Transgene-Induced Silencing of the Zoosporogenesis-Specific NIFC Gene Cluster of Phytophthora infestans Involves Chromatin Alterations

ABSTRACT Clustered within the genome of the oomycete phytopathogen Phytophthora infestans are four genes encoding spore-specific nuclear LIM interactor-interacting factors (NIF proteins, a type of transcriptional regulator) that are moderately conserved in DNA sequence. NIFC1, NIFC2, and NIFC3 are zoosporogenesis-induced and grouped within 4 kb, and 20 kb away resides a sporulation-induced form, NIFS. To test the function of the NIFC family, plasmids expressing full-length hairpin constructs of NIFC1 or NIFC2 were stably transformed into P. infestans. This triggered silencing of the cognate gene in about one-third of transformants, and all three NIFC genes were usually cosilenced. However, NIFS escaped silencing despite its high sequence similarity to the NIFC genes. Silencing of the three NIFC genes impaired zoospore cyst germination by 60% but did not affect other aspects of the life cycle. Silencing was transcriptional based on nuclear run-on assays and associated with tighter chromatin packing based on nuclease accessibility experiments. The chromatin alterations extended a few hundred nucleotides beyond the boundaries of the transcribed region of the NIFC cluster and were not associated with increased DNA methylation. A plasmid expressing a short hairpin RNA having sequence similarity only to NIFC1 silenced both that gene and an adjacent member of the gene cluster, likely due to the expansion of a heterochromatic domain from the targeted locus. These data help illuminate the mechanism of silencing in Phytophthora and suggest that caution should be used when interpreting silencing experiments involving closely spaced genes.

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Meiotic Recombination Between Paralogous RBCSB Genes on Sister Chromatids of Arabidopsis thaliana

Genetics ◽

10.1093/genetics/166.2.947 ◽

2004 ◽

Vol 166 (2) ◽

pp. 947-957 ◽

Cited By ~ 1

Author(s):

John G Jelesko ◽

Kristy Carter ◽

Whitney Thompson ◽

Yuki Kinoshita ◽

Wilhelm Gruissem

Keyword(s):

Gene Cluster ◽

Dna Sequences ◽

Meiotic Recombination ◽

Sequence Similarity ◽

Specific Gene ◽

High Sequence Similarity ◽

Paralogous Genes ◽

Chimeric Genes ◽

Unequal Recombination ◽

Sister Chromatids

Abstract Paralogous genes organized as a gene cluster can rapidly evolve by recombination between misaligned paralogs during meiosis, leading to duplications, deletions, and novel chimeric genes. To model unequal recombination within a specific gene cluster, we utilized a synthetic RBCSB gene cluster to isolate recombinant chimeric genes resulting from meiotic recombination between paralogous genes on sister chromatids. Several F1 populations hemizygous for the synthRBCSB1 gene cluster gave rise to Luc+ F2 plants at frequencies ranging from 1 to 3 × 10-6. A nonuniform distribution of recombination resolution sites resulted in the biased formation of recombinant RBCS3B/1B::LUC genes with nonchimeric exons. The positioning of approximately half of the mapped resolution sites was effectively modeled by the fractional length of identical DNA sequences. In contrast, the other mapped resolution sites fit an alternative model in which recombination resolution was stimulated by an abrupt transition from a region of relatively high sequence similarity to a region of low sequence similarity. Thus, unequal recombination between paralogous RBCSB genes on sister chromatids created an allelic series of novel chimeric genes that effectively resulted in the diversification rather than the homogenization of the synthRBCSB1 gene cluster.

