In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis

Corynebacterium pseudotuberculosis is a pathogen of veterinary relevance diseases, being divided into two biovars: equi and ovis; causing ulcerative lymphangitis and caseous lymphadenitis, respectively. The isolation and sequencing of C. pseudotuberculosis biovar ovis strains in the Northern and Northeastern regions of Brazil exhibited the emergence of this pathogen, which causes economic losses to small ruminant producers, and condemnation of carcasses and skins of animals. Through the pan-genomic approach, it is possible to determine and analyze genes that are shared by all strains of a species—the core genome. However, many of these genes do not have any predicted function, being characterized as hypothetical proteins (HP). In this study, we considered 32 C. pseudotuberculosis biovar ovis genomes for the pan-genomic analysis, where were identified 172 HP present in a core genome composed by 1255 genes. We are able to functionally annotate 80 sequences previously characterized as HP through the identification of structural features as conserved domains and families. Furthermore, we analyzed the physicochemical properties, subcellular localization and molecular function. Additionally, through RNA-seq data, we investigated the differential gene expression of the annotated HP. Genes inserted in pathogenicity islands had their virulence potential evaluated. Also, we have analyzed the existence of functional associations for their products based on protein–protein interaction networks, and perform the structural prediction of three targets. Due to the integration of different strategies, this study can underlie deeper in vitro researches in the characterization of these HP and the search for new solutions for combat this pathogen.

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Genomic Analysis of Curtobacterium Flaccumfaciens Reveals the Differences Between Pathogenic and Nonpathogenic Strains

10.21203/rs.3.rs-335330/v1 ◽

2021 ◽

Author(s):

Qingde Li ◽

Lianjun Sun

Keyword(s):

Core Genome ◽

Genomic Analysis ◽

Pectate Lyase ◽

Economic Losses ◽

Positive Bacterium ◽

Citrate Cycle ◽

The Core ◽

Genomic Level ◽

Genes Encoding ◽

Genome Phylogeny

Abstract Purpose Curtobacterium flaccumfaciens is a Gram-positive bacterium which has been isolated from different plants and abiotic environment. Curtobacterium. flaccumfaciens pv. flaccumfaciens (Cff) is a pathogenic bacterium that infects legume, which is causing great economic losses. At the genomic level, the metabolic and phylogenetic characteristics, and differences in pathogenicity between pathogenic and nonpathogenic C. flaccumfaciens strains have not been analyzed in detail. Methods Therefore, in order to discuss the differences in genome, phylogeny, gene function and mobile genetic elements between pathogenic and nonpathogenic strains, pangenomics and comparative genomics were used in this study to analyze 12 C. flaccumfaciens strains. Result The pangenome of C. flaccumfaciens is open. Phylogenetic analysis showed that there was no correlation between the phylogeny and pathogenicity of C. flaccumfaciens. KAAS annotation of the core genome shows that the citrate cycle was incomplete. In addition, gene islands analysis of the three pathogenicity-related genes encoding for pectate lyase, serine protease and cellulases showed that they only existed in the Cffs and LMG3645 strains. LMG3645 might be a pathogenic strain. Conclusion This study clearly and reliably revealed the differences between the pathogenic and nonpathogenic strains of C. flaccumfaciens at the genomic level, and paves the way for further research on its pathogenicity.

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First Steps in the Analysis of Prokaryotic Pan-Genomes

Bioinformatics and Biology Insights ◽

10.1177/1177932220938064 ◽

2020 ◽

Vol 14 ◽

pp. 117793222093806

Author(s):

Sávio Souza Costa ◽

Luís Carlos Guimarães ◽

Artur Silva ◽

Siomar Castro Soares ◽

Rafael Azevedo Baraúna

Keyword(s):

Genome Analysis ◽

Core Genome ◽

Bacterial Species ◽

Genomic Analysis ◽

Gene Families ◽

Specific Group ◽

The Core ◽

Pan Genome ◽

Research Areas ◽

Key Concepts

Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open pan-genome, the number of gene families will continuously increase with the addition of new genomes to the analysis, while in a closed pan-genome, the number of gene families will not increase considerably. The first step of a pan-genome analysis is the homogenization of genome annotation. The same software should be used to annotate genomes, such as GeneMark or RAST. Subsequently, several software are used to calculate the pan-genome such as BPGA, GET_HOMOLOGUES, PGAP, among others. This review presents all these initial steps for those who want to perform a pan-genome analysis, explaining key concepts of the area. Furthermore, we present the pan-genomic analysis of 9 bacterial species. These are the species with the highest number of genomes deposited in GenBank. We also show the influence of the identity and coverage parameters on the prediction of orthologous and paralogous genes. Finally, we cite the perspectives of several research areas where pan-genome analysis can be used to answer important issues.

