Revisiting the Neurospora crassa mitochondrial genome

The mitochondrial genome of Neurospora crassa has been less studied than its nuclear counterpart, yet it holds great potential for understanding the diversity and evolution of this important fungus. Here we describe a new mitochondrial DNA (mtDNA) complete sequence of a N. crassa wild type strain. The genome with 64 839 bp revealed 21 protein-coding genes and several hypothetical open reading frames with no significant homology to any described gene. Five large repetitive regions were identified across the genome, including partial or complete genes. The largest repeated region holds a partial nd2 section that was also detected in Neurospora intermedia, suggesting a rearrangement that occurred before the N. crassa speciation. Interestingly, N. crassa has a palindrome adjacent to the partial nd2 repeated region possibly related to the genomic rearrangement, which is absent in N. intermedia. Finally, we compared the sequences of the three available N. crassa complete mtDNAs and found low levels of intraspecific variability. Most differences among strains were due to small indels in noncoding regions. The revisiting of the N. crassa mtDNA forms the basis for future studies on mitochondrial genome organization and variability.

Quantification of Neurospora crassa mitochondrial DNA using quantitative real-time PCR

The filamentous fungus Neurospora crassa is a popular model organism used in a wide range of biochemical and genetic studies and vastly used in mitochondrial research. Despite the relevance of mitochondria in N. crassa biology, no method for quantification of mitochondrial DNA (mtDNA) is currently available. Quantitative real-time PCR (qPCR) is a powerful tool, with a wide range of applications, and has been used for the quantification of nucleic acids in humans and a few other species. Here we present a new qPCR assay for relative quantification of N. crassa mtDNA. Three sets of qPCR primers targeting different regions of the mitochondrial genome were tested for mtDNA quantification. The qPCR was successfully validated in N. crassa strains from different geographical locations, representing the vast genetic diversity of this species, and knockout mutant strains. Moreover the assay proved to be efficient in templates with varied amounts of mitochondria, obtained through different DNA extraction methods. The qPCR performed well in all tested samples revealing a higher amount of mtDNA than nuclear DNA in all cases. This technique will facilitate the characterization of mtDNA of N. crassa in future studies and can be used as a tool to validate methods of mitochondria isolation. SIGNIFICANCE AND IMPACT OF THE STUDY: The standardization of quantitative real-time PCR (qPCR) techniques is essential to enable and facilitate future comparisons. Neurospora crassa is a model organism with a lot of potential in different fields of study. Here we use N. crassa to develop and establish an assay to quantify mitochondrial DNA using qPCR. We tested strains with different geographical background and our data demonstrated the usefulness of this assay to quantify mitochondrial DNA in N. crassa. This technique can be useful in a wide variety of applications and in different types of studies.

The external calcium-dependent NADPH dehydrogenase from Neurospora crassa mitochondria

We have inactivated the nuclear gene coding for a putative NAD(P)H dehydrogenase from the inner membrane of Neurospora crassa mitochondria by repeat-induced point mutations. The respiratory rates of mitochondria from the resulting mutant (nde-1) were measured, using NADH or NADPH as substrates under different assay conditions. The results showed that the mutant lacks an external calcium-dependent NADPH dehydrogenase. The observation of NADH and NADPH oxidation by intact mitochondria from the nde-1 mutant suggests the existence of a second external NAD(P)H dehydrogenase. The topology of the NDE1 protein was further studied by protease accessibility, in vitro import experiments, and in silico analysis of the amino acid sequence. Taken together, it appears that most of the NDE1 protein extends into the intermembrane space in a tightly folded conformation and that it remains anchored to the inner mitochondrial membrane by an N-terminal transmembrane domain.

