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Background: Using a previously unreported Peruvian registry of patients treated for early-stage non-small cell lung cancer (NSCLC), this study explored whether wedge resection and lobectomy were equivalent regarding survival and impact on radiologic-pathologic variables. Methods: This observational, analytical, longitudinal study used propensity score-matched (PSM) analysis of a single-center retrospective registry of 2,570 patients with pathologic stage I-II NSCLC who were treated with wedge resection (n=1,845) or lobectomy (n=725) during 2000-2020. After PSM, 650 cases were analyzed (resection, n=325; lobectomy, n=325) through preoperative and clinical variables, including patients with ≥1 lymph node removed. Kaplan-Meier curves and multivariable Cox proportional hazard models were created for 5-year overall survival (OS), disease-free survival (DFS), and locoregional-recurrence-free survival (LRFS). Results: The principal complication was operative pain persisting >7 days for lobectomy versus wedge resection (58% vs. 23%, p=0.034) and shorter hospital stays for resection than for lobectomy (5.3 days vs. 12.8 days, p=0.009). The 5-year OS (84.3% vs. 81.2%, p=0.09) and DFS (79.1% vs. 74.1%, p=0.07) were similar and statistically insignificant between resections and lobectomies, respectively. LRFS was worse overall following wedge resection than lobectomy (79.8% vs. 91.1%, p<0.02). Nevertheless, in the PSM analysis, both groups experienced similar LRFS when the resection margin was >10 mm (90.9% vs. 87.3%, p<0.048) and ≥4 lymph nodes were removed (82.8% vs. 79.1%, p<0.011). Conclusion: Both techniques led to similar OS and DFS at 5 years; however, successful LRFS required a wedge resection with a surgical margin and adequate lymph node removal to obtain outcomes similar to lobectomy.

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Oxygenic photosynthesis conducted by cyanobacteria has dramatically transformed the geochemistry of our planet. These organisms have colonized most habitats, including extreme environments such as the driest warm desert on Earth: the Atacama Desert. In particular, cyanobacteria highly tolerant to desiccation are of particular interest for clean energy production. These microorganisms are promising candidates for designing bioelectrodes for photocurrent generation owing to their ability to perform oxygenic photosynthesis and to withstand long periods of desiccation. Here, we present bioelectrochemical assays in which graphite electrodes were modified with the extremophile cyanobacterium Gloeocapsopsis sp. UTEXB3054 for photocurrent generation. Optimum working conditions for photocurrent generation were determined by modifying directly graphite electrode with the cyanobacterial culture (direct electron transfer), as well as using an Os polymer redox mediator (mediated electron transfer). Besides showing outstanding photocurrent production for Gloeocapsopsis sp. UTEXB3054, both in direct and mediated electron transfer, our results provide new insights into the metabolic basis of photocurrent generation and the potential applications of such an assisted bioelectrochemical system in a worldwide scenario in which clean energies are imperative for sustainable development.

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Multicellularity in Cyanobacteria played a key role in their habitat expansion, contributing to the Great Oxidation Event around 2.45 billion to 2.32 billion years ago. Evolutionary studies have indicated that some unicellular cyanobacteria emerged from multicellular ancestors, yet little is known about how the emergence of new unicellular morphotypes from multicellular ancestors occurred. Our results give new insights into the evolutionary reversion from which the Gloeocapsopsis lineage emerged. Flow cytometry and microscopy results revealed morphological plasticity involving the patterned formation of multicellular morphotypes sensitive to environmental stimuli. Genomic analyses unveiled the presence of multicellularity-associated genes in its genome. Calcein-fluorescence recovery after photobleaching (FRAP) experiments confirmed that Gloeocapsopsis sp. strain UTEX B3054 carries out cell-to-cell communication in multicellular morphotypes but at slower time scales than filamentous cyanobacteria. Although traditionally classified as unicellular, our results suggest that Gloeocapsopsis displays facultative multicellularity, a condition that may have conferred ecological advantages for thriving as an extremophile for more than 1.6 billion years.IMPORTANCECyanobacteria are among the few prokaryotes that evolved multicellularity. The early emergence of multicellularity in Cyanobacteria (2.5 billion years ago) entails that some unicellular cyanobacteria reverted from multicellular ancestors. We tested this evolutionary hypothesis by studying the unicellular strain Gloeocapsopsis sp. UTEX B3054 using flow cytometry, genomics, and cell-to-cell communication experiments. We demonstrate the existence of a well-defined patterned organization of cells in clusters during growth, which might change triggered by environmental stimuli. Moreover, we found genomic signatures of multicellularity in the Gloeocapsopsis genome, giving new insights into the evolutionary history of a cyanobacterial lineage that has thrived in extreme environments since the early Earth. The potential benefits in terms of resource acquisition and the ecological relevance of this transient behavior are discussed.

