Subtelomeric regions and a repeat-rich chromosome harbor multicopy effector gene clusters with variable conservation in multiple plant pathogenic Colletotrichum species

AbstractMembers of the Colletotrichum gloeosporioides species complex are causal agents of anthracnose in a wide range of commercially important plants. To provide an in-depth overview of its diversity, we sequenced the genomes of fungi belonging to this group, including multiple strains of C. fructicola (Cf) and C. siamense (Cs), as well as representatives of three previously unsequenced species, C. aenigma (Ca), C. tropicale and C. viniferum. Comparisons between multiple Cf and Cs strains led to the identification of accessory regions that show variable conservation in both lineages. These accessory regions encode effector candidate genes, including homologs of previously characterized effectors, organized in clusters of conserved synteny with copy number variations in different strains of Cf, Cs and Ca. Analysis of highly contiguous assemblies of Cf, Cs and Ca strains revealed the association of such accessory effector gene clusters with subtelomeric regions and repeat-rich minichromosomes and provided evidence of gene transfer between these two genomic compartments. In addition, expression analysis indicated that paralogs associated with clusters of conserved synteny showed a tendency for correlated gene expression. These data highlight the importance of subtelomeric regions and repeat-rich chromosomes to the genome plasticity of Colletotrichum fungi.

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Telomeres and a repeat‐rich chromosome encode effector gene clusters in plant pathogenic Colletotrichum fungi

Environmental Microbiology ◽

10.1111/1462-2920.15490 ◽

2021 ◽

Author(s):

Pamela Gan ◽

Ryoko Hiroyama ◽

Ayako Tsushima ◽

Sachiko Masuda ◽

Arisa Shibata ◽

...

Keyword(s):

Gene Clusters ◽

Effector Gene

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Biodiversity of Secondary Metabolites Compounds Isolated from Phylum Actinobacteria and Its Therapeutic Applications

Molecules ◽

10.3390/molecules26154504 ◽

2021 ◽

Vol 26 (15) ◽

pp. 4504

Author(s):

Muhanna Al-shaibani ◽

Radin Maya Saphira Radin Mohamed ◽

Nik Sidik ◽

Hesham Enshasy ◽

Adel Al-Gheethi ◽

...

Keyword(s):

Secondary Metabolites ◽

Bioactive Compounds ◽

Extreme Environments ◽

Software Tool ◽

Gene Clusters ◽

Well Being ◽

Bioactive Substances ◽

Diverse Range ◽

Wide Range ◽

Potential Applications

The current review aims to summarise the biodiversity and biosynthesis of novel secondary metabolites compounds, of the phylum Actinobacteria and the diverse range of secondary metabolites produced that vary depending on its ecological environments they inhabit. Actinobacteria creates a wide range of bioactive substances that can be of great value to public health and the pharmaceutical industry. The literature analysis process for this review was conducted using the VOSviewer software tool to visualise the bibliometric networks of the most relevant databases from the Scopus database in the period between 2010 and 22 March 2021. Screening and exploring the available literature relating to the extreme environments and ecosystems that Actinobacteria inhabit aims to identify new strains of this major microorganism class, producing unique novel bioactive compounds. The knowledge gained from these studies is intended to encourage scientists in the natural product discovery field to identify and characterise novel strains containing various bioactive gene clusters with potential clinical applications. It is evident that Actinobacteria adapted to survive in extreme environments represent an important source of a wide range of bioactive compounds. Actinobacteria have a large number of secondary metabolite biosynthetic gene clusters. They can synthesise thousands of subordinate metabolites with different biological actions such as anti-bacterial, anti-parasitic, anti-fungal, anti-virus, anti-cancer and growth-promoting compounds. These are highly significant economically due to their potential applications in the food, nutrition and health industries and thus support our communities’ well-being.

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Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.013528 ◽

2020 ◽

Vol 295 (44) ◽

pp. 14826-14839

Author(s):

Serina L. Robinson ◽

Barbara R. Terlouw ◽

Megan D. Smith ◽

Sacha J. Pidot ◽

Timothy P. Stinear ◽

...