Respiratory chain complex I is essential for sexual development in neurospora and binding of iron sulfur clusters are required for enzyme assembly

We have cloned and disrupted in vivo, by repeat-induced point mutations, the nuclear gene coding for an iron sulfur subunit of complex I from Neurospora crassa, homologue of the mammalian TYKY protein. Analysis of the obtained mutant nuo21.3c revealed that complex I fails to assemble. The peripheral arm of the enzyme is disrupted while its membrane arm accumulates. Furthermore, mutated 21.3c-kD proteins, in which selected cysteine residues were substituted with alanines or serines, were expressed in mutant nuo21. 3c. The phenotypes of these strains regarding the formation of complex I are similar to that of the original mutant, indicating that binding of iron sulfur centers to protein subunits is a prerequisite for complex I assembly. Homozygous crosses of nuo21.3c strain, and of other complex I mutants, are unable to complete sexual development. The crosses are blocked at an early developmental stage, before fusion of the nuclei of opposite mating types. This phenotype can be rescued only by transformation with the intact gene. Our results suggest that this might be due to the compromised capacity of complex I-defective strains in energy production.

NADH dehydrogenase in Neurospora crassa contains myristic acid covalently linked to the ND5 subunit peptide

The mitochondrial, proton-pumping NADH:ubiquinone oxidoreductase consists of at least 35 subunits whose synthesis is divided between the cytosol and mitochondria; this complex I catalyzes the first steps of mitochondrial electron transfer and proton translocation. Radiolabel from [(3)H]myristic acid was incorporated by Neurospora crassa into the mitochondrial-encoded, approximately 70 kDa ND5 subunit of NADH dehydrogenase, as shown by immunoprecipitation. This myristate apparently was linked to the peptide through an amide linkage at an invariant lysine residue (Lys546), based upon analyses of proteolysis products. The myristoylated lysine residue occurs in the predicted transmembrane helix 17 (residues 539-563) of ND5. A consensus amino acid sequence around this conserved residue exists in homologous subunits of NADH dehydrogenase. Cytochrome c oxidase subunit 1, in all prokaryotes and eukaryotes, contains this same consensus sequence surrounding the lysine which is myristoylated in N. crassa.

The 24-kDa iron-sulphur subunit of complex I is required for enzyme activity

We have cloned the nuclear gene encoding the 24-kDa iron-sulphur subunit of complex I from Neurospora crassa. The gene was inactivated in vivo by repeat-induced point-mutations, and mutant strains lacking the 24-kDa protein were isolated. Mutant nuo24 appears to assemble an almost intact complex I only lacking the 24-kDa subunit. However, we also found reduced levels of the NADH-binding, 51-kDa subunit of the enzyme. Surprisingly, the complex I from the nuo24 strain lacks NADH:ferricyanide reductase activity. In agreement with this, the respiration of intact mitochondria or mitochondrial membranes from the mutant strain is insensitive to rotenone inhibition. These results suggest that the nuo24 complex is not functioning in electron transfer and the 24-kDa protein is absolutely required for complex I activity. This phenotype may explain the findings that the 24-kDa iron-sulphur protein is reduced or absent in human mitochondrial diseases. In addition, selected substitutions of cysteine to alanine residues in the 24-kDa protein suggest that binding of the iron-sulphur centre is a requisite for protein assembly.

Effects of disrupting the 21 kDa subunit of complex I from Neurospora crassa

We have cloned and inactivated in vivo, by repeat-induced point mutations, the nuclear gene encoding a 21 kDa subunit of complex I from Neurospora crassa. Mitochondria from the nuo21 mutant lack this specific protein but retain other subunits of complex I in approximately normal amounts. In addition, this mutant is able to assemble an almost intact enzyme. The electron transfer activities from NADH to artificial acceptors of mitochondrial membranes from nuo21 differ from those of the wild-type strain, suggesting that the absence of the 21 kDa polypeptide results in conformational changes in complex I. Nevertheless, complex I of nuo21 is able to perform NADH:ubiquinone reductase activity, as judged by the observation that the respiration of mutant mitochondria is sensitive to inhibition by rotenone. We discuss these findings in relation to the involvement of complex I in mitochondrial diseases.

