Role of the Pathotype-Specific ACRTS1 Gene Encoding a Hydroxylase Involved in the Biosynthesis of Host-Selective ACR-Toxin in the Rough Lemon Pathotype of Alternaria alternata

The rough lemon pathotype of Alternaria alternata produces host-selective ACR-toxin and causes Alternaria leaf spot disease of the rootstock species rough lemon (Citrus jambhiri) and Rangpur lime (C. limonia). Genes controlling toxin production were localized to a 1.5-Mb chromosome carrying the ACR-toxin biosynthesis gene cluster (ACRT) in the genome of the rough lemon pathotype. A genomic BAC clone containing a portion of the ACRT cluster was sequenced which allowed identification of three open reading frames present only in the genomes of ACR-toxin producing isolates. We studied the functional role of one of these open reading frames, ACRTS1 encoding a putative hydroxylase, in ACR-toxin production by homologous recombination-mediated gene disruption. There are at least three copies of ACRTS1 gene in the genome and disruption of two copies of this gene significantly reduced ACR-toxin production as well as pathogenicity; however, transcription of ACRTS1 and production of ACR-toxin were not completely eliminated due to remaining functional copies of the gene. RNA-silencing was used to knock down the remaining ACRTS1 transcripts to levels undetectable by reverse transcription-polymerase chain reaction. The silenced transformants did not produce detectable ACR-toxin and were not pathogenic. These results indicate that ACRTS1 is an essential gene in ACR-toxin biosynthesis in the rough lemon pathotype of A. alternata and is required for full virulence of this fungus.

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Role of the Host-Selective ACT-Toxin Synthesis Gene ACTTS2 Encoding an Enoyl-Reductase in Pathogenicity of the Tangerine Pathotype of Alternaria alternata

Phytopathology ◽

10.1094/phyto-100-2-0120 ◽

2010 ◽

Vol 100 (2) ◽

pp. 120-126 ◽

Cited By ~ 33

Author(s):

Naoya Ajiro ◽

Yoko Miyamoto ◽

Akira Masunaka ◽

Takashi Tsuge ◽

Mikihiro Yamamoto ◽

...

Keyword(s):

Alternaria Alternata ◽

Essential Gene ◽

Toxin Production ◽

Brown Spot ◽

Gene Encoding ◽

Bac Clone ◽

Biosynthesis Gene Cluster ◽

Enoyl Reductase ◽

Alternaria Brown Spot ◽

Rapid Amplification

The tangerine pathotype of Alternaria alternata produces host-selective ACT-toxin and causes Alternaria brown spot disease of tangerines and tangerine hybrids. Sequence analysis of a genomic BAC clone identified a previously uncharacterized portion of the ACT-toxin biosynthesis gene cluster (ACTT). A 1,034-bp gene encoding a putative enoyl-reductase was identified by using rapid amplification of cDNA ends and polymerase chain reaction and designated ACTTS2. Genomic Southern blots demonstrated that ACTTS2 is present only in ACT-toxin producers and is carried on a 1.9 Mb conditionally dispensable chromosome by the tangerine pathotype. Targeted gene disruption of ACTTS2 led to a reduction in ACT-toxin production and pathogenicity, and transcriptional knockdown of ACTTS2 using RNA silencing resulted in complete loss of ACT-toxin production and pathogenicity. These results indicate that ACTTS2 is an essential gene for ACT-toxin biosynthesis in the tangerine pathotype of A. alternata and is required for pathogenicity of this fungus.

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ACTTS3 Encoding a Polyketide Synthase Is Essential for the Biosynthesis of ACT-Toxin and Pathogenicity in the Tangerine Pathotype of Alternaria alternata

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-23-4-0406 ◽

2010 ◽

Vol 23 (4) ◽

pp. 406-414 ◽

Cited By ~ 27

Author(s):

Y. Miyamoto ◽

A. Masunaka ◽

T. Tsuge ◽

M. Yamamoto ◽

K. Ohtani ◽

...

Keyword(s):

Alternaria Alternata ◽

Polyketide Synthase ◽

Essential Gene ◽

Attachment Site ◽

Toxin Production ◽

Open Reading Frames ◽

Brown Spot ◽

Bac Clone ◽

Chain Reactions ◽

Highly Correlated

The tangerine pathotype of Alternaria alternata produces host-selective ACT-toxin and causes Alternaria brown spot disease of tangerine and tangerine hybrids. Sequence analysis of a genomic BAC clone identified part of the ACT-toxin TOX (ACTT) gene cluster, and knockout experiments have implicated several open reading frames (ORF) contained within the cluster in the biosynthesis of ACT-toxin. One of the ORF, designated ACTTS3, encoding a putative polyketide synthase, was isolated by rapid amplification of cDNA ends and genomic/reverse transcription-polymerase chain reactions using the specific primers designed from the BAC sequences. The 7,374-bp ORF encodes a polyketide synthase with putative β-ketoacyl synthase, acyltransferase, methyltransferase, β-ketoacyl reductase, and phosphopantetheine attachment site domains. Genomic Southern blots demonstrated that ACTTS3 is present on the smallest chromosome in the tangerine pathotype of A. alternata, and the presence of ACTTS3 is highly correlated with ACT-toxin production and pathogenicity. Targeted gene disruption of two copies of ACTTS3 led to a complete loss of ACT-toxin production and pathogenicity. These results indicate that ACTTS3 is an essential gene for ACT-toxin biosynthesis in the tangerine pathotype of A. alternata and is required for pathogenicity of this fungus.

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A Polyketide Synthase Gene, ACRTS2, Is Responsible for Biosynthesis of Host-Selective ACR-Toxin in the Rough Lemon Pathotype of Alternaria alternata

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-06-12-0155-r ◽

2012 ◽

Vol 25 (11) ◽

pp. 1419-1429 ◽

Cited By ~ 18

Author(s):

Y. Izumi ◽

K. Ohtani ◽

Y. Miyamoto ◽

A. Masunaka ◽

T. Fukumoto ◽

...

Keyword(s):

Alternaria Alternata ◽

Polyketide Synthase ◽

Attachment Site ◽

Toxin Production ◽

Leaf Spot Disease ◽

Predicted Amino Acid Sequence ◽

Type I ◽

Methyl Transferase ◽

Reading Frame ◽

Rough Lemon

The rough lemon pathotype of Alternaria alternata produces host-selective ACR-toxin and causes Alternaria leaf spot disease of rough lemon (Citrus jambhiri). The structure of ACR-toxin I (MW = 496) consists of a polyketide with an α-dihydropyrone ring in a 19-carbon polyalcohol. Genes responsible for toxin production were localized to a 1.5-Mb chromosome in the genome of the rough lemon pathotype. Sequence analysis of this chromosome revealed an 8,338-bp open reading frame, ACRTS2, that was present only in the genomes of ACR-toxin-producing isolates. ACRTS2 is predicted to encode a putative polyketide synthase of 2,513 amino acids and belongs to the fungal reducing type I polyketide synthases. Typical polyketide functional domains were identified in the predicted amino acid sequence, including β-ketoacyl synthase, acyl transferase, methyl transferase, dehydratase, β-ketoreductase, and phosphopantetheine attachment site domains. Combined use of homologous recombination-mediated gene disruption and RNA silencing allowed examination of the functional role of multiple paralogs in ACR-toxin production. ACRTS2 was found to be essential for ACR-toxin production and pathogenicity of the rough lemon pathotype of A. alternata.

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DNA Microarray Analysis of Central Carbohydrate Metabolism: Glycolytic/Gluconeogenic Carbon Switch in the Hyperthermophilic Crenarchaeum Thermoproteus tenax

Journal of Bacteriology ◽

10.1128/jb.01524-07 ◽

2008 ◽

Vol 190 (6) ◽

pp. 2231-2238 ◽

Cited By ~ 16

Author(s):

Melanie Zaparty ◽

Alexander Zaigler ◽

Claudia Stamme ◽

Jörg Soppa ◽

Reinhard Hensel ◽

...

Keyword(s):

Carbohydrate Metabolism ◽

Dna Microarray ◽

Transcript Level ◽

Open Reading Frames ◽

Transcriptional Analysis ◽

Heterotrophic Growth ◽

Thermoproteus Tenax ◽

Central Carbohydrate Metabolism ◽

Reading Frames

ABSTRACT In order to unravel the role of regulation on transcript level in central carbohydrate metabolism (CCM) of Thermoproteus tenax, a focused DNA microarray was constructed by using 85 open reading frames involved in CCM. A transcriptional analysis comparing heterotrophic growth on glucose versus autotrophic growth on CO2-H2 was performed.