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Genetic Investigation of the Catabolic Pathway for Degradation of Abietane Diterpenoids by Pseudomonas abietaniphilaBKME-9

Journal of Bacteriology ◽

10.1128/jb.182.13.3784-3793.2000 ◽

2000 ◽

Vol 182 (13) ◽

pp. 3784-3793 ◽

Cited By ~ 39

Author(s):

Vincent J. J. Martin ◽

William W. Mohn

Keyword(s):

Gene Cluster ◽

Sequence Similarity ◽

Open Reading Frames ◽

Ring Cleavage ◽

Catabolic Pathway ◽

Transcriptional Fusion ◽

Abietane Diterpenoids ◽

Genes Encoding ◽

Dna Fragment ◽

Reading Frames

ABSTRACT We have cloned and sequenced the dit gene cluster encoding enzymes of the catabolic pathway for abietane diterpenoid degradation by Pseudomonas abietaniphila BKME-9. Thedit gene cluster is located on a 16.7-kb DNA fragment containing 13 complete open reading frames (ORFs) and 1 partial ORF. The genes ditA1A2A3 encode the α and β subunits and the ferredoxin of the dioxygenase which hydroxylates 7-oxodehydroabietic acid to 7-oxo-11,12-dihydroxy-8,13-abietadien acid. The dioxygenase mutant strain BKME-941 (ditA1::Tn5) did not grow on nonaromatic abietanes, and transformed palustric and abietic acids to 7-oxodehydroabietic acid in cell suspension assays. Thus, nonaromatic abietanes are aromatized prior to further degradation. Catechol 2,3-dioxygenase activity of xylEtranscriptional fusion strains showed induction of ditA1and ditA3 by abietic, dehydroabietic, and 7-oxodehydroabietic acids, which support the growth of strain BKME-9, as well as by isopimaric and 12,14-dichlorodehydroabietic acids, which are diterpenoids that do not support the growth of strain BKME-9. In addition to the aromatic-ring-hydroxylating dioxygenase genes, thedit cluster includes ditC, encoding an extradiol ring cleavage dioxygenase, and ditR, encoding an IclR-type transcriptional regulator. Although ditR is not strictly required for the growth of strain BKME-9 on abietanes, aditR::Kmr mutation in aditA3::xylE reporter strain demonstrated that it encodes an inducer-dependent transcriptional activator of ditA3. An ORF with sequence similarity to genes encoding permeases (ditE) is linked with genes involved in abietane degradation.

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Novel 4-Chlorophenol Degradation Gene Cluster and Degradation Route via Hydroxyquinol in Arthrobacter chlorophenolicus A6

Applied and Environmental Microbiology ◽

10.1128/aem.71.11.6538-6544.2005 ◽

2005 ◽

Vol 71 (11) ◽

pp. 6538-6544 ◽

Cited By ~ 81

Author(s):

Karolina Nordin ◽

Maria Unell ◽

Janet K. Jansson

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Gene Cluster ◽

Microbial Degradation ◽

Codon Bias ◽

Sequence Similarity ◽

Open Reading Frames ◽

Genes Encoding ◽

Arthrobacter Chlorophenolicus ◽

Reading Frames

ABSTRACT Arthrobacter chlorophenolicus A6, a previously described 4-chlorophenol-degrading strain, was found to degrade 4-chlorophenol via hydroxyquinol, which is a novel route for aerobic microbial degradation of this compound. In addition, 10 open reading frames exhibiting sequence similarity to genes encoding enzymes involved in chlorophenol degradation were cloned and designated part of a chlorophenol degradation gene cluster (cph genes). Several of the open reading frames appeared to encode enzymes with similar functions; these open reading frames included two genes, cphA-I and cphA-II, which were shown to encode functional hydroxyquinol 1,2-dioxygenases. Disruption of the cphA-I gene yielded a mutant that exhibited negligible growth on 4-chlorophenol, thereby linking the cph gene cluster to functional catabolism of 4-chlorophenol in A. chlorophenolicus A6. The presence of a resolvase pseudogene in the cph gene cluster together with analyses of the G+C content and codon bias of flanking genes suggested that horizontal gene transfer was involved in assembly of the gene cluster during evolution of the ability of the strain to grow on 4-chlorophenol.