Primary structure and characterisation of a 64 kDa NADH dehydrogenase from the inner membrane of Neurospora crassa mitochondria

A cDNA clone encoding a mitochondrial NADH dehydrogenase from Neurospora crassa was sequenced. The total DNA sequence encompasses 2570 base pairs and contains an open reading frame of 2019 base pairs coding for a precursor polypeptide of 673 amino acid residues. The protein is encoded by a single-copy gene located to the right side of the centromere in linkage group IV of the fungal genome. The N-terminus of the precursor protein has characteristics of a mitochondrial targeting pre-sequence. The protein displays homology with mitochondrial NADH dehydrogenases from yeast. In contrast to these polypeptides, however, analysis of its primary structure revealed that it contains a well-conserved calcium-binding domain. Rabbit antiserum against the protein expressed in an heterologous system recognises a mitochondrial protein of N. crassa with an apparent molecular mass of 64 kDa. Analysis of the fungal mitochondria by swelling, digitonin fractionation and alkaline treatment indicate that the protein is located in the inner membrane of the organelles, possibly facing the matrix side.

Characterisation of the last Fe-S cluster-binding subunit of Neurospora crassa complex I

We have cloned cDNAs encoding the last iron-sulphur protein of complex I from Neurospora crassa. The cDNA sequence contains an open reading frame that codes for a precursor polypeptide of 226 amino acid residues with a molecular mass of 24972 Da. Our results indicate that the mature protein belongs probably to the peripheral arm of complex I and is rather unstable when not assembled into the enzyme. The protein is highly homologous to the PSST subunit of bovine complex I, the most likely candidate to bind iron-sulphur cluster N-2. All the amino acid residues proposed to bind such a cluster are conserved in the fungal protein.

The membrane domain of complex I is not assembled in the stopper mutant E35 of Neurospora

The assembly of mitochondrial NADH: ubiquinone oxidoreductase (complex I) was studied in the E35 stopper mutant of Neurospora crassa at different times during growth in liquid media. Assembly of complex I as well as of its membrane domain is impaired in this strain throughout the growth period. Nevertheless, a structure that resembles the peripheral aim of the enzyme is still formed in the mitochondria of this mutant. The absence of the membrane domain of complex I in E35 can be attributed to the specific deletion of the mitochondrial ND2 and ND3 subunits of the enzyme.

Complex I from the fungus Neurospora crassa

Respiratory chain complex I is a complicated enzyme of mitochondria, that couples electron transfer from NADH to ubiquinone to the proton translocation across the inner membrane of the organelle. The fungus Neurospora crassa has been used as one of the main model organisms to study this enzyme. Complex I is composed of multiple polypeptide subunits of dual genetic origin and contains several prosthetic groups involved in its activity. Most subunits have been cloned and those binding redox centres have been identified. Yet, the functional role of certain complex I proteins remains unknown. Insight into the possible origin and the mechanisms of complex I assembly has been gained. Several mutant strains of N. crassa, in which specific subunits of complex I were disrupted, have been isolated and characterised. This review concerns many aspects of the structure, function and biogenesis of complex I that are being elucidated.

Inactivation of the gene coding for the 30.4-kDa subunit of respiratory chain NADH dehydrogenase: is the enzyme essential for Neurospora?

We have isolated and characterised the nuclear gene that codes for the 30.4-kDa subunit of the peripheral arm of complex I from Neurospora crassa. The single-copy gene was localised on chromosome VI of the fungal genome by restriction fragment length polymorphism mapping. An extra copy of the gene was introduced into a strain of N. crassa by transformation. This strain was crossed with another strain in order to inactivate, by repeat-induced point mutations, both copies of the duplication carried by the parental transformant. Ascospore progeny from the cross were analysed and a mutant strain lacking the 30.4-kDa protein, nuo30.4, was isolated and further characterised. The mutant appears to assemble the membrane arm of complex I, while formation of the peripheral arm is prevented. Nevertheless, the mutant grows reasonably well--indicating that this well conserved protein is not essential for vegetative growth--and is able to mate with other strains both as male or female. Strains with multiple mutations are readily obtained from heterozygous crosses between different complex I mutants of N. crassa. On the other hand, homozygous crosses between several mutants, including nuo30.4, fail to produce ascospores. These results suggest that complex I plays an essential role during the sexual phase of the life cycle of the fungus.

