scholarly journals The Azurin Coding Gene: Origin and Phylogenetic Distribution

2021 ◽  
Vol 10 (1) ◽  
pp. 9
Author(s):  
Leandro Gammuto ◽  
Carolina Chiellini ◽  
Marta Iozzo ◽  
Renato Fani ◽  
Giulio Petroni
Keyword(s):  
Anticancer Activity ◽  
Bacterial Genomes ◽  
Patchy Distribution ◽  
Vertical Inheritance ◽  
Bacterial Phyla ◽  
Conserved Domain ◽  
Domains Of Life ◽  
Gene Origin ◽  
Bacterial Domain ◽  
Cancer Diseases

Azurin is a bacterial-derived cupredoxin, which is mainly involved in electron transport reactions. Interest in azurin protein has risen in recent years due to its anticancer activity and its possible applications in anticancer therapies. Nevertheless, the attention of the scientific community only focused on the azurin protein found in Pseudomonas aeruginosa (Proteobacteria, Gammaproteobacteria). In this work, we performed the first comprehensive screening of all the bacterial genomes available in online repositories to assess azurin distribution in the three domains of life. The Azurin coding gene was not detected in the domains Archaea and Eucarya, whereas it was detected in phyla other than Proteobacteria, such as Bacteroidetes, Verrucomicrobia and Chloroflexi, and a phylogenetic analysis of the retrieved sequences was performed. Observed patchy distribution and phylogenetic data suggest that once it appeared in the bacterial domain, the azurin coding gene was lost in several bacterial phyla and/or anciently horizontally transferred between different phyla, even though a vertical inheritance appeared to be the major force driving the transmission of this gene. Interestingly, a shared conserved domain has been found among azurin members of all the investigated phyla. This domain is already known in P. aeruginosa as p28 domain and its importance for azurin anticancer activity has been widely explored. These findings may open a new and intriguing perspective in deciphering the azurin anticancer mechanisms and to develop new tools for treating cancer diseases.

scholarly journals SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes

2020 ◽  
Vol 16 (12) ◽  
pp. e1008439
Author(s):  
Jennifer Lu ◽  
Steven L. Salzberg
Keyword(s):  
Large Scale ◽  
Analysis Tool ◽  
Index Test ◽  
Bacterial Genomes ◽  
Phylogenetic Groups ◽  
Bacterial Phyla ◽  
Link Type ◽  
Gc Skew ◽  
A Genome ◽  
Web App

GC skew is a phenomenon observed in many bacterial genomes, wherein the two replication strands of the same chromosome contain different proportions of guanine and cytosine nucleotides. Here we demonstrate that this phenomenon, which was first discovered in the mid-1990s, can be used today as an analysis tool for the 15,000+ complete bacterial genomes in NCBI’s Refseq library. In order to analyze all 15,000+ genomes, we introduce a new method, SkewIT (Skew Index Test), that calculates a single metric representing the degree of GC skew for a genome. Using this metric, we demonstrate how GC skew patterns are conserved within certain bacterial phyla, e.g. Firmicutes, but show different patterns in other phylogenetic groups such as Actinobacteria. We also discovered that outlier values of SkewIT highlight potential bacterial mis-assemblies. Using our newly defined metric, we identify multiple mis-assembled chromosomal sequences in previously published complete bacterial genomes. We provide a SkewIT web app https://jenniferlu717.shinyapps.io/SkewIT/ that calculates SkewI for any user-provided bacterial sequence. The web app also provides an interactive interface for the data generated in this paper, allowing users to further investigate the SkewI values and thresholds of the Refseq-97 complete bacterial genomes. Individual scripts for analysis of bacterial genomes are provided in the following repository: https://github.com/jenniferlu717/SkewIT.

scholarly journals The Distribution of Tryptophan-Dependent Indole-3-Acetic Acid Synthesis Pathways in Bacteria Unraveled by Large-Scale Genomic Analysis

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1411 ◽  
Author(s):  
Pengfan Zhang ◽  
Tao Jin ◽  
Sunil Kumar Sahu ◽  
Jin Xu ◽  
Qiong Shi ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Large Scale ◽  
Growth Promotion ◽  
Plant Root ◽  
Genomic Analysis ◽  
Acid Synthesis ◽  
Metagenomic Data ◽  
Bacterial Genomes ◽  
Bacterial Phyla ◽  
Indole 3 Acetic Acid

