Actinoporin-like Proteins Are Widely Distributed in the Phylum Porifera

Actinoporins are proteinaceous toxins known for their ability to bind to and create pores in cellular membranes. This quality has generated interest in their potential use as new tools, such as therapeutic immunotoxins. Isolated historically from sea anemones, genes encoding for similar actinoporin-like proteins have since been found in a small number of other animal phyla. Sequencing and de novo assembly of Irish Haliclona transcriptomes indicated that sponges also possess similar genes. An exhaustive analysis of publicly available sequencing data from other sponges showed that this is a potentially widespread feature of the Porifera. While many sponge proteins possess a sequence similarity of 27.70–59.06% to actinoporins, they show consistency in predicted structure. One gene copy from H. indistincta has significant sequence similarity to sea anemone actinoporins and possesses conserved residues associated with the fundamental roles of sphingomyelin recognition, membrane attachment, oligomerization, and pore formation, indicating that it may be an actinoporin. Phylogenetic analyses indicate frequent gene duplication, no distinct clade for sponge-derived proteins, and a stronger signal towards actinoporins than similar proteins from other phyla. Overall, this study provides evidence that a diverse array of Porifera represents a novel source of actinoporin-like proteins which may have biotechnological and pharmaceutical applications.

Download Full-text

Genomic comparison of archaeal conjugative plasmids fromSulfolobus

Archaea ◽

10.1155/2004/151926 ◽

2004 ◽

Vol 1 (4) ◽

pp. 231-239 ◽

Cited By ~ 66

Author(s):

Bo Greve ◽

Susanne Jensen ◽

Kim Brügger ◽

Wolfram Zillig ◽

Roger A. Garrett

Keyword(s):

Sequence Similarity ◽

Comparative Sequence Analysis ◽

Genomic Comparison ◽

Variable Regions ◽

Integrase Gene ◽

Significant Sequence Similarity ◽

Genes Encoding ◽

Putative Origin ◽

Main Components ◽

Intercellular Exchange

All of the known self-transmissable plasmids of the Archaea have been found in the genusSulfolobus. To gain more insight into archaeal conjugative processes, four newly isolated self-transmissable plasmids, pKEF9, pHVE14, pARN3 and pARN4, were sequenced and subjected to a comparative sequence analysis with two earlier sequenced plasmids, pNOB8 and pING1. The analyses revealed three conserved and functionally distinct sections in the genomes. Section A is considered to encode the main components of the conjugative apparatus, where two genes show low but significant sequence similarity to sections of genes encoding bacterial conjugative proteins. A putative origin of replication is located in section B, which is highly conserved in sequence and contains several perfect and imperfect direct and inverted repeats. Further downstream, in section C, an operon encoding six to nine smaller proteins is implicated in the initiation and regulation of replication. Each plasmid carries an integrase gene of the type that does not partition on integration, and there is strong evidence for their integration into host chromosomes, where they may facilitate intercellular exchange of chromosomal genes. Two plasmids contain hexameric short regularly spaced repeats (SRSR), which have been implicated in plasmid maintenance, and each plasmid carries multiple recombination motifs, concentrated in the variable regions, which likely provide sites for genomic rearrangements.

Download Full-text

Characterization of the transcriptome and EST-SSR development in Boea clarkeana, a desiccation-tolerant plant endemic to China

10.7287/peerj.preprints.2603v1 ◽

2016 ◽

Author(s):

Ying Wang ◽

Kun Liu ◽

De Bi ◽

Biao Shou Zhou ◽

Wen Jian Shao

Keyword(s):