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Distribution and Characterization of AKT Homologs in the Tangerine Pathotype of Alternaria alternata

Phytopathology ◽

10.1094/phyto.2000.90.7.762 ◽

2000 ◽

Vol 90 (7) ◽

pp. 762-768 ◽

Cited By ~ 63

Author(s):

A. Masunaka ◽

A. Tanaka ◽

T. Tsuge ◽

T. L. Peever ◽

L. W. Timmer ◽

...

Keyword(s):

Alternaria Alternata ◽

Sequence Similarity ◽

Structural Similarity ◽

Toxin Production ◽

Brown Spot ◽

Japanese Pear ◽

Black Rot ◽

Acid Moiety ◽

High Sequence Similarity ◽

Rough Lemon

The tangerine pathotype of Alternaria alternata produces a host-selective toxin (HST), known as ACT-toxin, and causes Alternaria brown spot disease of citrus. The structure of ACT-toxin is closely related to AK- and AF-toxins, which are HSTs produced by the Japanese pear and strawberry pathotypes of A. alternata, respectively. AC-, AK-, and AF-toxins are chemically similar and share a 9,10-epoxy-8-hydroxy-9-methyl-decatrienoic acid moiety. Two genes controlling AK-toxin biosynthesis (AKT1 and AKT2) were recently cloned from the Japanese pear pathotype of A. alternata. Portions of these genes were used as heterologous probes in Southern blots, that detected homologs in 13 isolates of A. alternata tangerine pathotype from Minneola tangelo in Florida. Partial sequencing of the homologs in one of these isolates demonstrated high sequence similarity to AKT1 (89.8%) and to AKT2 (90.7%). AKT homologs were not detected in nine isolates of A. alternata from rough lemon, six isolates of nonpathogenic A. alternata, and one isolate of A. citri that causes citrus black rot. The presence of homologs in the Minneola isolates and not in the rough lemon isolates, nonpathogens or black rot isolates, correlates perfectly to pathogenicity on Iyo tangerine and ACT-toxin production. Functionality of the homologs was demonstrated by detection of transcripts using reverse transcription-polymerase chain reaction (RT-PCR) in total RNA of the tangerine pathotype of A. alternata. The high sequence similarity of AKT and AKT homologs in the tangerine patho-type, combined with the structural similarity of AK-toxin and ACT-toxin, may indicate that these homologs are involved in the biosynthesis of the decatrienoic acid moiety of ACT-toxin.

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Autophagy Intertwines with Different Diseases—Recent Strategies for Therapeutic Approaches

Diseases ◽

10.3390/diseases7010015 ◽

2019 ◽

Vol 7 (1) ◽

pp. 15 ◽

Cited By ~ 6

Author(s):

Janani Ramesh ◽

Larance Ronsard ◽

Anthony Gao ◽

Bhuvarahamurthy Venugopal

Keyword(s):

Inflammatory Diseases ◽

Therapeutic Strategies ◽

Open Reading Frames ◽

Signaling Cascades ◽

Progression Rate ◽

Therapeutic Approaches ◽

Genes Encoding ◽

Novel Therapeutic Strategies ◽

Reading Frames

Autophagy is a regular and substantial “clear-out process” that occurs within the cell and that gets rid of debris that accumulates in membrane-enclosed vacuoles by using enzyme-rich lysosomes, which are filled with acids that degrade the contents of the vacuoles. This machinery is well-connected with many prevalent diseases, including cancer, HIV, and Parkinson’s disease. Considering that autophagy is well-known for its significant connections with a number of well-known fatal diseases, a thorough knowledge of the current findings in the field is essential in developing therapies to control the progression rate of diseases. Thus, this review summarizes the critical events comprising autophagy in the cellular system and the significance of its key molecules in manifesting this pathway in various diseases for down- or upregulation. We collectively reviewed the role of autophagy in various diseases, mainly neurodegenerative diseases, cancer, inflammatory diseases, and renal disorders. Here, some collective reports on autophagy showed that this process might serve as a dual performer: either protector or contributor to certain diseases. The aim of this review is to help researchers to understand the role of autophagy-regulating genes encoding functional open reading frames (ORFs) and its connection with diseases, which will eventually drive better understanding of both the progression and suppression of different diseases at various stages. This review also focuses on certain novel therapeutic strategies which have been published in the recent years based on targeting autophagy key proteins and its interconnecting signaling cascades.