Bacterial indole-3-acetic acid (IAA), an effector molecule in microbial physiology, plays an important role in plant growth-promotion. Here, we comprehensively analyzed about 7282 prokaryotic genomes representing diverse bacterial phyla, combined with root-associated metagenomic data to unravel the distribution of tryptophan-dependent IAA synthesis pathways and to quantify the IAA synthesis-related genes in the plant root environments. We found that 82.2% of the analyzed bacterial genomes were potentially capable of synthesizing IAA from tryptophan (Trp) or intermediates. Interestingly, several phylogenetically diverse bacteria showed a preferential tendency to utilize different pathways and tryptamine and indole-3-pyruvate pathways are most prevalent in bacteria. About 45.3% of the studied genomes displayed multiple coexisting pathways, constituting complex IAA synthesis systems. Furthermore, root-associated metagenomic analyses revealed that rhizobacteria mainly synthesize IAA via indole-3-acetamide (IAM) and tryptamine (TMP) pathways and might possess stronger IAA synthesis abilities than bacteria colonizing other environments. The obtained results refurbished our understanding of bacterial IAA synthesis pathways and provided a faster and less labor-intensive alternative to physiological screening based on genome collections. The better understanding of IAA synthesis among bacterial communities could maximize the utilization of bacterial IAA to augment the crop growth and physiological function.

PPK1 and PPK2 — which polyphosphate kinase is older?

Biologia ◽  
2014 ◽  
Vol 69 (3) ◽  
Author(s):  
Lucia Achbergerová ◽  
Jozef Nahálka
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Phylogenetic Analyses ◽  
Linear Molecule ◽  
Polyphosphate Kinase ◽  
Hypothetical Proteins ◽  
Bacterial Genomes ◽  
Metabolic Balance ◽  
Domains Of Life

AbstractPolyphosphate kinases (PPKs) catalyse the polymerisation and degradation of polyphosphate chains. As a result of this process, PPK produces or consumes energy in the form of ATP. Polyphosphate is a linear molecule that contains tens to hundreds of phosphate residues connected by macroergic bonds, and it appears to be an easily obtainable and rich source of energy from prebiotic times to the present. Notably, polyphosphate is present in the cells of all three domains of life, but PPKs are widely distributed only in Bacteria, as Archaea and Eucarya use various unrelated or “nonhomologous” proteins for energy and metabolic balance. The present study focuses on PPK1 and PPK2 homologues, which have been described to some extent in Bacteria, and the aim was to determine which homologue group, PPK1 or PPK2, is older. Phylogenetic analyses of 109 sequence homologues of Escherichia coli PPK1 and 109 sequence homologues of Pseudomonas aeruginosa PPK2 from 109 bacterial genomes imply that polyphosphate consumption (PPK2) evolved first and that phosphate polymerisation (PPK1) evolved later. Independently, a theory of the trends in amino acid loss and gain also confirms that PPK2 is older than PPK1. According to the results of this study, we propose 68 hypothetical proteins to mark as PPK2 homologues and 3 hypothetical proteins to mark as PPK1 homologues.

scholarly journals Holins in Bacteria, Eukaryotes, and Archaea: Multifunctional Xenologues with Potential Biotechnological and Biomedical Applications

2014 ◽  
Vol 197 (1) ◽  
pp. 7-17 ◽  
Author(s):  
Milton H. Saier ◽  
Bhaskara L. Reddy
Keyword(s):  
Cell Death ◽  
Biomedical Applications ◽  
Cell Lysis ◽  
Gram Negative Bacteria ◽  
Bacterial Genomes ◽  
Future Studies ◽  
Virion Release ◽  
Cytoplasmic Membranes ◽  
Domains Of Life ◽  
The Many

Holins form pores in the cytoplasmic membranes of bacteria for the primary purpose of releasing endolysins that hydrolyze the cell wall and induce cell death. Holins are encoded within bacteriophage genomes, where they promote cell lysis for virion release, and within bacterial genomes, where they serve a diversity of potential or established functions. These include (i) release of gene transfer agents, (ii) facilitation of programs of differentiation such as those that allow sporulation and spore germination, (iii) contribution to biofilm formation, (iv) promotion of responses to stress conditions, and (v) release of toxins and other proteins. There are currently 58 recognized families of holins and putative holins with members exhibiting between 1 and 4 transmembrane α-helical spanners, but many more families have yet to be discovered. Programmed cell death in animals involves holin-like proteins such as Bax and Bak that may have evolved from bacterial holins. Holin homologues have also been identified in archaea, suggesting that these proteins are ubiquitous throughout the three domains of life. Phage-mediated cell lysis of dual-membrane Gram-negative bacteria also depends on outer membrane-disrupting “spanins” that function independently of, but in conjunction with, holins and endolysins. In this minireview, we provide an overview of their modes of action and the first comprehensive summary of the many currently recognized and postulated functions and uses of these cell lysis systems. It is anticipated that future studies will result in the elucidation of many more such functions and the development of additional applications.