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For tolerating extreme desiccation, cyanobacteria are known to produce both compatible solutes at intracellular level and a copious amount of exopolysaccharides as a protective coat. However, these molecules make cyanobacterial cells refractory to a broad spectrum of cell disruption methods, hindering genome sequencing, and molecular studies. In fact, few genomes are already available from cyanobacteria from extremely desiccated environments such as deserts. In this work, we report the 5.4 Mbp draft genome (with 100% of completeness in 105 contigs) of Gloeocapsopsis sp. UTEX B3054 (subsection I; Order Chroococcales), a cultivable sugar-rich and hardly breakable hypolithic cyanobacterium from the Atacama Desert. Our in silico analyses focused on genomic features related to sugar-biosynthesis and adaptation to dryness. Among other findings, screening of Gloeocapsopsis genome revealed a unique genetic potential related to the biosynthesis and regulation of compatible solutes and polysaccharides. For instance, our findings showed for the first time a novel genomic arrangement exclusive of Chroococcaceae cyanobacteria associated with the recycling of trehalose, a compatible solute involved in desiccation tolerance. Additionally, we performed a comparative genome survey and analyses to entirely predict the highly diverse pool of glycosyltransferases enzymes, key players in polysaccharide biosynthesis and the formation of a protective coat to dryness. We expect that this work will set the fundamental genomic framework for further research on microbial tolerance to desiccation and to a wide range of other extreme environmental conditions. The study of microorganisms like Gloeocapsopsis sp. UTEX B3054 will contribute to expand our limited understanding regarding water optimization and molecular mechanisms allowing extremophiles to thrive in xeric environments such as the Atacama Desert.

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The Atacama Desert is the driest and oldest desert on Earth. Eleven years ago, the Yungay region was established as the driest site of this hyperarid desert and also close to the dry limit for life on Earth. Since then, much has been published about the extraordinary characteristics of this site and its pertinence as a Mars analogue model. However, as a result of a more systematic search in the Atacama here, we describe a new site, María Elena South (MES), which is much drier than Yungay. The mean atmospheric relative humidity (RH) at MES was 17.3%, with the RH of its soils remaining at a constant 14% at the depth of 1 m, a value that matches the lowest RH measurements taken by the Mars Science Laboratory at Gale Crater. Remarkably, we found a number of viable bacterial species in the soil profile at MES using a combination of molecular dependent and independent methods, unveiling the presence of life in the driest place on the Atacama Desert reported to date.

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Martian surface microbial inhabitants would be challenged by a constant and unimpeded flux of UV radiation, and the study of analog model terrestrial environments may be of help to understand how such life forms could survive under this stressful condition. One of these environments is the Atacama Desert (Chile), a well-known Mars analog due to its extreme dryness and intense solar UV radiation. Here, we report the microbial diversity at five locations across this desert and the isolation of UVC-tolerant microbial strains found in these sites. Denaturing gradient gel electrophoresis (DGGE) of 16S rDNA sequences obtained from these sites showed banding patterns that suggest distinct and complex microbial communities. Analysis of 16S rDNA sequences obtained from UV-tolerant strains isolated from these sites revealed species related to the Bacillus and Pseudomonas genera. Vegetative cells of one of these isolates, Bacillus S3.300-2, showed the highest UV tolerance profile (LD(10) = 318 J m(2)), tenfold higher than a wild-type strain of Escherichia coli. Thus, our results show that the Atacama Desert harbors a noteworthy microbial community that may be considered for future astrobiological-related research in terms of UV tolerance.

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We have recently discovered a variety of unrelated phototrophic microorganisms (two microalgae and one cyanobacteria) in specialized terrestrial habitats at The Coastal Range of the Atacama Desert. Interestingly, morphological and molecular evidence suggest that these three species are all recent colonists that came from aquatic habitats. The first case is Cyanidiales inhabiting coastal caves. Cyanidiales are microalgae that are commonly found in warm acid springs, but have also been recently discovered as cave flora in Italy. The case is Dunaliella biofilms colonizing spider webs in coastal caves; Dunaliella are microalgae typically found in hypersaline habitats. The third case is Chroococcidiopsis, a genus of Cyanobacteria commonly found in deserts around the world that has also been described in warm springs. Thus, we show that the traits found in the closest ancestors of the aforementioned species (which inhabited other unrelated extreme environments) seem to be now useful for the described species in their current subaerial habitats and may likely correspond to cases of exaptations. Altogether, the Coastal Range of the Atacama Desert may be considered as a place where key steps on the colonization of land by phototrophic organisms seem to be being repeated by convergent evolution of extant microalgae and Cyanobacteria.

