Phenolic degradation by catechol dioxygenases is associated with pathogenic fungi with a necrotrophic lifestyle in the Ceratocystidaceae

Fungal species of the Ceratocystidaceae grow on their host plants using a variety of different lifestyles, from saprophytic to highly pathogenic. Although many genomes of fungi in the Ceratocystidaceae are publicly available, it is not known how the genes that encode catechol dioxygenases (CDOs), enzymes involved in the degradation of phenolic plant defence compounds, differ among members of the Ceratocystidaceae. The aim of this study was therefore to identify and characterize the genes encoding CDOs in the genomes of Ceratocystidaceae representatives. We found that genes encoding CDOs are more abundant in pathogenic necrotrophic species of the Ceratocystidaceae and less abundant in saprophytic species. The loss of the CDO genes and the associated 3-oxoadipate catabolic pathway appears to have occurred in a lineage-specific manner. Taken together, this study revealed a positive association between CDO gene copy number and fungal lifestyle in Ceratocystidaceae representatives.

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Differential elimination of rDNA genes in bobbed mutants of Drosophila melanogaster

Molecular and Cellular Biology ◽

10.1128/mcb.6.4.1023-1031.1986 ◽

1986 ◽

Vol 6 (4) ◽

pp. 1023-1031

Author(s):

R Terracol ◽

N Prud'homme

Keyword(s):

Drosophila Melanogaster ◽

Gene Copy Number ◽

Rdna Locus ◽

Gene Copy ◽

Specific Gene ◽

Type I ◽

28S Rrna ◽

Wild Type ◽

Y Chromosomes ◽

Genes Encoding

In Drosophila melanogaster, the multiply repeated genes encoding 18S and 28S rRNA are located on the X and Y chromosomes. A large percentage of these repeats are interrupted in the 28S region by insertions of two types. We compared the restriction patterns from a subcloned wild-type Oregon R strain to those of spontaneous and ethyl methanesulfonate-induced bobbed mutants. Bobbed mutations were found to be deficiencies that modified the organization of the rDNA locus. Genes without insertions were deleted about twice as often as genes with type I insertions. Type II insertion genes were not decreased in number, except in the mutant having the most bobbed phenotype. Reversion to wild type was associated with an increase in gene copy number, affecting exclusively genes without insertions. One hypothesis which explains these results is the partial clustering of genes by type. The initial deletion could then be due either to an unequal crossover or to loss of material without exchange. Some of our findings indicated that deletion may be associated with an amplification phenomenon, the magnitude of which would be dependent on the amount of clustering of specific gene types at the locus.

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Optimization of Yarrowia lipolytica-based consolidated biocatalyst through synthetic biology approach: transcription units and signal peptides shuffling

10.21203/rs.3.rs-17224/v1 ◽

2020 ◽

Author(s):

Ewelina Celińska ◽

Monika Borkowska ◽

Paulina Korpys-Woźniak ◽

Monika Kubiak ◽

Jean-Marc Nicaud ◽

...

Keyword(s):

Gene Copy Number ◽

Regulatory Elements ◽

Gene Copy ◽

Signal Peptides ◽

Synthetic Dna ◽

Batch Bioreactor ◽

Genes Encoding ◽

Valuable Compounds ◽

Synthetic Biology Approach ◽

Lipids Accumulation

Abstract Background: Nowadays considerable effort is being pursued towards development of consolidated microbial biocatalysts that will be able to utilize complex, non-pretreated substrates and produce valuable compounds. In such engineered microbes, synthesis of extracellular hydrolases may be fine-tuned by different approaches, like strength of promoter, type of secretory tag, gene copy number etc. In this study, we investigated if organization of a multi-element expression cassette impacts the resultant Y. lipolytica transformants’ phenotype, presuming that different variants of the cassette are composed of the same regulatory elements and encode the same hydrolases. Results: To this end, Y. lipolytica cells were transformed with expression cassettes bearing a pair of genes encoding exactly the same mature amylases, but fused to four different signal peptides (SP), and located interchangeably in either first or second position of a synthetic DNA construction. The resultant strains were tested for growth on raw and pre-treated complex substrates of different plant origin for comprehensive examination of the strains’ acquired characteristics. The best strain’s performance was tested in batch bioreactor cultivations for growth and lipids accumulation. Conclusions: Based on the conducted research we concluded that the positional order of transcription units (TU) and the type of exploited SP affect final characteristics of the resultant consolidated biocatalyst strains, and thus could be considered as additional factors to be evaluated upon consolidated biocatalysts optimization.