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Structure and Sequence Conservation of hao Cluster Genes of Autotrophic Ammonia-Oxidizing Bacteria: Evidence for Their Evolutionary History

Applied and Environmental Microbiology ◽

10.1128/aem.71.9.5371-5382.2005 ◽

2005 ◽

Vol 71 (9) ◽

pp. 5371-5382 ◽

Cited By ~ 46

Author(s):

David J. Bergmann ◽

Alan B. Hooper ◽

Martin G. Klotz

Keyword(s):

Gene Cluster ◽

Sequence Similarity ◽

Molecular Ecology ◽

Gene Clusters ◽

Nitrite Reduction ◽

Divergent Evolution ◽

Ammonia Oxidizing Bacteria ◽

High Sequence Similarity ◽

Hydroxylamine Oxidoreductase ◽

Transfer Event

ABSTRACT Comparison of the organization and sequence of the hao (hydroxylamine oxidoreductase) gene clusters from the gammaproteobacterial autotrophic ammonia-oxidizing bacterium (aAOB) Nitrosococcus oceani and the betaproteobacterial aAOB Nitrosospira multiformis and Nitrosomonas europaea revealed a highly conserved gene cluster encoding the following proteins: hao, hydroxylamine oxidoreductase; orf2, a putative protein; cycA, cytochrome c 554; and cycB, cytochrome c m 552. The deduced protein sequences of HAO, c 554, and c m 552 were highly similar in all aAOB despite their differences in species evolution and codon usage. Phylogenetic inference revealed a broad family of multi-c-heme proteins, including HAO, the pentaheme nitrite reductase, and tetrathionate reductase. The c-hemes of this group also have a nearly identical geometry of heme orientation, which has remained conserved during divergent evolution of function. High sequence similarity is also seen within a protein family, including cytochromes c m 552, NrfH/B, and NapC/NirT. It is proposed that the hydroxylamine oxidation pathway evolved from a nitrite reduction pathway involved in anaerobic respiration (denitrification) during the radiation of the Proteobacteria. Conservation of the hydroxylamine oxidation module was maintained by functional pressure, and the module expanded into two separate narrow taxa after a lateral gene transfer event between gamma- and betaproteobacterial ancestors of extant aAOB. HAO-encoding genes were also found in six non-aAOB, either singly or tandemly arranged with an orf2 gene, whereas a c 554 gene was lacking. The conservation of the hao gene cluster in general and the uniqueness of the c 554 gene in particular make it a suitable target for the design of primers and probes useful for molecular ecology approaches to detect aAOB.

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A Carbohydrate Hydrolysis Enzymes encoding Genes in Neurospora crassa

JOURNAL OF ADVANCES IN BIOTECHNOLOGY ◽

10.24297/jbt.v5i3.1539 ◽

2015 ◽

Vol 5 (3) ◽

pp. 711-727

Author(s):

Ravi Gedela

Keyword(s):

Neurospora Crassa ◽

Sequence Similarity ◽

Bacterial Species ◽

High Sequence Similarity ◽

Physiochemical Properties ◽

Carbohydrate Hydrolysis ◽

Genes Encoding ◽

Multiple Sequences ◽

Encoding Genes ◽

Sequences Alignment

Neurospora crassa, NCU05882.7 (423aa) and NCU09774.7 (303 aa) (NCU, Neurospora 7 crassa unit) genes encoding a Cellulase, which hydrolysis the Cellulose. In addition to that, 8 reporting here other 35 Carbohydrate hydrolysis enzymes encoding genes in N.crassa. A 9 metagenomic analysis for multiple sequences alignment and Phylogenetics analysis, the evaluated 10 result showed high sequence similarity and 99% homology to the other class of fungi; in the 11 bacterial species showed extremely very less sequence similarities and 100 % homology. 12 Where as in inter species between fungi and bacteria, the results showed extremely less sequence 13 similarities and 97 % homology. The studies on physiochemical properties of Cellulase using 14 GeneDoc, the evaluated results showed Cellulase was an amphoteric (polor), aromatic, aliphatic 15 and highly repeated amino acids of glycine and proline. These metagenomic studies could help 16 to straightforward isolation of Cellulase enzymes from NCU05882.7 (Chromosome/Linkage 17 Group-VII), NCU09774.7 (Chromosome Linkage Group- II) and other 35 Carbohydrate 18 hydrolysis enzymes encoding genes in N.crassa.

