Genes encoding intrinsic disorder in Eukaryota have high GC content

Abstract Until recently, research has focused on Clostridium perfringens in clinical settings without considering environmental isolates. In this study, environmental genomes were used to investigate possible antibiotic resistance and the presence of virulence traits in C. perfringens strains from raw surface water. In silico assembly of three C. perfringens strains, DNA generated almost complete genomes setting their length ranging from 3.4 to 3.6 Mbp with GC content of 28.18%. An average of 3,175 open reading frames was identified, with the majority associated with carbohydrate and protein metabolisms. The genomes harboured several antibiotic resistance genes for glycopeptides, macrolide–lincosamide–streptogramin B, β-lactam, trimethoprim, tetracycline and aminoglycosides and also the presence of several genes encoding for polypeptides and multidrug resistance efflux pumps and 35 virulence genes. Some of these encode for haemolysins, sialidase, hyaluronidase, collagenase, perfringolysin O and phospholipase C. All three genomes contained sequences indicating phage, antibiotic resistance and pathogenic islands integration sites. A genomic comparison of these three strains confirmed high similarity and shared core genes with clinical C. perfringens strains, highlighting their health security risks. This study provides a genomic insight into the potential pathogenicity of C. perfringens present in the environment and emphasises the importance of monitoring this niche in the future.

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Polycyclic aromatic hydrocarbon degrading gene islands in five pyrene-degrading Mycobacterium isolates from different geographic locations

Canadian Journal of Microbiology ◽

10.1139/w11-093 ◽

2012 ◽

Vol 58 (1) ◽

pp. 102-111 ◽

Cited By ~ 9

Author(s):

Chun Zhang ◽

Anne J. Anderson

Keyword(s):

Polycyclic Aromatic Hydrocarbon ◽

Aromatic Hydrocarbon ◽

Gc Content ◽

The United States ◽

Pcr Analysis ◽

Transcript Accumulation ◽

Circular Plasmid ◽

Genes Encoding ◽

Polycyclic Aromatic ◽

Induced Proteins

Mycobacterium sp. strain KMS utilizes pyrene, a high-molecular weight polycyclic aromatic hydrocarbon (PAH), as a sole carbon source. Bioinformatic analysis of the genome of isolate KMS predicted 25 genes with the potential to encode 17 pyrene-induced proteins identified by proteomics; these genes were clustered on both the chromosome and a circular plasmid. RT-PCR analysis of total RNA isolated from KMS cells grown with or without pyrene showed that the presence of pyrene increased the transcript accumulation of 20 of the predicted chromosome- and plasmid-located genes encoding pyrene-induced proteins. The transcribed genes from both the chromosome and a circular plasmid were within larger regions containing genes required for PAH degradation constituting PAH-degrading gene islands. Genes encoding integrases and transposases were found within and outside the PAH-degrading gene islands. The lower GC content of the genes within the gene island (61%–64%) compared with the average genome content (68%) suggested that these mycobacteria initially acquired these genes by horizontal gene transfer. Synteny was detected for the PAH-degrading islands in the genomes of two additional Mycobacterium isolates from the same PAH-polluted site and of two other pyrene-degrading Mycobacterium from different sites in the United States of America. Consequently, the gene islands have been conserved from a common ancestral strain.

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Identifying candidate Aspergillus pathogenicity factors by annotation frequency

BMC Microbiology ◽

10.1186/s12866-020-02031-y ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Kayla K. Pennerman ◽

Guohua Yin ◽

Anthony E. Glenn ◽

Joan W. Bennett

Keyword(s):

Gc Content ◽

Sugar Metabolism ◽

Principal Component ◽

Amino Sugar ◽

Human Immune System ◽

Protein Coding ◽

Functional Annotations ◽

Pathogenicity Factors ◽

Genes Encoding ◽

Effective Use

Abstract Background Members of the genus Aspergillus display a variety of lifestyles, ranging from saprobic to pathogenic on plants and/or animals. Increased genome sequencing of economically important members of the genus permits effective use of “-omics” comparisons between closely related species and strains to identify candidate genes that may contribute to phenotypes of interest, especially relating to pathogenicity. Protein-coding genes were predicted from 216 genomes of 12 Aspergillus species, and the frequencies of various structural aspects (exon count and length, intron count and length, GC content, and codon usage) and functional annotations (InterPro, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes terms) were compared. Results Using principal component analyses, the three sets of functional annotations for each strain were clustered by species. The species clusters appeared to separate by pathogenicity on plants along the first dimensions, which accounted for over 20% of the variance. More annotations for genes encoding pectinases and secondary metabolite biosynthetic enzymes were assigned to phytopathogenic strains from species such as Aspergillus flavus. In contrast, Aspergillus fumigatus strains, which are pathogenic to animals but not plants, were assigned relatively more terms related to phosphate transferases, and carbohydrate and amino-sugar metabolism. Analyses of publicly available RNA-Seq data indicated that one A. fumigatus protein among 17 amino-sugar processing candidates, a hexokinase, was up-regulated during co-culturing with human immune system cells. Conclusion Genes encoding hexokinases and other proteins of interest may be subject to future manipulations to further refine understanding of Aspergillus pathogenicity factors.