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Gene copy number is associated with phytochemistry in Cannabis sativa

AoB Plants ◽

10.1093/aobpla/plz074 ◽

2019 ◽

Vol 11 (6) ◽

Cited By ~ 4

Author(s):

Daniela Vergara ◽

Ezra L Huscher ◽

Kyle G Keepers ◽

Robert M Givens ◽

Christian G Cizek ◽

...

Keyword(s):

Copy Number ◽

Cannabis Sativa ◽

Sequence Data ◽

Gene Copy Number ◽

Gene Copy ◽

Multiple Points ◽

Transcriptome Sequence Data ◽

Cannabidiolic Acid ◽

Genes Encoding ◽

Genome Shotgun Sequence

Abstract Gene copy number (CN) variation is known to be important in nearly every species where it has been examined. Alterations in gene CN may provide a fast way of acquiring diversity, allowing rapid adaptation under strong selective pressures, and may also be a key component of standing genetic variation within species. Cannabis sativa plants produce a distinguishing set of secondary metabolites, the cannabinoids, many of which have medicinal utility. Two major cannabinoids—THCA (delta-9-tetrahydrocannabinolic acid) and CBDA (cannabidiolic acid)—are products of a three-step biochemical pathway. Using whole-genome shotgun sequence data for 69 Cannabis cultivars from diverse lineages within the species, we found that genes encoding the synthases in this pathway vary in CN. Transcriptome sequence data show that the cannabinoid paralogs are differentially expressed among lineages within the species. We also found that CN partially explains variation in cannabinoid content levels among Cannabis plants. Our results demonstrate that biosynthetic genes found at multiple points in the pathway could be useful for breeding purposes, and suggest that natural and artificial selection have shaped CN variation. Truncations in specific paralogs are associated with lack of production of particular cannabinoids, showing how phytochemical diversity can evolve through a complex combination of processes.

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Differential elimination of rDNA genes in bobbed mutants of Drosophila melanogaster.

Molecular and Cellular Biology ◽

10.1128/mcb.6.4.1023 ◽

1986 ◽

Vol 6 (4) ◽

pp. 1023-1031 ◽

Cited By ~ 20

Author(s):

R Terracol ◽

N Prud'homme

Keyword(s):

Drosophila Melanogaster ◽

Gene Copy Number ◽

Rdna Locus ◽

Gene Copy ◽

Specific Gene ◽

Type I ◽

28S Rrna ◽

Wild Type ◽

Y Chromosomes ◽

Genes Encoding

In Drosophila melanogaster, the multiply repeated genes encoding 18S and 28S rRNA are located on the X and Y chromosomes. A large percentage of these repeats are interrupted in the 28S region by insertions of two types. We compared the restriction patterns from a subcloned wild-type Oregon R strain to those of spontaneous and ethyl methanesulfonate-induced bobbed mutants. Bobbed mutations were found to be deficiencies that modified the organization of the rDNA locus. Genes without insertions were deleted about twice as often as genes with type I insertions. Type II insertion genes were not decreased in number, except in the mutant having the most bobbed phenotype. Reversion to wild type was associated with an increase in gene copy number, affecting exclusively genes without insertions. One hypothesis which explains these results is the partial clustering of genes by type. The initial deletion could then be due either to an unequal crossover or to loss of material without exchange. Some of our findings indicated that deletion may be associated with an amplification phenomenon, the magnitude of which would be dependent on the amount of clustering of specific gene types at the locus.