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Identification of Sinorhizobium melilotiGenes Regulated during Symbiosis

Journal of Bacteriology ◽

10.1128/jb.182.13.3632-3637.2000 ◽

2000 ◽

Vol 182 (13) ◽

pp. 3632-3637 ◽

Cited By ~ 25

Author(s):

Didier Cabanes ◽

Pierre Boistard ◽

Jacques Batut

Keyword(s):

Sinorhizobium Meliloti ◽

Sequence Similarity ◽

Pyruvate Dehydrogenase Complex ◽

Surface Protein ◽

Symbiotic Interaction ◽

High Sequence Similarity ◽

Copper Transporter ◽

Genes Encoding ◽

A Cell ◽

Arbitrarily Primed Pcr

ABSTRACT RNA fingerprinting by arbitrarily primed PCR was used to isolateSinorhizobium meliloti genes regulated during the symbiotic interaction with alfalfa (Medicago sativa). Sixteen partial cDNAs were isolated whose corresponding genes were differentially expressed between symbiotic and free-living conditions. Thirteen sequences corresponded to genes up-regulated during symbiosis, whereas three were instead repressed during establishment of the symbiotic interaction. Seven cDNAs corresponded to known or predictednif and fix genes. Four presented high sequence similarity with genes not yet identified in S. meliloti, including genes encoding a component of the pyruvate dehydrogenase complex, a cell surface protein component, a copper transporter, and an argininosuccinate lyase. Finally, five cDNAs did not exhibit any similarity with sequences present in databases. A detailed expression analysis of the nine non-nif-fix genes provided evidence for an unexpected variety of regulatory patterns, most of which have not been described so far.

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CelR-mediated activation of the cellobiose-utilization gene cluster in Streptococcus pneumoniae

Microbiology ◽

10.1099/mic.0.051359-0 ◽

2011 ◽

Vol 157 (10) ◽

pp. 2854-2861 ◽

Cited By ~ 25

Author(s):

Sulman Shafeeq ◽

Tomas G. Kloosterman ◽

Oscar P. Kuipers

Keyword(s):

Streptococcus Pneumoniae ◽

Gene Cluster ◽

Transcriptional Activation ◽

Sole Carbon Source ◽

Transcriptional Regulator ◽

Regulatory Site ◽

Human Pathogen ◽

Direct Control ◽

Atp Binding Cassette Transporters ◽

Genes Encoding

The human pathogen Streptococcus pneumoniae harbours many genes encoding phosphotransferase systems and sugar ABC (ATP-binding cassette) transporters, including systems for the utilization of the β-glucoside sugar cellobiose. In this study, we show that the transcriptional regulator CelR, which has previously been found to be important for pneumococcal virulence, activates the expression of the cellobiose-utilization gene cluster (cel locus) of S. pneumoniae. Expression directed by the two promoters present in the cel locus was increased in the presence of cellobiose as sole carbon source in the medium, while expression decreased in the presence of glucose in the medium. Furthermore, we have predicted a 22 bp putative CelR regulatory site (5′-YTTTCCWTAWCAWTWAGGAAAA-3′) in the promoters of celA and celB, and in silico analysis showed that it is highly conserved in other pathogenic streptococci as well. Promoter truncations of celA and celB, where the half or full CelR regulatory site was deleted, confirmed that the CelR-binding site in PcelA and PcelB is functional. Transcriptome studies with the celR mutant and in silico prediction of the CelR regulatory site in the entire D39 genome sequence show that the cel locus is the only cluster of genes under the direct control of CelR. Therefore, CelR is a regulator dedicated to the cellobiose-dependent transcriptional activation of the cel locus.