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Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains

BMC Genomics ◽

10.1186/s12864-020-07263-w ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Eva Wagner ◽

Andreas Zaiser ◽

Rebekka Leitner ◽

Narciso M. Quijada ◽

Nadja Pracser ◽

...

Keyword(s):

Food Processing ◽

Genomic Analysis ◽

Comparative Genomic ◽

Specific Sequence ◽

Equal Distribution ◽

Genetic Traits ◽

Virulence Potential ◽

Genetic Features ◽

Source Category

Abstract Background Listeria (L.) monocytogenes strains show a high diversity regarding stress tolerance and virulence potential. Genome studies have mainly focused on specific sequence types (STs) predominantly associated with either food or human listeriosis. This study focused on the prevalent ST155, showing equal distribution among clinical and food isolates. We evaluated the virulence potential of 20 ST155 strains and performed comparative genomic analysis of 130 ST155 strains isolated from food, food processing environments and human listeriosis cases in different countries and years. Results The in vitro virulence assays using human intestinal epithelial Caco2 and hepatocytic HEPG2 cells showed an impaired virulence phenotype for six of the 20 selected ST155 strains. Genome analysis revealed no distinct clustering of strains from the same source category (food, food processing environment, and clinical isolates). All strains harbored an intact inlA and inlB locus, except four strains, which had an internal deletion in the inlA gene. All strains harbored LIPI-1, but prfA was present in a longer variant in six strains, all showing impaired virulence. The longer PrfA variant resulted in lower expression of inlA, inlB, and prfA, and no expression of hly and actA. Regarding stress-related gene content, SSI-1 was present, whereas qacH was absent in all strains. 34.6% of the strains harbored a plasmid. All but one ST155 plasmids showed high conservation and harbored cadA2, bcrABC, and a triphenylmethane reductase. Conclusions This study contributes to an enhanced understanding of L. monocytogenes ST155 strains, being equally distributed among isolates from humans, food, and food processing environments. The conservation of the present genetic traits and the absence of unique inherent genetic features makes these types of STs especially interesting since they are apparently equally adapted to the conditions in food processing environments, as well as in food as to the human host environment. However, a ST155-specific mutation resulting in a longer PrfA variant impaired the virulence potential of several ST155 strains.

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PANINI: Pangenome Neighbor Identification for Bacterial Populations

10.1101/174409 ◽

2017 ◽

Cited By ~ 2

Author(s):

Khalil Abudahab ◽

Joaquín M. Prada ◽

Zhirong Yang ◽

Stephen D. Bentley ◽

Nicholas J. Croucher ◽

...

Keyword(s):

Machine Learning ◽

Core Genome ◽

Population Genomics ◽

Genomic Analysis ◽

Diverse Populations ◽

Data Set ◽

Bacterial Populations ◽

Accessory Genome ◽

The Core ◽

Link Type

ABSTRACTThe standard workhorse for genomic analysis of the evolution of bacterial populations is phylogenetic modelling of mutations in the core genome. However, in the current era of population genomics, a notable amount of information about evolutionary and transmission processes in diverse populations can be lost unless the accessory genome is also taken into consideration. Here we introduce PANINI, a computationally scalable method for identifying the neighbours for each isolate in a data set using unsupervised machine learning with stochastic neighbour embedding. PANINI is browser-based and integrates with the Microreact platform for rapid online visualisation and exploration of both core and accessory genome evolutionary signals together with relevant epidemiological, geographic, temporal and other metadata. Several case studies with single-and multi-clone pneumococcal populations are presented to demonstrate ability to identify biologically important signals from gene content data. PANINI is available at http://panini.wgsa.net/ and code at http://gitlab.com/cgps/panini

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Evidence of Extensive Homologous Recombination in the Core Genome ofRickettsia

Comparative and Functional Genomics ◽

10.1155/2009/510270 ◽

2009 ◽

Vol 2009 ◽

pp. 1-5 ◽

Cited By ~ 2

Author(s):

Jinyu Wu ◽

Tonghai Yu ◽

Qiyu Bao ◽

Fangqing Zhao

Keyword(s):

Homologous Recombination ◽

Pathogenic Bacteria ◽

Core Genome ◽

Phylogenetic Network ◽

Genomic Analysis ◽

Intracellular Bacteria ◽

The Core ◽

Evolutionary Genomic ◽

The Impact

The important role of homologous recombination has been extensively demonstrated to be fundamental for genetic variation in bacterial genomes. In contrast to extracellular or facultative intracellular bacteria, obligate intracellular bacteria are considered to be less prone to recombination, especially for their core genomes. InRickettsia, only antigen-related genes were identified to have experienced homologous recombination. In this study, we employed evolutionary genomic approaches to investigate the impact of recombination on the core genome ofRickettsia. Phylogenetic network and phylogenetic compatibility matrix analyses are clearly consistent with the hypothesis that recombination has occurred frequently duringRickettsiaevolution. 28% ofRickettsiacore genes (194 out of 690) are found to present the evidence of recombination under four independent statistical methods. Further functional classification shows that these recombination events occur across all functional categories, with a significant overrepresentation in the cell wall/membrane/envelope biogenesis, which may provide a molecular basis for the parasite adaptation to host immunity. This evolutionary genomic analysis provides insight into the substantial role of recombination in the evolution of the intracellular pathogenic bacteriaRickettsia.