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Analysis of amplicons containing the esterase genes responsible for insecticide resistance in the peach-potato aphid Myzus persicae (Sulzer)

Biochemical Journal ◽

10.1042/bj3130543 ◽

1996 ◽

Vol 313 (2) ◽

pp. 543-547 ◽

Cited By ~ 18

Author(s):

Linda M. FIELD ◽

Alan L. DEVONSHIRE ◽

Chris TYLER-SMITH

Keyword(s):

Gene Amplification ◽

Myzus Persicae ◽

Gene Copy Number ◽

Fold Increase ◽

Gene Copy ◽

Potato Aphid ◽

Gene Copies ◽

Genes Encoding ◽

Aphid Clone ◽

Peach Potato Aphid

The amplification of genes encoding an insecticide-detoxifying esterase (E4) in the peach-potato aphid Myzus persicae is one of the few examples where this genetic phenomenon has been shown to be involved in the response of an intact higher organism to artificial selection. Here we report quantitative and qualitative studies of the repeat units (amplicons) containing the E4 genes in a highly resistant aphid clone. Initial studies to quantify esterase sequences showed a 5-11-fold increase in resistant aphids compared with susceptible aphids, suggesting the presence of 10-22 gene copies per diploid genome. A more incisive analysis by pulsed-field gel electrophoresis confirmed the presence of about 12 copies of the E4 gene and showed them to be on about 24 kb amplicons, arranged as a tandem array of direct repeats. This, together with previous results from crossing experiments and with recent in situ hybridization studies, confirms that the E4 gene amplification in this aphid clone is heterozygous at a single locus. However, these data show that the gene amplification alone cannot account for the approx. 60 times higher levels of E4 protein and its mRNA present in this aphid clone, and therefore resistance must involve changes in both esterase gene copy number and gene expression.

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Increased or Decreased Levels of Caenorhabditis elegans lon-3, a Gene Encoding a Collagen, Cause Reciprocal Changes in Body Length

Genetics ◽

10.1093/genetics/161.1.83 ◽

2002 ◽

Vol 161 (1) ◽

pp. 83-97 ◽

Cited By ~ 2

Author(s):

Josefin Nyström ◽

Zai-Zhong Shen ◽

Margareta Aili ◽

Anthony J Flemming ◽

Armand Leroi ◽

...

Keyword(s):

Body Length ◽

Gene Copy Number ◽

Gene Copy ◽

Loss Of Function ◽

Gene Encoding ◽

C Elegans ◽

Morphometric Analyses ◽

Genes Encoding ◽

New Mutations

Abstract Body length in C. elegans is regulated by a member of the TGFβ family, DBL-1. Loss-of-function mutations in dbl-1, or in genes encoding components of the signaling pathway it activates, cause worms to be shorter than wild type and slightly thinner (Sma). Overexpression of dbl-1 confers the Lon phenotype characterized by an increase in body length. We show here that loss-of-function mutations in dbl-1 and lon-1, respectively, cause a decrease or increase in the ploidy of nuclei in the hypodermal syncytial cell, hyp7. To learn more about the regulation of body length in C. elegans we carried out a genetic screen for new mutations causing a Lon phenotype. We report here the cloning and characterization of lon-3. lon-3 is shown to encode a putative cuticle collagen that is expressed in hypodermal cells. We show that, whereas putative null mutations in lon-3 (or reduction of lon-3 activity by RNAi) causes a Lon phenotype, increasing lon-3 gene copy number causes a marked reduction in body length. Morphometric analyses indicate that the lon-3 loss-of-function phenotype resembles that caused by overexpression of dbl-1. Furthermore, phenotypes caused by defects in dbl-1 or lon-3 expression are in both cases suppressed by a null mutation in sqt-1, a second cuticle collagen gene. However, whereas loss of dbl-1 activity causes a reduction in hypodermal endoreduplication, the reduction in body length associated with overexpression of lon-3 occurs in the absence of defects in hypodermal ploidy.

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Contribution to the pathogenic fungi on woody plants in North Korea

Phytotaxa ◽

10.11646/phytotaxa.299.2.3 ◽

2017 ◽

Vol 299 (2) ◽

pp. 185 ◽

Cited By ~ 1

Author(s):

KATARÍNA PASTIRČÁKOVÁ ◽

HYEON-DONG SHIN

Keyword(s):

Woody Plants ◽

North Korea ◽

Host Plants ◽

Pathogenic Fungi ◽

Fungal Species

This paper presents the first checklist of pathogenic fungi on woody plants in North Korea. The checklist enumerates 146 species of fungi belonging to 79 genera, growing on 108 host plants belonging to 58 genera and 35 families. Two hosts and 57 fungal species represent first records in North Korea.