Identification of the TYKY homologous subunit of complex I from Neurospora crassa

A polypeptide subunit of complex I from Neurospora crassa, homologous to bovine TYKY, was expressed in Escherichia coli, purified and used for the production of rabbit antiserum. The mature mitochondrial protein displays a molecular mass of 21280 Da and results from cleavage of a presequence consisting of the first 34 N-terminal amino acids of the precursor. This protein was found closely associated with the peripheral arm of complex I.

Purification, and biochemical and biological characterization of an immunosuppressive and lymphocyte mitogenic protein secreted by Streptococcus sobrinus

An immunosuppressive/mitogenic (ISM) protein was purified from the supernatants of cultures of Streptococcus sobrinus with an isoelectric point of 4.75 and a relative molecular mass of 38 kDa (p38). Treatment of C57BL/6 mice with p38 induced an increase in the numbers of non-specific splenic Ig-secreting plaque-forming cells (PFC) with peak responses on day 3 for IgM-secreting PFC and on day 5 for IgG-secreting PFC, with an isotype pattern consisting predominantly of IgG2a and IgG2b. This increase was accompanied by a lymphocyte blastogenic response of both T and B lymphocytes. The in vitro effects of p38 on pure B, T and total splenic lymphocytes indicated that this ISM protein was primarily a B cell mitogen, being T cells activated subsequently by the generation of B blasts. Suppression of the murine primary immune response against sheep red blood cells was observed in C57BL/6 mice treated 4 days before with p38. The amino acid sequence of the N-terminus of p38 has a significant similarity with several enolases, particularly with rabbit enolase. However, the biological effects ascribed to p38 have not been detected after in vivo treatment with that enolase. The immunosuppressive effect of p38 was abrogated by depletion of IL-10 but not of IL-4. In agreement with this observation IL-10 was the only cytokine detected in serum of C57BL/6 mice after p38 treatment and the peak of serum levels was observed as soon as 2 h after treatment.

Disruption of the nuclear gene encoding the 20.8-kDa subunit of NADH: ubiquinone reductase of Neurospora mitochondria

The nuclear gene coding for the 20.8-kDa subunit of the membrane arm of respiratory chain NADH: ubiquinone reductase (Complex I) from Neurospora crassa, nuo-20.8, was localized on linkage group I of the fungal genome. A genomic DNA fragment containing this gene was cloned and a duplication was created in a strain of N. crassa by transformation. To generate RIP (repeat-induced point) mutations in the duplicated sequence, the transformant was crossed with another strain carrying an auxotrophic marker on chromosome I. To increase the chance of finding an isolate with a non-functional nuo-20.8 gene, random progeny from the cross were selected against this auxotrophy since RIP of the target gene will only occur in the nucleus carrying the duplication. Among these, we isolated and characterised a mutant strain that lacks the 20.8 kDa mitochondrial protein, indicating that this cysteine-rich polypeptide is not essential. Nevertheless, the absence of the 20.8-kDa subunit prevents the full assembly of complex I. It appears that the peripheral arm and two intermediates of the membrane arm of the enzyme are still formed in the mutant mitochondria. The NADH: ubiquinone reductase activity of sonicated mitochondria from the mutant is rotenone insensitive. Electron microscopy of mutant mitochondria does not reveal any alteration in the structure or numbers of the organelles.