Keyword(s):

Machine Learning ◽

Natural Product ◽

Global Analysis ◽

Gene Clusters ◽

Divergent Evolution ◽

Acid Activation ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Predictive Tool ◽

Wide Range

Enzymes that cleave ATP to activate carboxylic acids play essential roles in primary and secondary metabolism in all domains of life. Class I adenylate-forming enzymes share a conserved structural fold but act on a wide range of substrates to catalyze reactions involved in bioluminescence, nonribosomal peptide biosynthesis, fatty acid activation, and β-lactone formation. Despite their metabolic importance, the substrates and functions of the vast majority of adenylate-forming enzymes are unknown without tools available to accurately predict them. Given the crucial roles of adenylate-forming enzymes in biosynthesis, this also severely limits our ability to predict natural product structures from biosynthetic gene clusters. Here we used machine learning to predict adenylate-forming enzyme function and substrate specificity from protein sequences. We built a web-based predictive tool and used it to comprehensively map the biochemical diversity of adenylate-forming enzymes across >50,000 candidate biosynthetic gene clusters in bacterial, fungal, and plant genomes. Ancestral phylogenetic reconstruction and sequence similarity networking of enzymes from these clusters suggested divergent evolution of the adenylate-forming superfamily from a core enzyme scaffold most related to contemporary CoA ligases toward more specialized functions including β-lactone synthetases. Our classifier predicted β-lactone synthetases in uncharacterized biosynthetic gene clusters conserved in >90 different strains of Nocardia. To test our prediction, we purified a candidate β-lactone synthetase from Nocardia brasiliensis and reconstituted the biosynthetic pathway in vitro to link the gene cluster to the β-lactone natural product, nocardiolactone. We anticipate that our machine learning approach will aid in functional classification of enzymes and advance natural product discovery.

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Additional Og-Typing PCR Techniques Targeting Escherichia coli-Novel and Shigella-Unique O-Antigen Biosynthesis Gene Clusters

Journal of Clinical Microbiology ◽

10.1128/jcm.01493-20 ◽

2020 ◽

Vol 58 (11) ◽

Author(s):

Atsushi Iguchi ◽

Hironobu Nishii ◽

Kazuko Seto ◽

Jiro Mitobe ◽

Kenichi Lee ◽

...

Keyword(s):

Escherichia Coli ◽

Strong Association ◽

Gene Clusters ◽

Epidemiological Studies ◽

Content Type ◽

E Coli ◽

O Antigen ◽

Wide Range ◽

Biosynthesis Gene ◽

Almost All

ABSTRACT The O-serogrouping of pathogenic Escherichia coli is a standard method for subtyping strains for epidemiological studies and controls. O-serogroup diversification shows a strong association with the genetic diversity in some O-antigen biosynthesis gene clusters. Through genomic studies, in addition to the types of O-antigen biosynthesis gene clusters (Og-types) from conventional O-serogroup strains, a number of novel Og-types have been found in E. coli isolates. To assist outbreak investigations and surveillance of pathogenic E. coli at inspection institutes, in previous studies, we developed PCR methods that could determine almost all conventional O-serogroups and some novel Og-types. However, there are still many Og-types that may not be determined by simple genetic methods such as PCR. Thus, in the present study, we aimed to develop an additional Og-typing PCR system. Based on the novel Og-types, including OgN32, OgN33, and OgN34, presented in this study, we designed an additional 24 PCR primer pairs targeting 14 novel and 2 diversified E. coli Og-types and 8 Shigella-unique Og-types. Subsequently, we developed 5 new multiplex PCR sets consisting of 33 primers, including the aforementioned 24 primers and 9 primers reported in previous studies. The accuracy and specificity of the PCR system was validated using approximately 260 E. coli and Shigella O-serogroup and Og-type reference strains. The Og-typing PCR system reported here can determine a wide range of Og-types of E. coli and may help epidemiological studies, in addition to the surveillance of pathogenic E. coli.

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Rapid and reliable detection of α-globin copy number variations by quantitative real-time PCR

BMC Hematology ◽

10.1186/2052-1839-14-4 ◽

2014 ◽

Vol 14 (1) ◽

Cited By ~ 21

Author(s):

Runa M Grimholt ◽

Petter Urdal ◽

Olav Klingenberg ◽

Armin P Piehler

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Copy Number ◽

Globin Gene ◽

Copy Number Variations ◽

Globin Genes ◽

Quantitative Real Time Pcr ◽

Human Genetic Disease ◽

Large Deletions ◽

Wide Range

Abstract Background Alpha-thalassemia is the most common human genetic disease worldwide. Copy number variations in the form of deletions of α-globin genes lead to α-thalassemia while duplications of α-globin genes can cause a severe phenotype in β-thalassemia carriers due to accentuation of globin chain imbalance. It is important to have simple and reliable methods to identify unknown or rare deletions and duplications in cases in which thalassemia is suspected but cannot be confirmed by multiplex gap-PCR. Here we describe a copy number variation assay to detect deletions and duplications in the α-globin gene cluster (HBA-CNV). Results Quantitative real-time PCR was performed using four TaqMan® assays which specifically amplify target sequences representing both the α-globin genes, the –α3.7 deletion and the HS-40 region. The copy number for each target was determined by the 2-ΔΔCq method. To validate our method, we compared the HBA-CNV method with traditional gap-PCR in 108 samples from patients referred to our laboratory for hemoglobinopathy evaluation. To determine the robustness of the four assays, we analyzed samples with and without deletions diluted to obtain different DNA concentrations. The HBA-CNV method identified the correct copy numbers in all 108 samples. All four assays showed the correct copy number within a wide range of DNA concentrations (3.2-100 ng/μL), showing that it is a robust and reliable method. By using the method in routine diagnostics of hemoglobinopathies we have also identified several deletions and duplications that are not detected with conventional gap-PCR. Conclusions HBA-CNV is able to detect all known large deletions and duplications affecting the α-globin genes, providing a flexible and simple workflow with rapid and reliable results.