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The effect of in vitro culture on unicellular eukaryotes: adaptation of Trypanosoma brucei brucei bloodstream forms results in gene copy-number changes.

10.1101/2021.06.10.446608 ◽

2021 ◽

Author(s):

Julius Mulindwa ◽

Geoffrey Ssentamu ◽

Enock Matovu ◽

Kevin Kamanyi Marucha ◽

Francisco Aresta-Branco ◽

...

Keyword(s):

In Vitro Culture ◽

Trypanosoma Brucei ◽

Gene Copy Number ◽

Gene Copy ◽

Trypanosoma Brucei Brucei ◽

Unicellular Eukaryotes ◽

Similar Work ◽

Genes Encoding ◽

Copy Number Changes

Most researchers who study unicellular eukaryotes work with an extremely limited number of laboratory-adapted isolates that were taken from the field decades ago, but the effects of passage in laboratory rodents, and adaptation to in vitro culture, have been little studied. For example, the vast majority of studies of Trypanosoma brucei biology have concentrated on just two strains, Lister 427 and EATRO1125, which were taken from the field over half a century ago and have since have undergone innumerable passages in rodents and culture. We here describe two new Trypanosoma brucei brucei strains. MAK65 and MAK98, which have undergone only 3 rodent passages since isolation from Ugandan cattle. Adaptation of these strains to culture was accompanied by changes in gene copy numbers, some of which were also evident when other lab-adapted strains, field isolates of T. rhodesiense, and the genome strain TREU927 were compared. Reproducible increases were seen for genes encoding histones, enzymes of mRNA processing and degradation, the cytosolic chaperone HSP70, and two proteins required for the DNA damage response. These results indicate that similar work with other eukaryotic pathogens would be worthwhile. Meanwhile, the two new T. brucei strains should be useful to researchers interested in trypanosome differentiation and pathogenicity. They have differing pathogenicities in mice and may also differ in their propensity for stumpy-form differentiation, as judged by morphology and mRNA expression. MAK65 grows better than MAK98 in bloodstream-form culture, and is uniformly diploid, whereas MAK98 is triploid for chromosome 5. Genome sequence exceeding 100-fold coverage is available for both strains.

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ZKSCAN3 Upregulation and Its Poor Clinical Outcome in Uterine Cervical Cancer

International Journal of Molecular Sciences ◽

10.3390/ijms19102859 ◽

2018 ◽

Vol 19 (10) ◽

pp. 2859 ◽

Cited By ~ 3

Author(s):

Sun Lee ◽

Young-Eun Cho ◽

Joo-Young Kim ◽

Jae-Hoon Park

Keyword(s):

Clinical Outcome ◽

Gene Copy Number ◽

Uterine Cervical Cancer ◽

Gene Copy ◽

Poor Clinical Outcome ◽

Poor Overall Survival ◽

Clinicopathological Findings ◽

Frequent Event ◽

Genes Encoding ◽

Domain 3

Zinc finger with KRAB and SCAN domain 3 (ZKSCAN3) upregulates genes encoding proteins involved in cell differentiation, proliferation and apoptosis. ZKSCAN3 has been reported to be overexpressed in several human cancers such as colorectal cancer and prostate cancer and is proposed as a candidate oncoprotein. However, the molecular mechanism by which ZKSCAN3 participates in carcinogenesis is largely unknown. Here, we evaluated ZKSCAN3 expression in uterine cervical cancers (CC) by immunohistochemistry using formalin-fixed, paraffin-embedded tissues from 126 biopsy samples from 126 patients. The clinicopathological findings were analyzed and compared with ZKSCAN3 expression levels. ZKSCAN3 was strongly overexpressed in CCs compared to adjacent non-neoplastic cervical mucosa tissues. Moreover, a gene copy number assay showed amplified ZKSCAN3 in CC samples. ZKSCAN3 overexpression was also significantly associated with poor overall survival of the patients. Overall, our findings indicate that ZKSCAN3 overexpression is a frequent event in uterine CC and is correlated with a poor clinical outcome. ZKSCAN3 could be developed as a molecular marker for prognostic prediction and early detection.

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