scholarly journals The Atacama Desert in Northern Chile as an Analog Model of Mars

2022 ◽  
Vol 8 ◽  
Author(s):  
Armando Azua-Bustos ◽  
Carlos González-Silva ◽  
Alberto G. Fairén
Keyword(s):  
Atacama Desert ◽  
Analog Model ◽  
Patchy Distribution ◽  
Microbial Life ◽  
Environmental Extremes ◽  
Life On Mars ◽  
Domains Of Life ◽  
Mars Analog ◽  
The Impact

The Atacama Desert is by far the driest and oldest desert on Earth, showing a unique combination of environmental extremes (extreme dryness, the highest UV radiation levels on Earth, and highly saline and oxidizing soils), explaining why the Atacama has been largely investigated as a Mars analog model for almost 20 years. Based on the source and the amount of water available for life and its analogy with Mars, two ecosystems are of interest in the Atacama: its Coastal Range and the much drier hyperarid core, which we here review in detail. Members of the three domains of life have been found across these ecosystems living at the limit of habitability, suggesting the potential dry limits for each domain and also unveiling the highly patchy distribution of microbial life in its most extreme regions. The thorough study of the Atacama has allowed us to understand how life has adapted to its extreme conditions, the specific habitats that life occupies in each case (thus suggesting the most likely places in which to search for evidence for life on Mars), and the number of biosignatures detected across this desert. Also, the characterization of west-to-east transects across this desert has shown to be of significant value to understand the potential adaptations that Martian microorganisms may have followed in an ever-drying planet. All of this explains why the Atacama is actively used as the testing ground of the technologies (detection instruments, rovers, etc.) that were sent and will be sent to Mars. We also highlight the need to better inform the exact locations of the sites studied to understand general trends, the need to identify the true native microbial species of the Atacama, and the impact of climate change on the most arid and most Martian desert of Earth.

scholarly journals Prophage genomics reveals patterns in phage genome organization and replication

2017 ◽  
Author(s):  
Han Suh Kang ◽  
Katelyn McNair ◽  
Daniel A. Cuevas ◽  
Barbara A. Bailey ◽  
Anca M. Segall ◽  
...  
Keyword(s):  
Gene Order ◽  
Transcriptional Control ◽  
Phage Genome ◽  
Translation Efficiency ◽  
Bacterial Genomes ◽  
Bacterial Host ◽  
Web Based ◽  
Bacterial Phyla ◽  
Low Copy Number ◽  
Rna Genes

AbstractTemperate phage genomes are highly variable mosaic collections of genes that infect a bacterial host, integrate into the host’s genome or replicate as low copy number plasmids, and are regulated to switch from the lysogenic to lytic cycles to generate new virions and escape their host. Genomes from most Bacterial phyla contain at least one or more prophages. We updated our PhiSpy algorithm to improve detection of prophages and to provide a web-based framework for PhiSpy. We have used this algorithm to identify 36,488 prophage regions from 11,941 bacterial genomes, including almost 600 prophages with no known homology to any proteins. Transfer RNA genes were abundant in the prophages, many of which alleviate the limits of translation efficiency due to host codon bias and presumably enable phages to surpass the normal capacity of the hosts’ translation machinery. We identified integrase genes in 15,765 prophages (43% of the prophages). The integrase was routinely located at either end of the integrated phage genome, and was used to orient and align prophage genomes to reveal their underlying organization. The conserved genome alignments of phages recapitulate early, middle, and late gene order in transcriptional control of phage genes, and demonstrate that gene order, presumably selected by transcription timing and/or coordination among functional modules has been stably conserved throughout phage evolution.

scholarly journals EnteroBase: Hierarchical clustering of 100,000s of bacterial genomes into species/sub-species and populations

2022 ◽  
Author(s):  
Mark Achtman ