 (19) ◽  
pp. 9062-9070 ◽  
Author(s):  
Richard Molenkamp ◽  
Sophie Greve ◽  
Willy J. M. Spaan ◽  
Eric J. Snijder
Keyword(s):  
Rna Virus ◽  
Rna Replication ◽  
Proximal Region ◽  
Full Length ◽  
Equine Arteritis Virus ◽  
Open Reading Frame ◽  
Replicase Gene ◽  
Rna Recombination ◽  
Reading Frame ◽  
A Genome

ABSTRACT Equine arteritis virus (EAV), the prototype arterivirus, is an enveloped plus-strand RNA virus with a genome of approximately 13 kb. Based on similarities in genome organization and protein expression, the arteriviruses have recently been grouped together with the coronaviruses and toroviruses in the newly established order Nidovirales. Previously, we reported the construction of pEDI, a full-length cDNA copy of EAV DI-b, a natural defective interfering (DI) RNA of 5.6 kb (R. Molenkamp et al., J. Virol. 74:3156–3165, 2000). EDI RNA consists of three noncontiguous parts of the EAV genome fused in frame with respect to the replicase gene. As a result, EDI RNA contains a truncated replicase open reading frame (EDI-ORF) and encodes a truncated replicase polyprotein. Since some coronavirus DI RNAs require the presence of an ORF for their efficient propagation, we have analyzed the importance of the EDI-ORF in EDI RNA replication. The EDI-ORF was disrupted at different positions by the introduction of frameshift mutations. These were found either to block DI RNA replication completely or to be removed within one virus passage, probably due to homologous recombination with the helper virus genome. Using recombination assays based on EDI RNA and full-length EAV genomes containing specific mutations, the rates of homologous RNA recombination in the 3′- and 5′-proximal regions of the EAV genome were studied. Remarkably, the recombination frequency in the 5′-proximal region was found to be approximately 100-fold lower than that in the 3′-proximal part of the genome.

A SEARCH FOR COMPLEXITY AT THE MATING-TYPE LOCUS OF NEUROSPORA CRASSA

1973 ◽  
Vol 15 (3) ◽  
pp. 577-585 ◽  
Author(s):  
Dorothy Newmeyer ◽  
H. Branch Howe Jr. ◽  
Donna R. Galeazzi
Keyword(s):  
Neurospora Crassa ◽  
Mating Type ◽  
Adjacent Gene ◽  
Opposite Mating Type ◽  
Type Locus ◽  
Linked Gene ◽  
Heterokaryon Incompatibility ◽  
Mating Type Locus ◽  
Incompatibility Reaction ◽  
The Right

Evidence for complexity at the mating-type locus of Neurospora crassa was sought by selecting recombinants between closely linked markers on either side. All recombinants were tested for crossing ability, to test the hypothesis that the two mating-type alleles are actually closely linked self-sterile mutants; such tests should also detect subunits analogous to the α and β subunits of the A factor of Schizophyllum or Coprinus. No change in crossing ability was found among the 5,019 recombinants tested, representing 235,000 viable ascospores. The results indicate that if subunits exist, they are not more than 0.002 units apart. Twelve hundred and forty of the recombinants were tested in a way that should also have detected subunits analogous to the A and B factors of Schizophyllum and Coprinus, except that A and B would be closely linked. No such subunits were detected.N. crassa strains of opposite mating type are heterokaryon-incompatible during vegetative growth, and observations of various investigators have suggested that the heterokaryon incompatibility might be controlled by a separate closely-linked gene rather than by mating type itself. A sample of the recombinants was therefore tested for separation of the heterokaryon-incompatibility and crossing-compatibility functions. (Heterokaryon-incompatibility was scored by the presence of an incompatibility reaction in duplications heterozygous for mating type; this technique is simple and eliminates complications due to unlinked heterokaryon-incompatibility loci, several of which are known in N. crassa.) No separation was found. The results indicate that if an adjacent gene is responsible for the heterokaryon-incompatibility, it is not more than 0.0078 units from mating type, if on the left, and not more than 0.018 units from mating type, if on the right.

scholarly journals Targeted Inactivation of a Tobacco Intron–containing Open Reading Frame Reveals a Novel Chloroplast-encoded Photosystem I–related Gene