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Cyanobacterial Two-Component Proteins: Structure,Diversity, Distribution, andEvolution

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.00046-05 ◽

2006 ◽

Vol 70 (2) ◽

pp. 472-509 ◽

Cited By ~ 91

Author(s):

Mark K. Ashby ◽

Jean Houmard

Keyword(s):

Regulatory Mechanisms ◽

Genome Plasticity ◽

Cyanobacterial Genome ◽

Response Regulators ◽

Genome Sequences ◽

Histidine Kinases ◽

Physiological Properties ◽

Two Component ◽

Different Strains ◽

Structure Diversity

SUMMARY A survey of the already characterized and potential two-component protein sequences that exist in the nine complete and seven partially annotated cyanobacterial genome sequences available (as of May 2005) showed that the cyanobacteria possess a much larger repertoire of such proteins than most other bacteria. By analysis of the domain structure of the 1,171 potential histidine kinases, response regulators, and hybrid kinases, many various arrangements of about thirty different modules could be distinguished. The number of two-component proteins is related in part to genome size but also to the variety of physiological properties and ecophysiologies of the different strains. Groups of orthologues were defined, only a few of which have representatives with known physiological functions. Based on comparisons with the proposed phylogenetic relationships between the strains, the orthology groups show that (i) a few genes, some of them clustered on the genome, have been conserved by all species, suggesting their very ancient origin and an essential role for the corresponding proteins, and (ii) duplications, fusions, gene losses, insertions, and deletions, as well as domain shuffling, occurred during evolution, leading to the extant repertoire. These mechanisms are put in perspective with the different genetic properties that cyanobacteria have to achieve genome plasticity. This review is designed to serve as a basis for orienting further research aimed at defining the most ancient regulatory mechanisms and understanding how evolution worked to select and keep the most appropriate systems for cyanobacteria to develop in the quite different environments that they have successfully colonized.

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Autism spectrum mixed neurodevelopmental disorder associated with 6q27 deletion and multiple copies within 20q11.23: a case study

Advances in Mental Health and Intellectual Disabilities ◽

10.1108/amhid-07-2013-0050 ◽

2014 ◽

Vol 8 (3) ◽

pp. 210-215

Author(s):

Stephen Hopkins ◽

Jeremy Turk ◽

Adeniyi Daramola ◽

Marinos Kyriakopoulos

Keyword(s):

Neurodevelopmental Disorder ◽

Autism Spectrum ◽

Copy Number Variations ◽

Comparative Genomic Hybridisation ◽

Comparative Genomic ◽

Content Type ◽

Effective Strategies ◽

Wide Range ◽

Multiple Copies

Purpose – Copy Number Variations (CNVs) are not infrequently observed in aberrant neurodevelopment. CNVs can alter gene expression and have been linked to a wide range of neuropsychiatric disorders. The purpose of this case study is to report the association of CNVs with a mixed neurodevelopmental disorder. Design/methodology/approach – Array-Comparative Genomic Hybridisation analysis was carried out in a case of an eight-year-old boy presenting with a mixed neurodevelopmental disorder including autism spectrum disorder, intellectual disability, tic disorder, anxiety and severe aggression. The child's parents also underwent the same investigation. Findings – A 6q27 deletion and multiple copies within 20q11.23 were identified. The boy's father shared the 6q27 deletion and his mother also had multiple copies within 20q11.23. Originality/value – This is the first report linking the combination of 6p27 and 20q11 CNVs with a mixed neurodevelopmental presentation. Identifying CNVs that may underlie aberrant neurodevelopment is likely to assist in unravelling the aetiology of neurodevelopmental and psychiatric disorders and lead to more effective strategies for their characterisation and management.

