Genome-Wide Analysis Reveals Genetic Potential for Aromatic Compounds Biodegradation of Sphingopyxis

Members of genus Sphingopyxis are frequently found in diverse eco-environments worldwide and have been traditionally considered to play vital roles in the degradation of aromatic compounds. Over recent decades, many aromatic-degrading Sphingopyxis strains have been isolated and recorded, but little is known about their genetic nature related to aromatic compounds biodegradation. In this study, bacterial genomes of 19 Sphingopyxis strains were used for comparative analyses. Phylogeny showed an ambiguous relatedness between bacterial strains and their habitat specificity, while clustering based on Cluster of Orthologous Groups suggested the potential link of functional profile with substrate-specific traits. Pan-genome analysis revealed that 19 individuals were predicted to share 1,066 orthologous genes, indicating a high genetic homogeneity among Sphingopyxis strains. Notably, KEGG Automatic Annotation Server results suggested that most genes pertaining aromatic compounds biodegradation were predicted to be involved in benzoate, phenylalanine, and aminobenzoate metabolism. Among them, β-ketoadipate biodegradation might be the main pathway in Sphingopyxis strains. Further inspection showed that a number of mobile genetic elements varied in Sphingopyxis genomes, and plasmid-mediated gene transfer coupled with prophage- and transposon-mediated rearrangements might play prominent roles in the evolution of bacterial genomes. Collectively, our findings presented that Sphingopyxis isolates might be the promising candidates for biodegradation of aromatic compounds in pollution sites.

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PaReBrick: PArallel REarrangements and BReaks identification toolkit

Bioinformatics ◽

10.1093/bioinformatics/btab691 ◽

2021 ◽

Author(s):

Alexey Zabelkin ◽

Yulia Yakovleva ◽

Olga Bochkareva ◽

Nikita Alexeev

Keyword(s):

Antigenic Variation ◽

Phenotypic Diversity ◽

Genome Rearrangements ◽

Supplementary Information ◽

High Plasticity ◽

Bacterial Strains ◽

Bacterial Genomes ◽

Phyletic Pattern ◽

Bacterial Populations ◽

Different Strains

Abstract Motivation High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions, and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. Specifically, such rearrangements might be responsible for virulence, antibiotic resistance, and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. Results Here we define the term “parallel rearrangements” as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial populations as a tool PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved.We demonstrated PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes. Availability PaReBrick is written in Python and is available on GitHub https://github.com/ctlab/parallelrearrangements Supplementary information Supplementary data are available at Bioinformatics online.

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Differential evolution in 3′UTRs leads to specific gene expression in Staphylococcus

Nucleic Acids Research ◽

10.1093/nar/gkaa047 ◽

2020 ◽

Vol 48 (5) ◽

pp. 2544-2563 ◽

Cited By ~ 2

Author(s):

Pilar Menendez-Gil ◽

Carlos J Caballero ◽

Arancha Catalan-Moreno ◽

Naiara Irurzun ◽

Inigo Barrio-Hernandez ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Regulation ◽

Bacterial Species ◽

Regulatory Elements ◽

Specific Gene ◽

Species Differentiation ◽

Orthologous Genes ◽

Genome Wide ◽

Sequence Variations ◽

Species Specific

Abstract The evolution of gene expression regulation has contributed to species differentiation. The 3′ untranslated regions (3′UTRs) of mRNAs include regulatory elements that modulate gene expression; however, our knowledge of their implications in the divergence of bacterial species is currently limited. In this study, we performed genome-wide comparative analyses of mRNAs encoding orthologous proteins from the genus Staphylococcus and found that mRNA conservation was lost mostly downstream of the coding sequence (CDS), indicating the presence of high sequence diversity in the 3′UTRs of orthologous genes. Transcriptomic mapping of different staphylococcal species confirmed that 3′UTRs were also variable in length. We constructed chimeric mRNAs carrying the 3′UTR of orthologous genes and demonstrated that 3′UTR sequence variations affect protein production. This suggested that species-specific functional 3′UTRs might be specifically selected during evolution. 3′UTR variations may occur through different processes, including gene rearrangements, local nucleotide changes, and the transposition of insertion sequences. By extending the conservation analyses to specific 3′UTRs, as well as the entire set of Escherichia coli and Bacillus subtilis mRNAs, we showed that 3′UTR variability is widespread in bacteria. In summary, our work unveils an evolutionary bias within 3′UTRs that results in species-specific non-coding sequences that may contribute to bacterial diversity.

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T4SP Database 2.0: An Improved Database for Type IV Secretion Systems in Bacterial Genomes with New Online Analysis Tools

Computational and Mathematical Methods in Medicine ◽

10.1155/2016/9415459 ◽

2016 ◽

Vol 2016 ◽

pp. 1-4 ◽

Cited By ~ 3

Author(s):

Na Han ◽

Weiwen Yu ◽

Yujun Qiang ◽

Wen Zhang

Keyword(s):

Recipient Cell ◽

Bacterial Species ◽

Genetic Material ◽

Type Iv Secretion ◽

Bacterial Strains ◽

Secretion Systems ◽

Bacterial Genomes ◽

Type Iv ◽

Type Iv Secretion Systems ◽

User Friendly

Type IV secretion system (T4SS) can mediate the passage of macromolecules across cellular membranes and is essential for virulent and genetic material exchange among bacterial species. The Type IV Secretion Project 2.0 (T4SP 2.0) database is an improved and extended version of the platform released in 2013 aimed at assisting with the detection of Type IV secretion systems (T4SS) in bacterial genomes. This advanced version provides users with web server tools for detecting the existence and variations of T4SS genes online. The new interface for the genome browser provides a user-friendly access to the most complete and accurate resource of T4SS gene information (e.g., gene number, name, type, position, sequence, related articles, and quick links to other webs). Currently, this online database includes T4SS information of 5239 bacterial strains.Conclusions. T4SS is one of the most versatile secretion systems necessary for the virulence and survival of bacteria and the secretion of protein and/or DNA substrates from a donor to a recipient cell. This database on virB/D genes of the T4SS system will help scientists worldwide to improve their knowledge on secretion systems and also identify potential pathogenic mechanisms of various microbial species.

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Exploring the genetic potential of a fosmid metagenomic library from an oil-impacted mangrove sediment for metabolism of aromatic compounds

Ecotoxicology and Environmental Safety ◽

10.1016/j.ecoenv.2019.109974 ◽

2020 ◽

Vol 189 ◽

pp. 109974 ◽

Cited By ~ 3

Author(s):

Sanderson Tarciso Pereira de Sousa ◽

Lucélia Cabral ◽

Gileno Vieira Lacerda-Júnior ◽

Melline Fontes Noronha ◽

Júlia Ronzella Ottoni ◽

...

Keyword(s):

Aromatic Compounds ◽

Metagenomic Library ◽

Mangrove Sediment ◽

Genetic Potential

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A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammals

Royal Society Open Science ◽

10.1098/rsos.150156 ◽

2015 ◽

Vol 2 (9) ◽

pp. 150156 ◽

Cited By ~ 19

Author(s):

Georgia Tsagkogeorga ◽

Michael R. McGowen ◽

Kalina T. J. Davies ◽

Simon Jarman ◽

Andrea Polanowski ◽

...

Keyword(s):

Protein Interactions ◽

Dna Sequences ◽

Brain Function ◽

Molecular Adaptation ◽

Phylogenomic Analysis ◽

Protein Protein Interactions ◽

Orthologous Genes ◽

Genome Wide ◽

A Genome ◽

The Common

Recent studies have reported multiple cases of molecular adaptation in cetaceans related to their aquatic abilities. However, none of these has included the hippopotamus, precluding an understanding of whether molecular adaptations in cetaceans occurred before or after they split from their semi-aquatic sister taxa. Here, we obtained new transcriptomes from the hippopotamus and humpback whale, and analysed these together with available data from eight other cetaceans. We identified more than 11 000 orthologous genes and compiled a genome-wide dataset of 6845 coding DNA sequences among 23 mammals, to our knowledge the largest phylogenomic dataset to date for cetaceans. We found positive selection in nine genes on the branch leading to the common ancestor of hippopotamus and whales, and 461 genes in cetaceans compared to 64 in hippopotamus. Functional annotation revealed adaptations in diverse processes, including lipid metabolism, hypoxia, muscle and brain function. By combining these findings with data on protein–protein interactions, we found evidence suggesting clustering among gene products relating to nervous and muscular systems in cetaceans. We found little support for shared ancestral adaptations in the two taxa; most molecular adaptations in extant cetaceans occurred after their split with hippopotamids.