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The Atacama Desert, located in northern Chile, is the driest and oldest desert on Earth. Research aimed at the understanding of this unique habitat and its diverse microbial ecosystems begun only a few decades ago, mainly driven by NASA's astrobiology program. A milestone in these efforts was a paper published in 2003, when the Atacama was shown to be a proper model of Mars. From then on, studies have been focused to examine every possible niche suitable for microbial life in this extreme environment. Habitats as different as the underside of quartz rocks, fumaroles at the Andes Mountains, the inside of halite evaporates and caves of the Coastal Range, among others, have shown that life has found ingenious ways to adapt to extreme conditions such as low water availability, high salt concentration and intense UV radiation.

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Iron, although toxic in excess, is an essential element for biological systems. Therefore, its homeostasis is of critical importance and tight mechanisms participate in its acquisition by microbial organisms. Lately, the relevance of this metal for biomass conversion by wood-degrading fungi has been gaining increasing attention. Iron plays a critical role as cofactor of key enzymes such as lignin and manganese peroxidases in lignin-degrading white-rot fungi, while Fe(II) also serves a pivotal role in Fenton reactions that are central in cellulose depolymerization by brown-rotters. It has been hypothesized that multicopper oxidases with ferroxidase activity might participate in controlling the bioavailability of iron in the hyphal proximity, fine-tuning Fenton chemistry and balancing lignin versus cellulose degradation. In order to further explore the dynamics of iron regulation in the well known white-rot fungus Phanerochaete chrysosporium, we analyzed the mRNA levels of the multicopper oxidases genes (mcos) in response to iron supplementation, confirming down-regulation of their expression in response to this metal. To gain a better understanding on the transcriptional mechanisms mediating this effect, we searched for a gene encoding a GATA-type transcription factor with homology to URBS1, the major transcriptional regulator of iron homeostasis in Ustilago maydis. Due to the limitation of experimental tools in P. chrysosporium, the alleged Phanerochaete iron regulator (PIR1) was studied by complementation of a Neurospora SRE/URBS1-deficient strain, where phenotypic and molecular characteristics of this transcriptional regulator could be easily assessed. In addition, using a genome-wide in silico strategy, we searched for putative cis-acting iron-responsive elements in P. chrysosporium. Some of the identified genes showed reduced transcript levels after 30 min in the presence of the metal, consistent with an SRE/URBS1-mediated mechanism, and suggesting a broad effect of iron on the regulation of several cellular processes.

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The Atacama Desert is one of the driest places on Earth, with an arid core highly adverse to the development of hypolithic cyanobacteria. Previous work has shown that when rain levels fall below ~1 mm per year, colonization of suitable quartz stones falls to virtually zero. Here, we report that along the coast in these arid regions, complex associations of cyanobacteria, archaea, and heterotrophic bacteria inhabit the undersides of translucent quartz stones. Colonization rates in these areas, which receive virtually no rain but mainly fog, are significantly higher than those reported inland in the hyperarid zone at the same latitude. Here, hypolithic colonization rates can be up to 80%, with all quartz rocks over 20 g being colonized. This finding strongly suggests that hypolithic microbial communities thriving in the seaward face of the Coastal Range can survive with fog as the main regular source of moisture. A model is advanced where the development of the hypolithic communities under quartz stones relies on a positive feedback between fog availability and the higher thermal conductivity of the quartz rocks, which results in lower daytime temperatures at the quartz-soil interface microenvironment.

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The ligninolytic machinery of the widely used model fungus Ceriporiopsis subvermispora includes the enzymes manganese-peroxidase (MnP) and laccase (Lcs). In this work the effect of Mn(II) on the secretion of MnP was studied. Cultures grown in the absence of Mn(II) showed high levels of mnp transcripts. However, almost no MnP enzyme was detected in the extracellular medium, either by enzymatic activity assays or Western blot hybridizations. In the corresponding mycelia, immuno-electron microscopy experiments showed high levels of MnP enzyme within intracellular compartments. These results suggest that in addition to its well-known effect on transcription regulation of mnp genes, manganese influences secretion of MnP to the extracellular medium. Experiments carried out in the presence of cycloheximide confirmed that the metal is required to secrete MnP already synthesized and retained within the cell.