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Characterization of Haemophilus parasuis Serovar 2 CL120103, a Moderately Virulent Strain in China

Open Life Sciences ◽

10.1515/biol-2018-0026 ◽

2018 ◽

Vol 13 (1) ◽

pp. 217-226

Author(s):

Yongliang Che ◽

Longbai Wang ◽

Xuemin Wu ◽

Rujing Chen ◽

Chenyan Wang ◽

...

Keyword(s):

Virulence Factors ◽

Genomic Sequence ◽

Virulent Strain ◽

Sequence Similarity ◽

Gc Content ◽

Trna Genes ◽

Haemophilus Parasuis ◽

Protein Coding ◽

Query Cover ◽

Genes Encoding

AbstractHaemophilus parasuisis an important bacterium affecting pigs, causing Glässer’s disease. To further characterize this species, we determined the complete genomic sequence ofH. parasuisCL120103, which was isolated from diseased pigs. The strainH. parasuisCL120103 was identified as serovar 2. The size of the largest scaffold is 2,326,318 bp and contains 145 large contigs, with the N50 contig being 20,573 bp in length. The complete genome ofH. parasuisCL120103 is 2,305,354 bp in length with 39.97% GC content and contains 2227 protein-coding genes, 19 ribosomal rRNA operons and 60 tRNA genes. Sequence similarity of the genome ofH. parasuisCL120103 to the previously sequenced genome ofH. parasuiswas up to 96% and query cover to 86%. Annotation of the genome ofH. parasuisCL120103 identified a number of genes encoding potential virulence factors. These virulence factors are involved in metabolism, adhesion, secretion and LPS biosynthesis. These related genes pave the way to better understand mechanisms underlying metabolic capabilities. The comprehensive genetic and phylogenetic analysis shows thatH. parasuisis closely related toActinobacillus pleuropneumoniaeand provides a foundation for future experimental confirmation of the virulence and pathogen-host interactions inH. parasuis.

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Penicillin resistance in the intestinal spirochaete Brachyspira pilosicoli associated with OXA-136 and OXA-137, two new variants of the class D β-lactamase OXA-63

Journal of Medical Microbiology ◽

10.1099/jmm.0.2008/001552-0 ◽

2008 ◽

Vol 57 (9) ◽

pp. 1122-1128 ◽

Cited By ~ 8

Author(s):

Sheila M. Mortimer-Jones ◽

Nyree D. Phillips ◽

Tom La ◽

Ram Naresh ◽

David J. Hampson

Keyword(s):

Amino Acid ◽

Gc Content ◽

Penicillin Resistance ◽

Predicted Amino Acid Sequence ◽

Gene Encoding ◽

Brachyspira Pilosicoli ◽

Class D ◽

Genes Encoding ◽

Pcr Products ◽

Additional Amino Acid

Penicillin resistance mediated by β-lactamase activity has been reported previously in the anaerobic intestinal spirochaete Brachyspira pilosicoli, and a novel class D β-lactamase (OXA-63) hydrolysing oxacillin was described recently in a resistant human strain from France. In the current study, 18 B. pilosicoli strains from Australia and Papua New Guinea were tested for ampicillin and oxacillin susceptibility, and investigated for the presence of the class D β-lactamase gene bla OXA-63 using PCR. PCR products were amplified from seven human and four porcine strains that were penicillin resistant, but not from seven penicillin-sensitive strains. Sequence analysis of the whole gene amplified from seven of the resistant strains from humans and pigs revealed only minor nucleotide differences among them, but there were significant differences compared with bla OXA-63. The predicted amino acid sequence of the enzyme from all seven strains had the same key structural motifs as the previously reported OXA-63, but two variants with 94–95 % identity with OXA-63 were identified. OXA-136 had an additional amino acid and 12 other consistent amino acid substitutions compared with OXA-63. OXA-137 had the same differences compared with OXA-63 as OXA-136, but had an additional amino acid substitution at position 16. No structures consistent with integrons or transposons were found in the nucleotide sequences in the vicinity of bla OXA-136 in partially sequenced B. pilosicoli strain 95/1000, and the GC content (25.2 mol%) of the gene was similar to that of the whole genome. The gene encoding OXA-136 from B. pilosicoli strain Cof-10 conferred penicillin resistance on Escherichia coli. This study shows that penicillin resistance in human and porcine B. pilosicoli strains from Australia is associated with the production of two variants of OXA-63, and that susceptible strains lack the genes encoding OXA-63 or the variants.