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bcgTree: automatized phylogenetic tree building from bacterial core genomes

Genome ◽

10.1139/gen-2015-0175 ◽

2016 ◽

Vol 59 (10) ◽

pp. 783-791 ◽

Cited By ~ 46

Author(s):

Markus J. Ankenbrand ◽

Alexander Keller

Keyword(s):

Markov Models ◽

Bacterial Species ◽

Single Copy ◽

Bacterial Strains ◽

Bacterial Genomes ◽

Sequencing Technologies ◽

Genus Lactobacillus ◽

Standard Task ◽

Tree Building ◽

High Level

The need for multi-gene analyses in scientific fields such as phylogenetics and DNA barcoding has increased in recent years. In particular, these approaches are increasingly important for differentiating bacterial species, where reliance on the standard 16S rDNA marker can result in poor resolution. Additionally, the assembly of bacterial genomes has become a standard task due to advances in next-generation sequencing technologies. We created a bioinformatic pipeline, bcgTree, which uses assembled bacterial genomes either from databases or own sequencing results from the user to reconstruct their phylogenetic history. The pipeline automatically extracts 107 essential single-copy core genes, found in a majority of bacteria, using hidden Markov models and performs a partitioned maximum-likelihood analysis. Here, we describe the workflow of bcgTree and, as a proof-of-concept, its usefulness in resolving the phylogeny of 293 publically available bacterial strains of the genus Lactobacillus. We also evaluate its performance in both low- and high-level taxonomy test sets. The tool is freely available at github ( https://github.com/iimog/bcgTree ) and our institutional homepage ( http://www.dna-analytics.biozentrum.uni-wuerzburg.de ).

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Debromination of 2,4,6-tribromophenol coupled with biodegradation

Open Chemistry ◽

10.2478/s11532-013-0231-6 ◽

2013 ◽

Vol 11 (6) ◽

pp. 979-987 ◽

Cited By ~ 3

Author(s):

Tomáš Weidlich ◽

Lubomír Prokeš ◽

Dagmar Pospíšilová

Keyword(s):

Aromatic Compounds ◽

Room Temperature ◽

Ph Value ◽

Phenol Removal ◽

Bacterial Strains ◽

Dissolved Metals ◽

Reaction Conditions ◽

Combined Application ◽

Ni Alloy ◽

Naoh Solution

AbstractThe application effect of aluminium and their alloys and mixtures with nickel was studied for the complete hydrodebromination of 2,4,6-tribromophenol (TBP) to phenol in aqueous NaOH solution at room temperature. It was found that the Raney Al-Ni alloy can rapidly transform TBP to phenol. Removal efficiency of 25 mM TBP solution in aqueous NaOH (15 g L−1) solution at the end of 1h reaction was 100% using 4 g L−1 Al-Ni. The hydrodebromination is accompanied by the dissolution of aluminium and formation of soluble Al(OH)4−1 anions under these reaction conditions. After completion of the hydrodebromination reaction removal of the dissolved metals was achieved by precipitation of appropriate hydroxides by adjustment of the pH value and filtration, the filtrate was treated with Pseudomonas or Rhodococcus bacterial strains to degrade dissolved phenol. The combined application of both (chemical-biological) treatments produced degradations of 100% of aromatic compounds.

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Genome-wide biases in the rate and molecular spectrum of spontaneous mutations in Vibrio cholerae and Vibrio fischeri

10.1101/066829 ◽

2016 ◽

Author(s):

Marcus M Dillon ◽

Way Sung ◽

Robert Sebra ◽

Michael Lynch ◽

Vaughn Cooper

Keyword(s):