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Prediction of new vaccine targets in the core genome of Corynebacterium pseudotuberculosis through omics approaches and reverse vaccinology

Gene ◽

10.1016/j.gene.2019.03.049 ◽

2019 ◽

Vol 702 ◽

pp. 36-45 ◽

Cited By ~ 5

Author(s):

Carlos Leonardo Araújo ◽

Jorianne Alves ◽

Wylerson Nogueira ◽

Lino César Pereira ◽

Anne Cybelle Gomide ◽

...

Keyword(s):

Core Genome ◽

Reverse Vaccinology ◽

Corynebacterium Pseudotuberculosis ◽

The Core

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Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526T and Zobellia laminariae KMM 3676T

Marine Drugs ◽

10.3390/md17120661 ◽

2019 ◽

Vol 17 (12) ◽

pp. 661 ◽

Cited By ~ 5

Author(s):

Nadezhda Chernysheva ◽

Evgeniya Bystritskaya ◽

Anna Stenkova ◽

Ilya Golovkin ◽

Olga Nedashkovskaya ◽

...

Keyword(s):

Comparative Genomics ◽

Core Genome ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Active Enzyme ◽

Comparative Genomic ◽

The Core ◽

Pan Genome ◽

Carbohydrate Active Enzyme ◽

Pharmaceutical Industries

We obtained two novel draft genomes of type Zobellia strains with estimated genome sizes of 5.14 Mb for Z. amurskyensis KMM 3526Т and 5.16 Mb for Z. laminariae KMM 3676Т. Comparative genomic analysis has been carried out between obtained and known genomes of Zobellia representatives. The pan-genome of Zobellia genus is composed of 4853 orthologous clusters and the core genome was estimated at 2963 clusters. The genus CAZome was represented by 775 GHs classified into 62 families, 297 GTs of 16 families, 100 PLs of 13 families, 112 CEs of 13 families, 186 CBMs of 18 families and 42 AAs of six families. A closer inspection of the carbohydrate-active enzyme (CAZyme) genomic repertoires revealed members of new putative subfamilies of GH16 and GH117, which can be biotechnologically promising for production of oligosaccharides and rare monomers with different bioactivities. We analyzed AA3s, among them putative FAD-dependent glycoside oxidoreductases (FAD-GOs) being of particular interest as promising biocatalysts for glycoside deglycosylation in food and pharmaceutical industries.

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Some Structural Features of Metaphase Chromosomes of Mice and Men

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100060969 ◽

1967 ◽

Vol 25 ◽

pp. 190-191

Author(s):

Godfrey C. Hoskins ◽

Betty B. Hoskins

Keyword(s):

Electron Microscopy ◽

Electron Micrographs ◽

Structural Features ◽

Metaphase Chromosomes ◽

The Future ◽

Of Mice And Men ◽

Mouse Cells ◽

Human And Mouse

Metaphase chromosomes from human and mouse cells in vitro are isolated by micrurgy, fixed, and placed on grids for electron microscopy. Interpretations of electron micrographs by current methods indicate the following structural features.Chromosomal spindle fibrils about 200Å thick form fascicles about 600Å thick, wrapped by dense spiraling fibrils (DSF) less than 100Å thick as they near the kinomere. Such a fascicle joins the future daughter kinomere of each metaphase chromatid with those of adjacent non-homologous chromatids to either side. Thus, four fascicles (SF, 1-4) attach to each metaphase kinomere (K). It is thought that fascicles extend from the kinomere poleward, fray out to let chromosomal fibrils act as traction fibrils against polar fibrils, then regroup to join the adjacent kinomere.

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Vibrio harveyi virulence gene expression in vitro and in vivo during infection in black tiger shrimp Penaeus monodon

Diseases of Aquatic Organisms ◽

10.3354/dao03475 ◽

2020 ◽

Vol 139 ◽

pp. 153-160

Author(s):

S Peeralil ◽

TC Joseph ◽

V Murugadas ◽

PG Akhilnath ◽

VN Sreejith ◽

...