1997 ◽  
Vol 139 (1) ◽  
pp. 95-102 ◽  
Author(s):  
Stephanie Ruf ◽  
Hans Kössel ◽  
Ralph Bock
Keyword(s):  
Photosystem I ◽  
Reverse Genetics ◽  
Higher Plants ◽  
Single Copy ◽  
Open Reading Frame ◽  
Higher Plant ◽  
Reading Frame ◽  
Chloroplast Genomes ◽  
Plant Chloroplast ◽  
Targeted Inactivation

The chloroplast genome of all higher plants encodes, in its large single-copy region, a conserved open reading frame of unknown function (ycf3), which is split by two group II introns and undergoes RNA editing in monocotyledonous plants. To elucidate the function of ycf3 we have deleted the reading frame from the tobacco plastid genome by biolistic transformation. We show here that homoplasmic Δycf3 plants display a photosynthetically incompetent phenotype. Molecular analyses indicate that this phenotype is not due to a defect in any of the general functions of the plastid genetic apparatus. Instead, the mutant plants specifically lack detectable amounts of all photosystem I (PSI) subunits analyzed. In contrast, at least under low light conditions, photosystem II subunits are still present and assemble into a physiologically active complex. Faithful transcription of photosystem I genes as well as correct mRNA processing and efficient transcript loading with ribosomes in the Δycf3 plants suggest a posttranslational cause of the PSI-defective phenotype. We therefore propose that ycf3 encodes an essential protein for the assembly and/or stability of functional PSI units. This study provides a first example for the suitability of reverse genetics approaches to complete our picture of the coding capacity of higher plant chloroplast genomes.

Characterization of mat A-2, mat A-3 and ΔmatA Mating-Type Mutants of Neurospora crassa

Genetics ◽  
1998 ◽  
Vol 148 (3) ◽  
pp. 1069-1079 ◽  
Author(s):  
Adlane V-B Ferreira ◽  
Zhiqiang An ◽  
Robert L Metzenberg ◽  
N Louise Glass
Keyword(s):  
Neurospora Crassa ◽  
Mating Type ◽  
Sexual Development ◽  
Vegetative Growth ◽  
Double Mutant ◽  
Sexual Cycle ◽  
Wild Type ◽  
Type Locus ◽  
Isolation And Characterization

AbstractThe mating-type locus of Neurospora crassa regulates mating identity and entry into the sexual cycle. The mat A idiomorph encodes three genes, mat A-1, mat A-2, and mat A-3. Mutations in mat A-1 result in strains that have lost mating identity and vegetative incompatibility with mat a strains. A strain containing mutations in both mat A-2 and mat A-3 is able to mate, but forms few ascospores. In this study, we describe the isolation and characterization of a mutant deleted for mat (ΔmatA), as well as mutants in either mat A-2 or mat A-3. The ΔmatA strain is morphologically wild type during vegetative growth, but it is sterile and heterokaryon compatible with both mat A and mat a strains. The mat A-2 and mat A-3 mutants are also normal during vegetative growth, mate as a mat A strain, and produce abundant biparental asci in crosses with mat a, and are thus indistinguishable from a wild-type mat A strain. These data and the fact that the mat A-2 mat A-3 double mutant makes few asci with ascospores indicate that MAT A-2 and MAT A-3 are redundant and may function in the same pathway. Analysis of the expression of two genes (sdv-1 and sdv-4) in the various mat mutants suggests that the mat A polypeptides function in concert to regulate the expression of some sexual development genes.

scholarly journals Deletion of a single-copy tRNA affects microtubule function in Saccharomyces cerevisiae.

Genetics ◽  
1993 ◽  
Vol 135 (4) ◽  
pp. 955-962 ◽  
Author(s):  
R A Reijo ◽  
D S Cho ◽  
T C Huffaker
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Single Copy ◽  
Open Reading Frame ◽  
Northern Analysis ◽  
Trna Genes ◽  
Heat Sensitivity ◽  
Gene Encoding ◽  
Yeast Saccharomyces Cerevisiae ◽  
Reading Frame ◽  
Sensitive Allele