De Novo ◽

Gene Annotation ◽

Sequence Similarity ◽

Molecular Study ◽

Sequence Information ◽

Sequencing Data ◽

Protein Database ◽

Illumina Hiseq ◽

Significant Similarity ◽

Assembly Technology

Background. Resurrection plants constitute a unique cadre within angiosperms. Boea clarkeana Hemsl. (Boea, Gesneriaceae) is a desiccation-tolerant dicotyledonous herb that is endemic to China. Although research on angiosperms with DT could be instructive for crops, genomic resources for B. clarkeana remain scarce. In addition, transcriptome sequencing could be an effective way to study desiccation-tolerant plants. Methods. In the present study, we used the platform Illumina HiSeqTM 2000 and de novo assembly technology to obtain leaf transcriptomes of B. clarkeana and conducted a BLASTX alignment of the sequencing data and protein databases for sequence classification and annotation. Then, based on the sequence information obtained, we developed EST-SSR markers by means of EST-SSR mining, primer design and polymorphism identification. Results. A total of 91,449 unigenes were generated from the leaf cDNA library of B. clarkeana in this study. Based on a sequence similarity search with a known protein database, 72,087 unigenes were annotated. Among the annotated unigenes, a total of 71,170 unigenes showed significant similarity to known proteins of 463 popular model species in the Nr database, and 59,962 unigenes and 32,336 unigenes were assigned to GO classifications and COG, respectively. In addition, 44,924 unigenes were mapped in 128 KEGG pathways. Furthermore, a total of 7,610 unigenes with 8,563 microsatellites were found. Seventy-four primer pairs were selected from 436 primer pairs designed for polymorphism validation. SSRs with higher polymorphism rates were concentrated on dinucleotides, pentanucleotides and hexanucleotides. Finally, 17 pairs with highly polymorphic and stable loci were selected for polymorphism screening. There were a total of 65 alleles, with 2–6 alleles at each locus. Mainly due to the unique biological characteristics of plants, the HE, HO and PIC per locus were very low, ranging from 0 to 0.196, 0.082 to 0.14 and 0 to 0.155, respectively. Discussion. A substantial fraction transcriptome sequences of B. clarkeana were generated in this study, which is the first molecular-level analysis of this plant. These sequences are valuable resources for gene annotation and discovery and molecular marker development. These sequences could also provide a valuable basis for the future molecular study of B. clarkeana.

Download Full-text

Synthetic promoter design in Escherichia coli based on a deep generative network

Nucleic Acids Research ◽

10.1093/nar/gkaa325 ◽

2020 ◽

Vol 48 (12) ◽

pp. 6403-6412 ◽

Cited By ~ 2

Author(s):

Ye Wang ◽

Haochen Wang ◽

Lei Wei ◽

Shuailin Li ◽

Liyang Liu ◽

...

Keyword(s):

Escherichia Coli ◽

Predictive Model ◽

De Novo ◽

Sequence Similarity ◽

Small Subset ◽

Vast Number ◽

Significant Sequence Similarity ◽

E Coli ◽

Synthetic Promoters ◽

Naturally Occurring

Abstract Promoter design remains one of the most important considerations in metabolic engineering and synthetic biology applications. Theoretically, there are 450 possible sequences for a 50-nt promoter, of which naturally occurring promoters make up only a small subset. To explore the vast number of potential sequences, we report a novel AI-based framework for de novo promoter design in Escherichia coli. The model, which was guided by sequence features learned from natural promoters, could capture interactions between nucleotides at different positions and design novel synthetic promoters in silico. We combined a deep generative model that guides the search for artificial sequences with a predictive model to preselect the most promising promoters. The AI-designed promoters were optimized based on the promoter activity in E. coli and the predictive model. After two rounds of optimization, up to 70.8% of the AI-designed promoters were experimentally demonstrated to be functional, and few of them shared significant sequence similarity with the E. coli genome. Our work provided an end-to-end approach to the de novo design of novel promoter elements, indicating the potential to apply deep learning methods to de novo genetic element design.

Download Full-text

Benchmarking topological accuracy of bacterial phylogenomic workflows using in silico evolution

10.1101/2021.08.03.454900 ◽

2021 ◽

Author(s):

Boas CL van der Putten ◽

Niek AH Huijsmans ◽

Daniel R Mende ◽

Constance Schultsz

Keyword(s):

De Novo ◽

Phylogenetic Analyses ◽

Bacterial Species ◽

Phylogenetic Reconstruction ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