Primary structure of a ferredoxin-like iron-sulfur subunit of complex I from Neurospora crassa

We have isolated cDNA clones encoding an iron-sulfur polypeptide subunit of the mitochondrial complex I of Neurospora crassa. The fungal cDNA library was screened by hybridisation with an heterologous probe from Paracoccus denitrificans. The DNA sequence of relevant isolates was determined and revealed an open reading frame encoding a precursor protein of 219 amino acid residues. The gene product is a ferredoxin-like protein that contains two cysteine-rich motives that may each bind a tetranuclear iron-sulfur cluster. The primary structure of the protein is highly homologous to the 23 kDa iron-sulfur subunit of complex I from bovine and P. denitrificans. Interestingly, an alanine residue within the second cluster-binding motif, which is conserved in complex I but replaced by tyrosine in similar chloroplast genes, is substituted for serine in N. crassa.

Immunoprotection against systemic candidiasis in mice

We have previously described an immunosuppressive B cell mitogenic (ISM) protein, p43, produced by Candida albicans, which plays an important role in the survival of the microorganism in the host. The N-terminal amino acid sequence of p43 was found to be different from all amino acid sequences registered in updated protein databanks. Immunization of BALB/c mice with p43 partially neutralized the biological effects of this protein, namely depletion of bone marrow pre-B and B cells, the increased numbers of total and large B and CD4+ lymphocytes, and the non-specific polyclonal response of splenic IgG2a-, IgG2b- and IgM-secreting plaque forming cells. Immunization of BALB/c mice with p43 fully protected the mice against the fungal infection. In contrast, immunization with C. albicans sonicates (Cs) was not protective. Our data indicated that specific antibodies against p43 protected, whereas those against Cs facilitated C. albicans infection. Thus, the ratio between anti-p43 and anti-Cs antibody titres was much lower in the non-protected mice (Cs-immunized and control non-immunized) than in p43-immunized mice. Moreover, passive administration of specific anti-p43 antibodies significantly protected against fungal infection, whereas passive administration of specific anti-Cs antibodies markedly increased the susceptibility to C. albicans infection. These observations are discussed on the basis of alternative approaches of immunointervention.

Inactivation of genes encoding subunits of the peripheral and membrane arms of neurospora mitochondrial complex I and effects on enzyme assembly

We have isolated and characterized the nuclear genes encoding the 12.3-kD subunit of the membrane arm and the 29.9-kD subunit of the peripheral arm of complex I from Neurospora crassa. The former gene was known to be located in linkage group I and the latter is now assigned to linkage group IV of the fungal genome. The genes were separately transformed into different N. crassa strains and transformants with duplicated DNA sequences were isolated. Selected transformants were then mated with other strains to generate repeat-induced point mutations in both copies of the genes present in the nucleus of the parental transformant. From the progeny of the crosses, we were then able to recover two individual mutants lacking the 12.3- and 29.9-kD proteins in their mitochondria, mutants nuo12.3 and nuo29.9, respectively. Several other subunits of complex I are present in the mutant organelles, although with altered stoichiometries as compared with those in the wild-type strain. Based on the analysis of Triton-solubilized mitochondrial complexes in sucrose gradients, neither mutant is able to fully assemble complex I. Our results indicate that mutant nuo12.3 separately assembles the peripheral arm and most of the membrane arm of the enzyme. Mutant nuo29.9 seems to accumulate the membrane arm of complex I and being devoid of the peripheral part. This implicates the 29.9-kD protein in an early step of complex I assembly.

Disruption of the gene encoding the 78-kilodalton subunit of the peripheral arm of complex I in Neurospora crassa by repeat induced point mutation (RIP)

We have used the procedure of sheltered RIP to generate mutants of the 78-kDa protein of the peripheral arm of Neurospora crassa complex I. The nuclei containing the mutations were initially isolated as one component of a heterokaryon but subsequent analysis showed that nuclei containing null alleles of the gene could be propagated as homokaryons. This demonstrates that the gene does not serve an essential function. Sequence analysis of one allele shows that 61 transition mutations were created resulting in 39 amino-acid changes including the introduction of four stop codons. Mutant strains grow at a slower rate than wild-type and exhibit a decrease in the production of conidia. Electron paramagnetic spectroscopy of mutant mitochondria suggest that they are deficient in Fe-S clusters N-1, N-3, and N-4.

Two nuclear-coded subunits of mitochondrial complex I are similar to different domains of a bacterial formate hydrogenlyase subunit

A computer comparison of protein sequences revealed similarity between the 30.4 kDa subunit of complex I from the fungus Neurospora crassa and the ORF5 subunit of formate hydrogenlyase from Escherichia coli. The ORF5 protein was previously known to be homologous to the 49 kDa component of the mitochondrial enzyme. We show that the 30.4 kDa corresponds to the N-terminal part while the 49 kDa subunit corresponds to the C-terminal portion of the bacterial protein. Thus, this bacterial protein represents a fusion of the two mitochondrial polypeptides suggesting that the two complex I genes arose from a single ancestor. Our results indicate that the 30.4 kDa and 49 kDa subunits are part of a structural and functional unit in complex I.

Complementary DNA sequences of the 24 kDa and 21 kDa subunits of complex I from Neurospora

We have cloned and sequenced cDNAs coding for two subunits of the peripheral arm of Neurospora crassa complex I. The two polypeptides are synthesized as precursor proteins which are processed to mature forms with predicted molecular masses of 24331 and 20982 Da.

Characterization of a membrane fragment of respiratory chain complex I from Neurospora crassa. Insights on the topology of the ubiquinone-binding site

1. A membrane fragment of complex I from the fungus Neurospora crassa was isolated by immunoprecipitation from alkaline-extracted mitochondrial membranes. 2. Analysis of the polypeptide composition of this hydrophobic domain of complex I has brought insights on the topology of two subunits of the enzyme, namely the 20.8 and 9.3 kDa components. 3. Our results indicate that the ubiquinone-binding site of complex I resides in the interface of the peripheral and membrane arms of the enzymes. The significance of these findings are discussed.

Disruption of the gene coding for the 21.3-kDa subunit of the peripheral arm of complex I from Neurospora crassa

A 21.3-kDa subunit of the peripheral arm of complex I from Neurospora is encoded by a single chromosomal gene, nuo-21.3b. It is located on linkage group V of the fungal genome, linked to inl. We have isolated and characterized a genomic clone containing this nuclear gene. A DNA fragment containing a portion of the coding region of the gene and upstream flanking sequences was introduced by transformation into a wild-type strain of Neurospora crassa. A single copy transformant was selected and crossed with another strain, leading to inactivation of nuo-21.3b through repeat-induced point mutations. We have analyzed random progeny from this cross and isolated two mutant strains lacking the 21.3-kDa subunit of complex I. One of them was further characterized. Our results suggest that most, if not all, other subunits of complex I are present in the mitochondria of the mutant and assembled in a structure similar to complex I, representing delta 25% of the amounts of enzyme found in the wild type. Nevertheless, a major intermediate, containing proteins of the peripheral arm of complex I, accumulates in the mutant mitochondria. This indicates that the absence of the 21.3-kDa polypeptide results in a disturbed assembly of the enzyme complex, suggesting a role for this polypeptide. We observed similar rates of rotenone-sensitive NADH:ubiquinone oxido-reductase activity in mitochondrial membranes from the mutant and wild-type strains and discuss the possibility that this electron transfer is independent of the more hydrophobic part of complex I. Transformation of the mutant with the intact gene and flanking sequences restored the wild-type phenotype.