Abstract rts1-1 was identified as an extragenic suppressor of tub2-104, a cold-sensitive allele of the sole gene encoding beta-tubulin in the yeast, Saccharomyces cerevisiae. In addition, rts1-1 cells are heat sensitive and resistant to the microtubule-destabilizing drug, benomyl. The rts1-1 mutation is a deletion of approximately 5 kb of genomic DNA on chromosome X that includes one open reading frame and three tRNA genes. Dissection of this region shows that heat sensitivity is due to deletion of the open reading frame (HIT1). Suppression and benomyl resistance are caused by deletion of the gene encoding a tRNA(Arg)AGG (HSX1). Northern analysis of rts1-1 cells indicates that HSX1 is the only gene encoding this tRNA. Deletion of HSX1 does not suppress the tub2-104 mutation by misreading at the AGG codons in TUB2. It also does not suppress by interfering with the protein arginylation that targets certain proteins for degradation. These results leave open the prospect that this tRNA(Arg)AGG plays a novel role in the cell.

scholarly journals RNA 2 of Citrus psorosis virus is of negative polarity and has a single open reading frame in its complementary strand

2002 ◽  
Vol 83 (7) ◽  
pp. 1777-1781 ◽  
Author(s):  
María Eugenia Sánchez de la Torre ◽  
Carmelo López ◽  
Oscar Grau ◽  
María Laura García
Keyword(s):  
Blot Hybridization ◽  
Negative Polarity ◽  
Open Reading Frame ◽  
Single Open Reading Frame ◽  
Northern Blot Hybridization ◽  
Complementary Strand ◽  
Significant Similarity ◽  
Reading Frame ◽  
A Genome ◽  
Citrus Psorosis Virus

Citrus psorosis virus (CPsV) causes a citrus disease occurring worldwide. Isolate CPV 4 has a genome with three single-stranded RNAs. The complete sequence of RNA 2 (1643 nucleotides) is reported here. Northern blot hybridization with strand-specific probes showed that most of the encapsidated RNA 2 is of negative polarity, although a small amount of the complementary strand may also be present in particles. The RNA 2 complementary strand contained a single open reading frame encoding a protein of 476 amino acids, which includes a motif resembling a nuclear localization signal. The sequence of this putative protein shows no significant similarity to any other in the databases. In the 3′-terminal untranslated region there is a putative polyadenylation signal. No subgenomic RNAs derived from RNA 2 were detected.

scholarly journals Subunit VII of ubiquinol:cytochrome-c oxidoreductase from Neurospora crassa is functional in yeast and has an N-terminal extension that is not essential for mitochondrial targeting

1996 ◽  
Vol 320 (3) ◽  
pp. 769-775 ◽  
Author(s):  
Gisele LOBO-HAJDU ◽  
Hans-Peter BRAUN ◽  
Nancy ROMP ◽  
Leslie A. GRIVELL ◽  
Jan A. BERDEN ◽  
...  
Keyword(s):  
Amino Acid ◽  
Neurospora Crassa ◽  
Direct Sequencing ◽  
Single Copy ◽  
Cdna Clones ◽  
Mitochondrial Targeting ◽  
Calculated Molecular Mass ◽  
Reading Frame ◽  
Isolated Mitochondria ◽  
Mitochondrial Intermediate Peptidase

cDNA clones encoding subunit VII of the Neurospora crassa bc1 complex (ubiquinol:cytochrome-c oxidoreductase), which is homologous with subunit VIII of the complex from yeast (encoded by QCR8), were identified on the basis of functional complementation of a yeast QCR8 deletion strain. The clones contain an open reading frame encoding a protein with a calculated molecular mass of 11.8 kDa. The N-terminal eight residues of the amino acid sequence deduced from the cDNA clones are absent from the mature protein, as revealed by direct sequencing of the isolated protein. To investigate the potential role of the N-terminal octapeptide in mitochondrial targeting, constructs were made encoding the precursor and the mature form of subunit VII from Neurospora. Incubation of isolated mitochondria with the two proteins revealed that the N-terminal extension of the precursor is removed on import. However, the presequence does not encode information for targeting, as the proteins encoded by both constructs can be imported into isolated mitochondria with equal efficiency. In contrast, the octapeptide seems to have functional importance: the defect in the yeast qcr8-null mutant is not complemented on transformation with the construct encoding mature subunit VII from N. crassa in a single-copy plasmid. We therefore speculate that the N-terminal extension plays a role in intramitochondrial sorting of N. crassa subunit VII. This is supported by the fact that the subunit VII precursor is processed by a protease other than the general mitochondrial processing peptidase. Interestingly, the presequence of N. crassa subunit VII has an amino acid composition similar to the octapeptides cleaved off by the mitochondrial intermediate peptidase.

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