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The cylindrospermopsin gene cluster of Aphanizomenon sp. strain 10E6: organization and recombination

Microbiology ◽

10.1099/mic.0.036988-0 ◽

2010 ◽

Vol 156 (8) ◽

pp. 2438-2451 ◽

Cited By ~ 62

Author(s):

Anke Stüken ◽

Kjetill S. Jakobsen

Keyword(s):

Gene Cluster ◽

Sequence Similarity ◽

Gc Content ◽

Orthologous Gene ◽

Gene Clusters ◽

Cylindrospermopsis Raciborskii ◽

Rrna Gene ◽

Full Genome Sequencing ◽

High Sequence Similarity ◽

Geographical Regions

Cylindrospermopsin (CYN), a potent hepatoxin, occurs in freshwaters worldwide. Several cyanobacterial species produce the toxin, but the producing species vary between geographical regions. Aphanizomenon flos-aquae, a common algae species in temperate fresh and brackish waters, is one of the three well-documented CYN producers in European waters. So far, no genetic information on the CYN genes of this species has been available. Here, we describe the complete CYN gene cluster, including flanking regions from the German Aphanizomenon sp. strain 10E6 using a full genome sequencing approach by 454 pyrosequencing and bioinformatic identification of the gene cluster. In addition, we have sequenced a ∼7 kb fragment covering the genes cyrC (partially), cyrA and cyrB (partially) of the same gene cluster in the CYN-producing Aphanizomenon sp. strains 10E9 and 22D11. Comparisons with the orthologous gene clusters of the Australian Cylindrospermopsis raciborskii strains AWT205 and CS505 and the partial gene cluster of the Israeli Aphanizomenon ovalisporum strain ILC-146 revealed a high gene sequence similarity, but also extensive rearrangements of gene order. The high sequence similarity (generally higher than that of 16S rRNA gene fragments from the same strains), atypical GC-content and signs of transposase activities support the suggestion that the CYN genes have been horizontally transferred.

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The Isolation of Pyrroloformamide Congeners and Characterization of Its Biosynthetic Gene Cluster from Streptomyces sp. CB02980 Revealed a Unified Mechanism for Dithiolopyrrolone Biosynthesis

10.26434/chemrxiv.10208717 ◽

2019 ◽

Author(s):

Wenqing Zhou ◽

Haoyu Liang ◽

Xiangjing Qin ◽

Danfeng Cao ◽

Xiangcheng Zhu ◽

...

Keyword(s):

Gene Cluster ◽

Sequence Similarity ◽

Biosynthetic Gene Cluster ◽

Gene Replacement ◽

Biosynthetic Gene ◽

High Sequence Similarity ◽

Bicyclic Structure ◽

Microbial Natural Products ◽

Drug Leads

Dithiolopyrrolones are microbial natural products containing a disulfide or thiosulfonate bridge embedded in a unique bicyclic structure. In the current study, two new dithiolopyrrolones, pyrroloformamide C (3) and pyrroloformamide D (4), were isolated from Streptomyces sp. CB02980, together with the known pyrroloformamides 1 and 2. The biosynthetic gene cluster for pyrroloformamides was identified from S. sp. CB02980, which shared high sequence similarity with those of dithiolopyrrolones, including holomycin and thiolutin. Gene replacement of pyfE, which encodes a non-ribosomal peptide synthetase, abolished the production of 1－4. Overexpression of pyfN, a type II thioesterase gene, increased the production of 1 and 2. The structure elucidation and biosynthetic characterization of pyrroloformamides 1 - 4 may inspire future efforts to discover new dithiolopyrrolones, which are promising drug leads for the treatment of infectious diseases or cancer.

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