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The biodegradation of lignin is a highly oxidative process in which various oxidases and peroxidases play a major role. During lignin decay, the generation of aromatic compounds and reactive oxygen species leads to oxidative stress. In this work, the effect of the oxidative compounds H(2)O(2) and hydroquinone in the ligninolytic fungus Ceriporiopsis subvermispora was studied, both at the ultrastructural and at the transcriptional level. Transmission electron microscopy revealed the presence of microvesicles and extensive cytoplasm degeneration after incubation with hydroquinone, but not with H(2)O(2). Studies of the intracellular redox state of the fungus showed that hydroquinone causes a transient decrease in the reduced glutathione/oxidized glutathione (GSH/GSSG) ratio and an increase in the glutathione-S-transferase mRNA levels. These results suggest that hydroquinone produces oxidative stress in this microorganism. On the other hand, it was observed that hydroquinone, but not H(2)O(2), affects Mn-dependent peroxide and laccase transcripts levels. We propose that the mechanism by which the fungus reacts against oxidative stress contributes to its selectivity toward lignin during wood decay.

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Cellobiose dehydrogenase (CDH), an extracellular flavocytochrome produced by several wood-degrading fungi, was detected in cultures of the selective delignifier Ceriporiopsis subvermispora when grown on a cellulose- and yeast extract-based liquid medium. CDH amounted to up to 2.5% of total extracellular protein during latter phases of the cultivation and thus suggested an important function for the fungus under the given conditions. The enzyme was purified 44-fold to apparent homogeneity. It was found to be present in two glycoforms of 98 kDa and 87 kDa with carbohydrate contents of 16 and 4%, respectively. The isoelectric point of both glycoforms is around 3.0, differing by 0.1 units, which is the most acidic value so far reported for a CDH. By using degenerated primers of known CDH sequences, one cdh gene was found in the genomic DNA, cloned, and sequenced. Alignment of the 774-amino-acid protein sequence revealed a high similarity to CDH from other white rot fungi. One notable difference was found in the longer interdomain peptide linker, which might affect the interdomain electron transfer at higher temperatures. The preferred substrate of C. subvermispora CDH is cellobiose, while glucose conversion is strongly discriminated by a 155,000-fold-lower catalytic efficiency. This is a typical feature of a basidiomycete CDH, as are the acidic pH optima for all tested electron acceptors in the range from 2.5 to 4.5.

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Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome, and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative beta-1-4 endoglucanase were expressed at high levels relative to glucose-grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Also up-regulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H(2)O(2). These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H(2)O(2) react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons with the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost.

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The effect of copper on the expression of genes encoding the ligninolytic enzymes laccase (lcs) and manganese peroxidase (mnp) in Ceriporiopsis subvermispora was evaluated. This metal increased transcript levels of lcs, mnp1 and mnp2. This finding was not unexpected in the case of lcs, since its promoter contains a putative ACE element. Originally characterized in the yeast Saccharomyces cerevisiae, ACE is the target sequence of the ACE1 copper-responsive transcription factor in this microorganism. Analysis of the promoter regions of mnp genes revealed the presence of formerly unnoticed ACE elements. Based on the ace1 gene from Phanerochaete chrysosporium, we isolated and characterized an ACE1-like transcription factor from C. subvermispora (Cs-ACE1) through complementation of a S. cerevisiae ace1Delta strain. Surprisingly, ACE1 factors from both basidiomycetes exhibit substantial differences, not only structurally but also in their ability to complement the aforementioned yeast strain. Specific binding of Cs-ACE1 to its cognate DNA sequence was confirmed by electrophoretic mobility-shift assays.

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In this work, we explore the use of the unbiased cDNA-AFLP strategy to identify genes involved in Mn(2+) homeostasis in Ceriporiopsis subvermispora. In this ligninolytic white-rot fungus, whose genome has not yet been sequenced, three Mn peroxidase genes responding to Mn(2+) have been characterized. Using cDNA-AFLP to identify transcript-derived fragments (TDFs), a total of 37 differentially expressed cDNA fragments were identified by comparing band intensities among cDNA-AFLP patterns obtained from mycelia from cultures supplemented with different concentrations of Mn(2+). Of 21 differentially expressed TDFs, nine were classified as upregulated, five as downregulated and seven as unregulated. Of these, six upregulated and two downregulated TDFs were selected for further characterization. The expected TDFs for the known Mn peroxidases were not isolated, but several genes encoding proteins related to protein sorting, storage and excretion of excess Mn(2+) were identified. Transcripts induced under Mn(2+) supplementation exhibited homologies to the elongation factor eEF3, a HDEL sequence binding protein and the ARD1 subunit of the N-acetyltransferase complex, among others. Overall, the results obtained in this study suggest a complex picture of Mn(2+) homeostasis and provide the possibility to search for common regulatory elements in the promoters of the novel putatively identified genes.