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Evolutionary and genomic comparisons of hybrid uninucleate and nonhybrid Rhizoctonia fungi

Communications Biology ◽

10.1038/s42003-021-01724-y ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Cheng Li ◽

Zejian Guo ◽

Shanyue Zhou ◽

Qingyue Han ◽

Manman Zhang ◽

...

Keyword(s):

Gc Content ◽

Long Terminal Repeat Retrotransposons ◽

Evolutionary Constraint ◽

Severe Damage ◽

Accelerated Evolution ◽

Evolutionary Changes ◽

Genes Encoding ◽

Host Cell Wall ◽

Mating Type Genes ◽

Genome Assemblies

AbstractThe basidiomycetous fungal genus, Rhizoctonia, can cause severe damage to many plants and is composed of multinucleate, binucleate, and uninucleate species differing in pathogenicity. Here we generated chromosome-scale genome assemblies of the three nuclear types of Rhizoctonia isolates. The genomic comparisons revealed that the uninucleate JN strain likely arose by somatic hybridization of two binucleate isolates, and maintained a diploid nucleus. Homeolog gene pairs in the JN genome have experienced both decelerated or accelerated evolution. Homeolog expression dominance occurred between JN subgenomes, in which differentially expressed genes show potentially less evolutionary constraint than the genes without. Analysis of mating-type genes suggested that Rhizoctonia maintains the ancestral tetrapolarity of the Basidiomycota. Long terminal repeat-retrotransposons displayed a reciprocal correlation with the chromosomal GC content in the three chromosome-scale genomes. The more aggressive multinucleate XN strain had more genes encoding enzymes for host cell wall decomposition. These findings demonstrate some evolutionary changes of a recently derived hybrid and in multiple nuclear types of Rhizoctonia.

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Comparative Analysis of Carbohydrate Active Enzymes in the Flammulina velutipes var. lupinicola Genome

Microorganisms ◽

10.3390/microorganisms9010020 ◽

2020 ◽

Vol 9 (1) ◽

pp. 20

Author(s):

Hye-Won Yu ◽

Ji-Hoon Im ◽

Won-Sik Kong ◽

Young-Jin Park

Keyword(s):

De Novo ◽

Animal Feed ◽

Gc Content ◽

Industrial Applications ◽

Glycoside Hydrolases ◽

Flammulina Velutipes ◽

Carbohydrate Binding ◽

Carbohydrate Active Enzymes ◽

Carbohydrate Binding Modules ◽

Genes Encoding

The purpose of this study was to determine the genome sequence of Flammulina velutipes var. lupinicola based on next-generation sequencing (NGS) and to identify the genes encoding carbohydrate-active enzymes (CAZymes) in the genome. The optimal assembly (71 kmer) based on ABySS de novo assembly revealed a total length of 33,223,357 bp (49.53% GC content). A total of 15,337 gene structures were identified in the F.velutipes var. lupinicola genome using ab initio gene prediction method with Funannotate pipeline. Analysis of the orthologs revealed that 11,966 (96.6%) out of the 15,337 predicted genes belonged to the orthogroups and 170 genes were specific for F. velutipes var. lupinicola. CAZymes are divided into six classes: auxiliary activities (AAs), glycosyltransferases (GTs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycoside hydrolases (GHs), and carbohydrate-binding modules (CBMs). A total of 551 genes encoding CAZymes were identified in the F. velutipes var. lupinicola genome by analyzing the dbCAN meta server database (HMMER, Hotpep, and DIAMOND searches), which consisted of 54–95 AAs, 145–188 GHs, 55–73 GTs, 6–19 PLs, 13–59 CEs, and 7–67 CBMs. CAZymes can be widely used to produce bio-based products (food, paper, textiles, animal feed, and biofuels). Therefore, information about the CAZyme repertoire of the F. velutipes var. lupinicola genome will help in understanding the lignocellulosic machinery and in-depth studies will provide opportunities for using this fungus for biotechnological and industrial applications.

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Hybrid genome assembly and gene repertoire of the root endophyte Clitopilus hobsonii QYL-10 (Entolomataceae, Agaricales, Basidiomycetes)

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-11-20-0328-a ◽

2021 ◽

Author(s):

LONG PENG ◽

Xiaoliang Shan ◽

Yuchen Wang ◽

Francis Martin ◽

Rytas Vilgalys ◽

...