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Role of two upstream open reading frames in the translational control of oncogene mdm2

Oncogene ◽

10.1038/sj.onc.1202949 ◽

1999 ◽

Vol 18 (41) ◽

pp. 5631-5637 ◽

Cited By ~ 59

Author(s):

Cheryl Y Brown ◽

Gregory J Mize ◽

Mario Pineda ◽

Donna L George ◽

David R Morris

Keyword(s):

Translational Control ◽

Open Reading Frames ◽

Upstream Open Reading Frames ◽

Reading Frames

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Phage composition of a fermented milk and colostrum product assessed by microbiome array; putative role of open reading frames in reference to cell signaling and neurological development

10.1101/714154 ◽

2019 ◽

Author(s):

Stefania Pacini ◽

Marco Ruggiero

Keyword(s):

Dna Sequences ◽

Bovine Milk ◽

Fermented Milk ◽

Open Reading Frames ◽

Neurological Development ◽

Putative Role ◽

Biological Entities ◽

Reading Frames

AbstractBacteriophages (phages), Earth’s most numerous biological entities, are natural constituents of alimentary matrices; in this study we describe the characterization of phage populations in a product obtained by fermentation of bovine milk and colostrum. Such characterizations were achieved using a microarray consisting of a chip covered in short DNA sequences that are specific to certain target organisms for a total of approximately 12,000 species. The only viruses evidenced by the array belonged to Siphoviridae, the largest phage family that targets bacteria and archea. The array yielded 27 iterations corresponding to a unique target. We discuss the putative role of some open reading frames of these phages in conferring health-supporting properties with particular reference to cells signaling and neurological development. We also describe the in vitro interaction of this fermented product with alpha-N-acetylgalactosaminidase, an enzyme whose activity in serum is elevated in neurodevelopmental disorders.

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Genetic Basis for Lipopolysaccharide O-Antigen Biosynthesis in Bordetellae

Infection and Immunity ◽

10.1128/iai.67.8.3763-3767.1999 ◽

1999 ◽

Vol 67 (8) ◽

pp. 3763-3767 ◽

Cited By ~ 64

Author(s):

Andrew Preston ◽

Andrew G. Allen ◽

Joanna Cadisch ◽

Richard Thomas ◽

Kim Stevens ◽

...

Keyword(s):

Insertion Sequence ◽

Genetic Basis ◽

Genetic Locus ◽

Bordetella Bronchiseptica ◽

Open Reading Frames ◽

Bordetella Parapertussis ◽

O Antigen ◽

Surface Polysaccharide ◽

Reading Frames

ABSTRACT Bordetella bronchiseptica and Bordetella parapertussis express a surface polysaccharide, attached to a lipopolysaccharide, which has been called O antigen. This structure is absent from Bordetella pertussis. We report the identification of a large genetic locus in B. bronchiseptica and B. parapertussis that is required for O-antigen biosynthesis. The locus is replaced by an insertion sequence in B. pertussis, explaining the lack of O-antigen biosynthesis in this species. The DNA sequence of the B. bronchiseptica locus has been determined and the presence of 21 open reading frames has been revealed. We have ascribed putative functions to many of these open reading frames based on database searches. Mutations in the locus in B. bronchiseptica andB. parapertussis prevent O-antigen biosynthesis and provide tools for the study of the role of O antigen in infections caused by these bacteria.

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Emerging role of long noncoding RNA-encoded micropeptides in cancer

Cancer Cell International ◽

10.1186/s12935-020-01589-x ◽

2020 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Mujie Ye ◽

Jingjing Zhang ◽

Meng Wei ◽

Baihui Liu ◽

Kuiran Dong

Keyword(s):

Noncoding Rna ◽

Cancer Metabolism ◽

Chain Complex ◽

Ribosome Profiling ◽

Open Reading Frames ◽

Clinical Value ◽

Anti Cancer ◽

Nascent Chain ◽

Reading Frames

Abstract Increasing evidence has indicated that long noncoding RNAs (lncRNAs) play various important roles in the development of cancers. The widespread applications of ribosome profiling and ribosome nascent chain complex sequencing revealed that some short open reading frames of lncRNAs have micropeptide-coding potential. The resulting micropeptides have been shown to participate in N6-methyladenosine modification, tumor angiogenesis, cancer metabolism, and signal transduction. This review summarizes current information regarding the reported roles of lncRNA-encoded micropeptides in cancer, and explores the potential clinical value of these micropeptides in the development of anti-cancer drugs and prognostic tumor biomarkers.

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