The 12.3 kDa subunit of complex I (respiratory-chain NADH dehydrogenase) from Neurospora crassa: cDNA cloning and chromosomal mapping of the gene

The 12.3 kDa subunit of complex I (respiratory-chain NADH dehydrogenase) is a nuclear-coded protein of the hydrophobic fragment of the enzyme. We have isolated and sequenced a full-length cDNA clone coding for this polypeptide. The deduced protein is 104 amino acid residues long with a molecular mass of 12305 Da. This particular subunit of complex I lacks a cleavable mitochondrial targeting sequence. In agreement with its localization within complex I, we have found that this subunit behaves like an intrinsic membrane protein. Nevertheless, the deduced protein is rather hydrophilic, exhibiting no hydrophobic domain long enough to traverse a membrane in an alpha-helical conformation. The 12.3 kDa subunit shows a significant similarity to the hinge protein of complex III, suggesting that these two polypeptides may be involved in identical functions. This complex I subunit is coded for by a single gene. Applying restriction-fragment-length-polymorphism mapping, we located the gene on the right side of the centromere in linkage group I, linked to the lys-4 locus.

Primary structure of the nuclear-encoded 10.5 kDa subunit of complex I from Neurospora crassa

We have isolated a cDNA clone for the nuclear encoded 10.5 kDa subunit of complex I from N. crassa. DNA sequencing revealed an open reading frame corresponding to a polypeptide with 94 amino acids and a calculated molecular mass of 10531 Da. The protein is synthesized without a cleavable mitochondrial targeting sequence. The N. crassa polypeptide is the fungal equivalent of subunit B8 of bovine complex I.

Primary structure and expression of a nuclear-coded subunit of complex I homologous to proteins specified by the chloroplast genome

A 31-kDa subunit of complex I from Neurospora crassa, of nuclear origin, was cloned. The precursor polypeptide (33 kDa) could be efficiently expressed in an in vitro system for transcription and translation. The processing of the precursor to the mature protein was also obtained in vitro. An open reading frame coding for a precursor protein of 283 amino acids (32247 Da) was found by DNA sequencing. The predicted primary structure shows significant homology with proteins made in chloroplast. This supports the hypothesis that an enzyme similar to respiratory chain NADH dehydrogenase might exist in these organelles.

Molecular cloning of subunits of complex I from Neurospora crassa. Primary structure and in vitro expression of a 22-kDa polypeptide

A lambda gt11 cDNA expression library was screened with antibodies directed against individual subunits of complex I from Neurospora crassa. Clones encoding cytoplasmically synthesized polypeptides with apparent molecular masses of 22, 29, 31, and 33 kDa were isolated. Northern blot analysis revealed that the corresponding genes are transcribed into mRNA species of about 0.85, 0.95, 1.3, and 1.4 kilobases, respectively. Further characterization of clones encoding the 22-kDa subunit was performed. A cDNA insert of 755 base pairs containing the complete coding sequence was used to express the polypeptide in vitro. A precursor of the protein is synthesized on cytoplasmic ribosomes without a cleavable signal sequence. Our data indicate that after import into the organelle and before assembly into complex I, the 22-kDa polypeptide forms intramolecular disulfide bridge(s). Nucleotide sequencing revealed an open reading frame coding for a protein of 183 amino acids. A molecular mass of 20,828 daltons was calculated. The polypeptide is hydrophilic and contains no obvious membrane-spanning domains. Eight cysteine residues arranged in a regular pattern are found in the primary structure of the protein. Therefore, this subunit is a good candidate to bind at least one of the iron-sulfur centers present in complex I of the respiratory chain.

Primary structure, in vitro expression and import into mitochondria of a 29/21-kDa subunit of complex I from Neurospora crassa

A full-length cDNA clone coding for a cytoplasmically-synthesized subunit of complex I from Neurospora crassa (apparent molecular mass of 29 kDa) was isolated. DNA sequencing revealed an open reading frame coding for a protein containing 201 amino acids. A molecular mass of 21323 Da was calculated. The precursor polypeptide was efficiently expressed in vitro and imported into isolated mitochondria. It is synthesized without a cleavable signal sequence and needs a membrane potential in order to bind to the mitochondrial membranes.