Keyword(s):

Gene Expression ◽

Virulence Genes ◽

Vibrio Harveyi ◽

Penaeus Monodon ◽

Challenge Test ◽

Virulence Gene ◽

Economic Losses ◽

Virulence Gene Expression

Luminescent Vibrio harveyi is common in sea and estuarine waters. It produces several virulence factors and negatively affects larval penaeid shrimp in hatcheries, resulting in severe economic losses to shrimp aquaculture. Although V. harveyi is an important pathogen of shrimp, its pathogenicity mechanisms have yet to be completely elucidated. In the present study, isolates of V. harveyi were isolated and characterized from diseased Penaeus monodon postlarvae from hatcheries in Kerala, India, from September to December 2016. All 23 tested isolates were positive for lipase, phospholipase, caseinase, gelatinase and chitinase activity, and 3 of the isolates (MFB32, MFB71 and MFB68) showed potential for significant biofilm formation. Based on the presence of virulence genes, the isolates of V. harveyi were grouped into 6 genotypes, predominated by vhpA+ flaB+ ser+ vhh1- luxR+ vopD- vcrD+ vscN-. One isolate from each genotype was randomly selected for in vivo virulence experiments, and the LD50 ranged from 1.7 ± 0.5 × 103 to 4.1 ± 0.1 × 105 CFU ml-1. The expression of genes during the infection in postlarvae was high in 2 of the isolates (MFB12 and MFB32), consistent with the result of the challenge test. However, in MFB19, even though all genes tested were present, their expression level was very low and likely contributed to its lack of virulence. Because of the significant variation in gene expression, the presence of virulence genes alone cannot be used as a marker for pathogenicity of V. harveyi.

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In-Vitro Effects of Ricinus Communis Seed Kernel Extract On Some Antioxidant And Hydrolytic Enzymes In Nymph And Adult Zonocerus Variegatus (Grasshopper)

Pan African Journal of Life Sciences ◽

10.36108/pajols/9102/30(0130) ◽

2019 ◽

Vol 3 (1) ◽

pp. 129-137

Author(s):

Gbadebo E . Adeleke ◽

Olaniyi T. Adedosu ◽

Rachael O. Adeyi ◽

John O. Fatoki

Keyword(s):

Ricinus Communis ◽

Hydrolytic Enzymes ◽

Crude Enzyme ◽

Economic Losses ◽

Seed Kernel ◽

Zonocerus Variegatus ◽

Sod Activity ◽

Enzyme Preparations ◽

In Vitro Effects

Background: Many plants have been identified for their insecticidal properties as alternatives to synthetic ones, which are toxic to untargeted organisms and environment. Ricinus communis (Castor) has been re-ported to exhibit insecticidal properties against insect pests. Zonocerus variegatus (Grasshopper) is a notable pest of several crops, and has been linked with great economic losses to farmers. The present study investigates the in-vitro toxicity of R. communis seed kernel extract (RCSKE) on the activities of selected antioxidant and hydrolytic enzymes in nymph and adult Zonocerus variegatus (Grasshopper), using cypermethrin (CYPER-M) and chlorpyrifos (CPF) as standard conventional pesticides. Methods: Seed kernel of Ricinus communis (Castor) was subjected to acidified aqueous extraction to obtain the extract (RCSKE). Crude enzyme preparations were obtained from nymph and adult Z. variegatus grass-hoppers. The in-vitro effects of different concentrations (15, 30, 45, 60, 75, 90 and 105μg/ml) each of RCSKE, CYPER-M and CPF on the activities of superoxide dismutase (SOD), catalase (CAT), acetylcholinesterase (AChE) and carboxylesterase (CES) in crude enzyme preparations were estimated spectrophotometrically. The level of statistical significance was 0.05. Results: The RCSKE significantly reduced the in-vitro SOD activity (p < 0.05) in nymph Z. variegatus at all the concentrations, whereas both CYPER-M and CPF significantly reduced the activity only at certain concentrations. The CAT activity in the nymph was significantly decreased by RCSKE and CPF at all the concentrations, but CYPER-M decreased it only at certain concentrations. In adult Z. variegatus, SOD activity was not significantly affected (p > 0.05), while CAT activity was significantly increased (p < 0.05) by the three agents at all the concentrations. The AChE and CES activities in the nymph were significantly reduced by RCSKE, CYPER-M and CPF at all the concentrations. The RCSKE and CPF significantly increased the CES activity, while CYPER-M caused a significant decrease in the activity in adult Z. variegatus. Conclusion: The seed kernel extract of Ricinus communis is an effective pesticidal agent and hence, it could be a source of biopesticide alternative with greater potential than cypermethrin and chlorpyrifos. In addition, the antioxidant, acetylcholinesterase and carboxylesterase enzymes in the nymphs of Z. variegatus grasshoppers are more susceptible to the effect of the extract than in the adult grasshoppers.

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