De Novo Genome Assembly ◽

Relevant Alternatives ◽

Wide Range ◽

Similar Accuracy

Phylogenetic analyses are widely used in microbiological research, for example to trace the progression of bacterial outbreaks based on whole-genome sequencing data. In practice, multiple analysis steps such as de novo assembly, alignment and phylogenetic inference are combined to form phylogenetic workflows. Comprehensive benchmarking of the accuracy of complete phylogenetic workflows is lacking. To benchmark different phylogenetic workflows, we simulated bacterial evolution under a wide range of evolutionary models, varying the relative rates of substitution, insertion, deletion, gene duplication, gene loss and lateral gene transfer events. The generated datasets corresponded to a genetic diversity usually observed within bacterial species (≥95% average nucleotide identity). We replicated each simulation three times to assess replicability. In total, we benchmarked seventeen distinct phylogenetic workflows using 8 different simulated datasets. We found that recently developed k-mer alignment methods such as kSNP and SKA achieve similar accuracy as reference mapping. The high accuracy of k-mer alignment methods can be explained by the large fractions of genomes these methods can align, relative to other approaches. We also found that the choice of de novo assembly algorithm influences the accuracy of phylogenetic reconstruction, with workflows employing SPAdes or SKESA outperforming those employing Velvet. Finally, we found that the results of phylogenetic benchmarking are highly variable between replicates. We conclude that for phylogenomic reconstruction k-mer alignment methods are relevant alternatives to reference mapping at species level, especially in the absence of suitable reference genomes. We show de novo genome assembly accuracy to be an underappreciated parameter required for accurate phylogenomic reconstruction.

Download Full-text

Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential

Marine Drugs ◽

10.3390/md19110621 ◽

2021 ◽

Vol 19 (11) ◽

pp. 621

Author(s):

Pedro Albuquerque ◽

Inês Ribeiro ◽

Sofia Correia ◽

Ana Paula Mucha ◽

Paula Tamagnini ◽

...

Keyword(s):

Genome Sequence ◽

Deep Sea ◽

In Silico ◽

De Novo ◽

Phylogenetic Analyses ◽

Gene Clusters ◽

Sequencing Data ◽

Innovative Drug ◽

Hybrid Strategy ◽

Madeira Archipelago

The deep-sea constitutes a true unexplored frontier and a potential source of innovative drug scaffolds. Here, we present the genome sequence of two novel marine actinobacterial strains, MA3_2.13 and S07_1.15, isolated from deep-sea samples (sediments and sponge) and collected at Madeira archipelago (NE Atlantic Ocean; Portugal). The de novo assembly of both genomes was achieved using a hybrid strategy that combines short-reads (Illumina) and long-reads (PacBio) sequencing data. Phylogenetic analyses showed that strain MA3_2.13 is a new species of the Streptomyces genus, whereas strain S07_1.15 is closely related to the type strain of Streptomyces xinghaiensis. In silico analysis revealed that the total length of predicted biosynthetic gene clusters (BGCs) accounted for a high percentage of the MA3_2.13 genome, with several potential new metabolites identified. Strain S07_1.15 had, with a few exceptions, a predicted metabolic profile similar to S. xinghaiensis. In this work, we implemented a straightforward approach for generating high-quality genomes of new bacterial isolates and analyse in silico their potential to produce novel NPs. The inclusion of these in silico dereplication steps allows to minimize the rediscovery rates of traditional natural products screening methodologies and expedite the drug discovery process.

Download Full-text

Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more

PLoS Computational Biology ◽

10.1371/journal.pcbi.1009428 ◽

2021 ◽

Vol 17 (10) ◽

pp. e1009428

Author(s):

Ryota Sugimoto ◽

Luca Nishimura ◽

Phuong Thanh Nguyen ◽

Jumpei Ito ◽

Nicholas F. Parrish ◽

...

Keyword(s):

De Novo ◽

Sequence Similarity ◽

Metagenomic Data ◽

Marker Genes ◽

Biological Entity ◽

Metagenomic Sequencing ◽

Sequencing Data ◽

Human Gut ◽

Protein Coding ◽

Viral Sequences

Viruses are the most numerous biological entity, existing in all environments and infecting all cellular organisms. Compared with cellular life, the evolution and origin of viruses are poorly understood; viruses are enormously diverse, and most lack sequence similarity to cellular genes. To uncover viral sequences without relying on either reference viral sequences from databases or marker genes that characterize specific viral taxa, we developed an analysis pipeline for virus inference based on clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR is a prokaryotic nucleic acid restriction system that stores the memory of previous exposure. Our protocol can infer CRISPR-targeted sequences, including viruses, plasmids, and previously uncharacterized elements, and predict their hosts using unassembled short-read metagenomic sequencing data. By analyzing human gut metagenomic data, we extracted 11,391 terminally redundant CRISPR-targeted sequences, which are likely complete circular genomes. The sequences included 2,154 tailed-phage genomes, together with 257 complete crAssphage genomes, 11 genomes larger than 200 kilobases, 766 genomes of Microviridae species, 56 genomes of Inoviridae species, and 95 previously uncharacterized circular small genomes that have no reliably predicted protein-coding gene. We predicted the host(s) of approximately 70% of the discovered genomes at the taxonomic level of phylum by linking protospacers to taxonomically assigned CRISPR direct repeats. These results demonstrate that our protocol is efficient for de novo inference of CRISPR-targeted sequences and their host prediction.