Keyword(s):

Genome Assembly ◽

Gc Content ◽

Gene Clusters ◽

Gene Repertoire ◽

Root Tips ◽

Protein Coding ◽

Root Endophyte ◽

Functional Studies ◽

Hybrid Genome ◽

Genes Encoding

Clitopilus hobsonii (Entolomataceae, Agaricales, Basidiomycetes) is a common soil saprotroph. There is also evidence that C. hobsonii can act as a root endophyte benefiting tree growth. Here, we report the genome assembly of C. hobsonii QYL-10 isolated from ectomycorrhizal root tips of Quercus lyrata. The genome size is 36.93 Mb, consisting of 13 contigs (N50=3.3 Mb) with 49.2% GC-content. Of them, 10 contigs approached the length of intact chromosomes, and 3 had telomeres at one end only. BUSCO analysis reported a completeness score of 98.4% using the Basidiomycota_odb10. Combining ab-initio, RNA-seq data, and homology-based predictions, we identified 12,710 protein-coding genes. Approximately, 1.43 Mb of Transposable elements (TEs) (3.88% of the assembly), 36 secondary metabolite biosynthetic gene clusters and 361 genes encoding putative CAZymes were identified. This genomic resource will allow functional studies aimed to characterize the symbiotic interactions between C. hobsonii and its host trees, but will also provide a valuable foundation for further research on comparative genomics of the Entolomataceae.

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Draft Genome Sequence of Lignin-Degrading Agrobacterium sp. Strain S2, Isolated from a Decaying Oil Palm Empty Fruit Bunch

Microbiology Resource Announcements ◽

10.1128/mra.00259-21 ◽

2021 ◽

Vol 10 (19) ◽

Author(s):

Ummu Habibah Faisal ◽

Nurul Syazwani Ahmad Sabri ◽

Nurtasbiyah Yusof ◽

Analhuda Abdullah Tahir ◽

Nuurul Nadrah Mohd Said ◽

...

Keyword(s):

Genome Sequence ◽

Oil Palm ◽

Lignin Degradation ◽

Draft Genome ◽

Gc Content ◽

Draft Genome Sequence ◽

Empty Fruit Bunch ◽

Genes Encoding

ABSTRACT We report the draft genome sequence of Agrobacterium sp. strain S2, isolated from a decaying oil palm empty fruit bunch (OPEFB) in Negeri Sembilan, Malaysia, which yields potential genes encoding lignin degradation enzymes. This genome of 9,722,071 bp exhibited 58.9% GC content, 10,416 coding genes, and 12 RNAs.

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Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172

Biotechnology for Biofuels ◽

10.1186/s13068-021-01975-1 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Monika Tõlgo ◽

Silvia Hüttner ◽

Peter Rugbjerg ◽

Nguyen Thanh Thuy ◽

Vu Nguyen Thanh ◽

...

Keyword(s):

Gc Content ◽

Carbohydrate Active Enzymes ◽

Lytic Polysaccharide Monooxygenase ◽

Thielavia Terrestris ◽

Biomass Saccharification ◽

Beechwood Xylan ◽

Genes Encoding ◽

Encoding Genes ◽

Polysaccharide Monooxygenase

Abstract Background Biomass-degrading enzymes with improved activity and stability can increase substrate saccharification and make biorefineries economically feasible. Filamentous fungi are a rich source of carbohydrate-active enzymes (CAZymes) for biomass degradation. The newly isolated LPH172 strain of the thermophilic Ascomycete Thielavia terrestris has been shown to possess high xylanase and cellulase activities and tolerate low pH and high temperatures. Here, we aimed to illuminate the lignocellulose-degrading machinery and novel carbohydrate-active enzymes in LPH172 in detail. Results We sequenced and analyzed the 36.6-Mb genome and transcriptome of LPH172 during growth on glucose, cellulose, rice straw, and beechwood xylan. 10,128 predicted genes were found in total, which included 411 CAZy domains. Compared to other fungi, auxiliary activity (AA) domains were particularly enriched. A higher GC content was found in coding sequences compared to the overall genome, as well as a high GC3 content, which is hypothesized to contribute to thermophilicity. Primarily auxiliary activity (AA) family 9 lytic polysaccharide monooxygenase (LPMO) and glycoside hydrolase (GH) family 7 glucanase encoding genes were upregulated when LPH172 was cultivated on cellulosic substrates. Conventional hemicellulose encoding genes (GH10, GH11 and various CEs), as well as AA9 LPMOs, were upregulated when LPH172 was cultivated on xylan. The observed co-expression and co-upregulation of genes encoding AA9 LPMOs, other AA CAZymes, and (hemi)cellulases point to a complex and nuanced degradation strategy. Conclusions Our analysis of the genome and transcriptome of T. terrestris LPH172 elucidates the enzyme arsenal that the fungus uses to degrade lignocellulosic substrates. The study provides the basis for future characterization of potential new enzymes for industrial biomass saccharification.

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