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We have previously identified and functionally characterized the transcription factor ACE1 (Pc-ACE1) from Phanerochaete chrysosporium. In Saccharomyces cerevisiae, ACE1 activates the copper-dependent transcription of target genes through a DNA sequence element named ACE. However, the possible target gene(s) of Pc-ACE1 were unknown. An in silico search led to the identification of putative ACE elements in the promoter region of mco1, one of the four clustered genes encoding multicopper oxidases (MCOs) in P. chrysosporium. Since copper exerts an effect at the transcriptional level in MCOs from several organisms, in this work we analysed the effect of copper on transcript levels of the clustered MCO genes from P. chrysosporium, with the exception of the transcriptionally inactive mco3. Copper supplementation of cultures produced an increment in transcripts from genes mco1 and mco2, but not from mco4. Electrophoretic mobility-shift assays revealed that Pc-ACE1 binds specifically to a probe containing one of the putative ACE elements found in the promoter of mco1. In addition, using a cell-free transcription system, we showed that in the presence of cuprous ion, Pc-ACE1 induces activation of the promoter of mco1, but not that of mco2.

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The authors have previously identified and characterized lcs, a gene encoding laccase in the white-rot basidiomycete Ceriporiopsis subvermispora. In this work, the effect of Mn2+ in the production of extracellular laccase in liquid cultures of this fungus has been assessed. It was observed that at low (0-10 microM) concentrations of Mn2+, high titers of lcs-mRNA were obtained, whereas at high (160-194 microM) concentrations of this metal ion, transcripts levels decreased markedly. This phenomenon was observed at different days of growth. On the other hand, Cu2+ or Ag+, but not Zn2+ or Cd2+, led to an accumulation of lcs transcripts only in cultures grown in the absence of Mn2+. A dramatic increase in lcs transcript levels was also obtained with syringic acid, a lignin-related aromatic compound. This effect was more pronounced in cultures lacking Mn2+. In the course of these studies it was observed that Mn2+ stimulates mycelium growth. Thus, although extracellular laccase activity appeared higher in cultures containing 160 or 194 microM Mn2+, i.e. when lcs transcripts were lower, a correlation between lcs-mRNA levels and enzymatic activity was observed when values of the latter were corrected by the amount of mycelium present in the cultures.

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MCO1, a multicopper oxidase from Phanerochaete chrysosporium exhibiting strong ferroxidase activity, has recently been described. This enzyme shows biochemical and structural similarities with the yeast Fet3p, a type I membrane glycoprotein that efficiently oxidizes Fe(II) to Fe(III) for its subsequent transport to the intracellular compartment by the iron permease Ftr1p. The genome database of P. chrysosporium was searched to verify whether it includes a canonical fet3 in addition to mco1, and single copies of fet3 and ftr1 orthologues were found, separated by a divergent promoter. Pc-fet3 encodes a 628 aa protein that exhibits overall identities of about 40 % with other reported Fet3 proteins. In addition to a secretion signal, it has a C-terminal transmembrane domain, characteristic of these cell-surface-attached ferroxidases. Structural modelling of Pc-Fet3 revealed that the active site has all the residues known to be essential for ferroxidase activity. Pc-ftr1 encodes a 393 aa protein that shows about 38 % identity with several Ftr1 proteins from ascomycetes. Northern hybridization studies showed that the mRNA levels of both genes are reduced upon supplementation of the growth medium with iron, supporting the functional coupling of Fet3 and Ftr1 proteins in vivo.

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We describe the structure, organization, and transcriptional impact of repetitive elements within the lignin-degrading basidiomycete, Phanerochaete chrysosporium. Searches of the P. chrysosporium genome revealed five copies of pce1, a ~1,750-nt non-autonomous, class II element. Alleles encoding a putative glucosyltransferase and a cytochrome P450 harbor pce insertions and produce incomplete transcripts. Class I elements included pcret1, an intact 8.14-kb gypsy-like retrotransposon inserted within a member of the multicopper oxidase gene family. Additionally, we describe a complex insertion of nested transposons within another putative cytochrome P450 gene. The disrupted allele lies within a cluster of >14 genes, all of which encode family 64 cytochrome P450s. Components of the insertion include a disjoint copia-like element, pcret3, the pol domain of a second retroelement, pcret2, and a duplication of an extended ORF of unknown function. As in the case of the pce elements, pcret1 and pcret2/3 insertions are confined to single alleles, transcripts of which are truncated. The corresponding wild-type alleles are apparently unaffected. In aggregate, P. chrysosporium harbors a complex array of repetitive elements, at least five of which directly influence expression of genes within families of structurally related sequences.

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