Download Full-text

Complete genome sequences of Streptomyces spp. isolated from disease-suppressive soils

10.21203/rs.2.10524/v1 ◽

2019 ◽

Author(s):

Stephen C Heinsch ◽

Suzie Hsu ◽

Lindsey Otto-Hanson ◽

Linda Kinkel ◽

Michael Smanski

Keyword(s):

Microbial Communities ◽

Natural Product ◽

De Novo ◽

Sequence Similarity ◽

Gene Clusters ◽

Sequencing Data ◽

Sample Number ◽

Genus Streptomyces ◽

Streptomyces Sp ◽

Streptomyces Spp

Abstract Background Bacteria within the genus Streptomyces remain a major source of new natural product discovery and as soil inoculants in agriculture where they promote plant growth and protect from disease. Recently, Streptomyces spp. have been implicated as important members of naturally disease-suppressive soils. To shine more light on the ecology and evolution of disease-suppressive microbial communities, we have sequenced the genome of three Streptomyces strains isolated from disease-suppressive soils and compared them to previously sequenced isolates. Strains selected for sequencing had previously showed strong phenotypes in competition or signaling assays. Results Here we present the de novo sequencing of three strains of the genus Streptomyces isolated from disease-suppressive soils to produce high-quality complete genomes. Streptomyces sp. GS93-23, Streptomyces sp. 3211-3, and Streptomyces sp. S3-4 were found to have linear chromosomes of 8.24 Mb, 8.23 Mb, and greater than 7.5 Mb, respectively. In addition, two of the strains were found to have large, linear plasmids. Each strain harbors between 26 and 38 natural product biosynthetic gene clusters, on par with previously sequenced Streptomyces spp.. We compared these newly-sequenced genomes with those of previously sequenced organisms. We see substantial natural product biosynthetic diversity between closely related strains, with the gain/loss of episomal DNA elements being a primary driver of genome evolution. Conclusions Long read sequencing data facilitates large contig assembly for high-GC Streptomyces genomes. While the sample number is too small for a definitive conclusion, we do not see evidence that disease suppressive soil isolates are particularly privileged in terms of numbers of BGCs. The strong sequence similarity between GS93-23 and previously isolated Streptomyces lydicus suggests that species recruitment may contribute to the evolution of disease-suppressive microbial communities.

Download Full-text

Identification and motif analyses of candidate nonreceptor olfactory genes of Dendroctonus adjunctus Blandford (Coleoptera: Curculionidae) from the head transcriptome

Scientific Reports ◽

10.1038/s41598-020-77144-5 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Brenda Torres-Huerta ◽

Obdulia L. Segura-León ◽

Marco A. Aragón-Magadan ◽

Héctor González-Hernández

Keyword(s):

Bark Beetles ◽

De Novo ◽

Phylogenetic Analyses ◽

Management Strategies ◽

Beetle Species ◽

Sequence Motifs ◽

Homologous Proteins ◽

Pine Beetle ◽

Genes Encoding ◽

Aggregation Behaviors

AbstractThe round-headed pine beetle Dendroctonus adjunctus, whose dispersion and colonization behaviors are linked to a communication system mediated by semiochemicals, is one of the five most critical primary pests in forest ecosystems in Mexico. This study provides the first head transcriptome analysis of D. adjunctus and the identification of the nonreceptor olfactory genes involved in the perception of odors. De novo assembly yielded 44,420 unigenes, and GO annotations were similar to those of antennal transcriptomes of other beetle species, which reflect metabolic processes related to smell and signal transduction. A total of 36 new transcripts of nonreceptor olfactory genes were identified, of which 27 encode OBPs, 7 encode CSPs, and 2 encode SNMP candidates, which were subsequently compared to homologous proteins from other bark beetles and Coleoptera species by searching for sequence motifs and performing phylogenetic analyses. Our study provides information on genes encoding nonreceptor proteins in D. adjunctus and broadens the knowledge of olfactory genes in Coleoptera and bark beetle species, and will help to understand colonization and aggregation behaviors for the development of tools that complement management strategies.