Assembly kinetics and identification of precursor proteins of complex I from Neurospora crassa

Complex I from Neurospora crassa was fractionated using chaotropic agents and various chromatographic techniques. Several subunits were isolated. Polyclonal antibodies directed against the holocomplex or individual subunits were raised in rabbits, and employed to analyse the composition and assembly of this respiratory chain enzyme in vivo. N. crassa cells were pulse-labelled with radioactive amino acids. The time course of incorporation of radioactivity into complex-I polypeptides was studied by immunoprecipitation. The labelling kinetics of whole complex I was found to be similar to that of cytochrome oxidase, displaying a half-maximal labelling time of 10 min. Newly synthesized individual polypeptide subunits (about 23 species) assembled into the holoenzyme at markedly different rates. Two mitochondrially synthesized proteins, a 29-kDa polypeptide (the ND-1 gene product) and a 12-kDa polypeptide were the fastest components to appear in the enzyme. We estimate that the precursor pool sizes of all components range between 1-25% of the amounts present in the final complex. Precursors of polypeptides of complex I were synthesized in an heterologous cell-free system and immunoprecipitated with subunit specific antibodies. Six isolated precursors were compared with the corresponding mature proteins. It appears that four subunits (apparent molecular masses of 22, 25, 31 and 33 kDa) are initially synthesized as larger-molecular-mass precursors. Two subunits (apparent molecular masses of 12.5 and 14 kDa) are made with the same size as their mature forms.

Mitochondrial gene expression in a nuclear mutant of Neurospora deficient in large subunits of mitochondrial ribosomes

A new cytochrome a and b deficient nuclear mutant of Neurospora crassa, cyt-U-28, is defective in the assembly of large subunits of mitochondrial ribosomes. Nonetheless, this mutant overproduces apparently normal small subunits of mitochondrial ribosomes, even though it should be deficient for the S5 ribosomal protein required for assembly of the particles beyond the CAP30S stage. The mitochondria of cyt-U-28 indeed synthesize only small amounts of most mitochondrial polypeptides, including cytochrome oxidase subunits I, II, and III, contain very low amounts of the normal seven-polypeptide cytochrome oxidase complex, and, unlike the organelles from other cytochrome a deficient mutants, do not accumulate the nuclear-encoded cytochrome oxidase subunits 5 and 6. Nonetheless, the mutant markedly oversynthesizes a mitochondrial protein that comigrates with subunit 9 of the mitochondrial ATPase on S DS–polyacrylamide electrophoresis gels. The overproduction of this protein and the accumulation of mature small subunits of mitochondrial ribosomes indicate that the cyt-U-28 mutant preferentially expresses two mitochondrial genes, one coding for ATPase subunit 9, the other for the S5 ribosomal protein.Key words: Neurospora, mitochondria, ribosomes, protein synthesis.

Identification of the polypeptide encoded by the URF-1 gene of Neurospora crassa mtDNA

Two peptides, potentially representing antigenic determinants of a proposed gene product, were synthesized. The peptide sequences were deduced from the nucleotide sequence of the unidentified reading frame (URF)1 of the Neurospora crassa mitochondrial genome. Specific antisera to the synthetic peptides were produced. The antibodies recognized a single polypeptide species with an apparent relative molecular mass of about 30 000. The mitochondrial origin of this polypeptide was verified by in vivo labelling experiments in the presence of cycloheximide, as well as by in vitro translation using isolated mitochondria. The chemical identification of the protein was performed by partial radiosequencing of the N-terminal portion of the immunoprecipitated URF-1 product. The amount of URF-1 polypeptide present in N. crassa mitochondria is in the range of 1-2%. The protein is a constituent of the inner envelope of the organelle and probably part of a more complex membrane unit.