Vibrio Cholerae ◽

Vibrio Fischeri ◽

Purifying Selection ◽

Base Substitution ◽

Chromosome 2 ◽

Spontaneous Mutations ◽

Wild Type ◽

Bacterial Genomes ◽

Genome Wide ◽

Mutation Spectra

The vast diversity in nucleotide composition and architecture among bacterial genomes may be partly explained by inherent biases in the rates and spectra of spontaneous mutations. Bacterial genomes with multiple chromosomes are relatively unusual but some are relevant to human health, none more so than the causative agent of cholera, Vibrio cholerae. Here, we present the genome-wide mutation spectra in wild-type and mismatch repair (MMR) defective backgrounds of two Vibrio species, the low-GC% squid symbiont V. fischeri and the pathogen V. cholerae, collected under conditions that greatly minimize the efficiency of natural selection. In apparent contrast to their high diversity in nature, both wild-type V. fischeri and V. cholerae have among the lowest rates for base-substitution mutations (bpsms) and insertion-deletion mutations (indels) that have been measured, below 10-3/genome/generation. V. fischeri and V. cholerae have distinct mutation spectra, but both are AT-biased and produce a surprising number of multi-nucleotide indels. Furthermore, the loss of a functional MMR system caused the mutation spectra of these species to converge, implying that the MMR system itself contributes to species-specific mutation patterns. Bpsm and indel rates varied among genome regions, but do not explain the more rapid evolutionary rates of genes on chromosome 2, which likely result from weaker purifying selection. More generally, the very low mutation rates of Vibrio species correlate inversely with their immense population sizes and suggest that selection may not only have maximized replication fidelity but also optimized other polygenic traits relative to the constraints of genetic drift.

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Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab181 ◽

2021 ◽

Author(s):

Ezequiel G Mogro ◽

Nicolás M Ambrosis ◽

Mauricio J Lozano

Keyword(s):

Insertion Sequence ◽

Bacterial Genome ◽

Draft Genome ◽

Genome Plasticity ◽

Bacterial Strains ◽

Bacterial Genomes ◽

A Genome ◽

Phenotypic Variations ◽

Genome Assemblies ◽

Straightforward Approach

Abstract Bacterial genomes are composed of core and accessory genomes. The first is composed of housekeeping and essential genes, while the second is highly enriched in mobile genetic elements, including transposable elements (TEs). Insertion sequences (ISs), the smallest TEs, have an important role in genome evolution, and contribute to bacterial genome plasticity and adaptability. ISs can spread in a genome, presenting different locations in nearly related strains, and producing phenotypic variations. Few tools are available which can identify differentially located ISs (DLISs) on assembled genomes. Here, we introduce ISCompare, a new program to profile IS mobilization events in related bacterial strains using complete or draft genome assemblies. ISCompare was validated using artificial genomes with simulated random IS insertions and real sequences, achieving the same or better results than other available tools, with the advantage that ISCompare can analyze multiple ISs at the same time and outputs a list of candidate DLISs. ISCompare provides an easy and straightforward approach to look for differentially located ISs on bacterial genomes.

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ISMapper: Identifying insertion sequences in bacterial genomes from short read sequence data

10.1101/016345 ◽

2015 ◽

Author(s):

Jane Hawkey ◽

Mohammad Hamidian ◽

Ryan R Wick ◽

David J Edwards ◽

Helen Billman-Jacobe ◽

...

Keyword(s):

Sequence Data ◽

Insertion Sequences ◽

Bacterial Genomes ◽

Short Read ◽

Phenotypic Resistance ◽

Genome Wide ◽

Wide Range ◽

Multiple Copies ◽

Short Read Sequence ◽

Insertion Sites

Background Insertion sequences (IS) are small transposable elements, commonly found in bacterial genomes. Identifying the location of IS in bacterial genomes can be useful for a variety of purposes including epidemiological tracking and predicting antibiotic resistance. However IS are commonly present in multiple copies in a single genome, which complicates genome assembly and the identification of IS insertion sites. Here we present ISMapper, a mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes, direct from paired-end short read data. Results ISMapper was validated using three types of short read data: (i) simulated reads from a variety of species, (ii) Illumina reads from 5 isolates for which finished genome sequences were available for comparison, and (iii) Illumina reads from 7 Acinetobacter baumannii isolates for which predicted IS locations were tested using PCR. A total of 20 genomes, including 13 species and 32 distinct IS, were used for validation. ISMapper correctly identified 96% of known IS insertions in the analysis of simulated reads, and 98% in real Illumina reads. Subsampling of real Illumina reads to lower depths indicated ISMapper was reliable for average genome-wide read depths >20x. All ISAba1 insertions identified by ISMapper in the A. baumannii genomes were confirmed by PCR. In each A. baumannii genome, ISMapper successfully identified an IS insertion upstream of the ampC beta-lactamase that could explain phenotypic resistance to third-generation cephalosporins. The utility of ISMapper was further demonstrated by profiling genome-wide IS6110 insertions in 138 publicly available Mycobacterium tuberculosis genomes, revealing lineage-specific insertions and multiple insertion hotspots. Conclusions ISMapper provides a rapid and robust method for identifying IS insertion sites direct from short read data, with a high degree of accuracy demonstrated across a wide range of bacteria.

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