Download Full-text

De Novo Sequencing of a Sparassis latifolia Genome and Its Associated Comparative Analyses

Canadian Journal of Infectious Diseases and Medical Microbiology ◽

10.1155/2018/1857170 ◽

2018 ◽

Vol 2018 ◽

pp. 1-12 ◽

Cited By ~ 6

Author(s):

Donglai Xiao ◽

Lu Ma ◽

Chi Yang ◽

Zhenghe Ying ◽

Xiaoling Jiang ◽

...

Keyword(s):

De Novo ◽

Phylogenetic Analyses ◽

Type I ◽

Fomitopsis Pinicola ◽

Total Size ◽

Postia Placenta ◽

Edible Fungus ◽

Genes Encoding ◽

Medicinal Properties ◽

Genome Content

Known to be rich in β-glucan, Sparassis latifolia (S. latifolia) is a valuable edible fungus cultivated in East Asia. A few studies have suggested that S. latifolia is effective on antidiabetic, antihypertension, antitumor, and antiallergen medications. However, it is still unclear genetically why the fungus has these medical effects, which has become a key bottleneck for its further applications. To provide a better understanding of this fungus, we sequenced its whole genome, which has a total size of 48.13 megabases (Mb) and contains 12,471 predicted gene models. We then performed comparative and phylogenetic analyses, which indicate that S. latifolia is closely related to a few species in the antrodia clade including Fomitopsis pinicola, Wolfiporia cocos, Postia placenta, and Antrodia sinuosa. Finally, we annotated the predicted genes. Interestingly, the S. latifolia genome encodes most enzymes involved in carbohydrate and glycoconjugate metabolism and is also enriched in genes encoding enzymes critical to secondary metabolite biosynthesis and involved in indole, terpene, and type I polyketide pathways. As a conclusion, the genome content of S. latifolia sheds light on its genetic basis of the reported medicinal properties and could also be used as a reference genome for comparative studies on fungi.

Download Full-text

Echinicola Salinicaeni sp. nov., A Novel Bacterium Isolated from Saltern

10.21203/rs.3.rs-474138/v1 ◽

2021 ◽

Author(s):

Han Zhao ◽

Chun-Yi Song ◽

Rui Yin ◽

Yan-Jun Yi ◽

Shuai-Ting Yun ◽

...

Keyword(s):

Sequence Similarity ◽

Phylogenetic Analyses ◽

Draft Genome ◽

Carotenoid Biosynthesis ◽

Amino Acid Identity ◽

Glycoside Hydrolases ◽

Rrna Gene ◽

Unidentified Phospholipid ◽

Resistance Pathway ◽

Genes Encoding

Abstract A Gram-stain-negative, aerobiotic, pink, motile, rod-shaped bacterium, designated P51 T was isolated from saline silt samples in Yantai, China. The novel isolate was able to grow at 4–42 °C (optimum 33 °C), pH 4.0–9.0 (optimum 7.0) and with 0–11.0% NaCl (optimum 4.0%, w/v). It could grow at 4 °C, which was different from the neighbour strains. The draft genome consisted of 4111 genes with a total length of 5139782 bp and 39.9% G + C content. The 16S rRNA gene sequence analysis indicated that strain P51 T was a member of the genus Echinicola and most closely related to ‘ Echinicola shivajiensis ’ with pair-wise sequence similarity of 97.7%. Genome analysis identified genes encoding proteins relating to carbon source utilization such as glycoside hydrolases and glycosyl transferases; carotenoid biosynthesis pathway and β -lactam resistance pathway were observed. Strain P51 T shared average nucleotide identity value below 84.7%, average amino acid identity value between of 70.8 – 89.3%, digital DNA-DNA hybridization identity of between 17.9–28.2% with the closely related type strains within the genus Echinicola . The sole menaquinone was MK-7; the major fatty acids were iso-C 15:0 , summed feature 3(C 16:1 ω 7 c and/or C 16:1 ω 6 c ), summed feature 4 (anteiso-C 17:1 B and/or iso-C 17:1 I) and summed feature 9 (iso-C 17:1 ω 9 c and/or 10-methyl C 16:0 ); the polar lipids included one phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, three unidentified aminolipids and one unknown lipid. Based on phenotypic, chemotaxonomic, and phylogenetic analyses, strain P51 T represents a novel species of the genus Echinicola , for which the name Echinicola salinicaeni sp. nov. is proposed. The type strain is P51 T (KCTC 82513 T = MCCC 1K04413 T ).

Download Full-text