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Genetic Variants of Alcohol Metabolizing Enzymes and Alcohol-Related Liver Cirrhosis Risk

Journal of Personalized Medicine ◽

10.3390/jpm11050409 ◽

2021 ◽

Vol 11 (5) ◽

pp. 409

Author(s):

Pedro Ayuso ◽

Elena García-Martín ◽

José A. Cornejo-García ◽

José A. G. Agúndez ◽

José María Ladero

Keyword(s):

Liver Cirrhosis ◽

Statistical Significance ◽

Alcohol Exposure ◽

Active Role ◽

Copy Number Variations ◽

Ethanol Metabolism ◽

Public Health Issue ◽

Excessive Alcohol Consumption ◽

Cyp2e1 Gene ◽

Wide Range

Alcohol-related liver disease (ARLD) is a major public health issue caused by excessive alcohol consumption. ARLD encompasses a wide range of chronic liver lesions, alcohol-related liver cirrhosis being the most severe and harmful state. Variations in the genes encoding the enzymes, which play an active role in ethanol metabolism, might influence alcohol exposure and hence be considered as risk factors of developing cirrhosis. We conducted a case-control study in which 164 alcohol-related liver cirrhosis patients and 272 healthy controls were genotyped for the following functional single nucleotide variations (SNVs): ADH1B gene, rs1229984, rs1041969, rs6413413, and rs2066702; ADH1C gene, rs35385902, rs283413, rs34195308, rs1693482, and rs35719513; CYP2E1 gene, rs3813867. Furthermore, copy number variations (CNVs) for ADH1A, ADH1B, ADH1C, and CYP2E1 genes were analyzed. A significant protective association with the risk of developing alcohol-related liver cirrhosis was observed between the mutant alleles of SNVs ADH1B rs1229984 (Pcvalue = 0.037) and ADH1C rs283413 (Pc value = 0.037). We identified CNVs in all genes studied, ADH1A gene deletions being more common in alcohol-related liver cirrhosis patients than in control subjects, although the association lost statistical significance after multivariate analyses. Our findings support that susceptibility to alcohol-related liver cirrhosis is related to variations in alcohol metabolism genes.

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Studies on lipopolysaccharides of Proteus

Canadian Journal of Microbiology ◽

10.1139/m71-221 ◽

1971 ◽

Vol 17 (11) ◽

pp. 1385-1394 ◽

Cited By ~ 8

Author(s):

B. A. Dmitriev ◽

N. A. Hinton ◽

R. W. Lowe ◽

J. K. N. Jones

Keyword(s):

Molecular Weight ◽

Acetic Acid ◽

Weight Fraction ◽

Low Molecular Weight ◽

The Core ◽

Wide Range ◽

Homologous Antiserum ◽

Main Components ◽

Different Strains ◽

Second Peak

The polysaccharide moieties of the lipopolysaccharides of serotyped strains of Proteus have been examined. The strains were selected to provide a wide range of serotypes. The primary acetic acid extracts of different strains of Proteus were fractionated on Sephadex G-50 and yielded three main components: a peak (I), which was composed mainly of polysaccharide; a second peak (II), the core polysaccharide, which contained heptose and phosphate; and a third component (III), which corresponded to a low molecular weight fraction and contained KDO and phosphate as well as other components. Peak I was not encountered in rough strains of Proteus. The chemical composition of the peaks obtained for S, SR, and R strains is discussed in relation to their agglutinating ability to homologous antiserum.

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Analysis of Coinfections with A/H1N1 Strain Variants among Pigs in Poland by Multitemperature Single-Strand Conformational Polymorphism

BioMed Research International ◽

10.1155/2015/535908 ◽

2015 ◽

Vol 2015 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Krzysztof Lepek ◽

Beata Pajak ◽

Lukasz Rabalski ◽

Kinga Urbaniak ◽

Krzysztof Kucharczyk ◽

...

Keyword(s):

Influenza A ◽

Cost Effective ◽

Single Strand ◽

Surveillance Systems ◽

Monitoring And Control ◽

Influenza A Viruses ◽

Single Strand Conformational Polymorphism ◽

Conformational Polymorphism ◽

Wide Range ◽

Different Strains

Monitoring and control of infections are key parts of surveillance systems and epidemiological risk prevention. In the case of influenza A viruses (IAVs), which show high variability, a wide range of hosts, and a potential of reassortment between different strains, it is essential to study not only people, but also animals living in the immediate surroundings. If understated, the animals might become a source of newly formed infectious strains with a pandemic potential. Special attention should be focused on pigs, because of the receptors specific for virus strains originating from different species, localized in their respiratory tract. Pigs are prone to mixed infections and may constitute a reservoir of potentially dangerous IAV strains resulting from genetic reassortment. It has been reported that a quadruple reassortant, A(H1N1)pdm09, can be easily transmitted from humans to pigs and serve as a donor of genetic segments for new strains capable of infecting humans. Therefore, it is highly desirable to develop a simple, cost-effective, and rapid method for evaluation of IAV genetic variability. We describe a method based on multitemperature single-strand conformational polymorphism (MSSCP), using a fragment of the hemagglutinin (HA) gene, for detection of coinfections and differentiation of genetic variants of the virus, difficult to identify by conventional diagnostic.

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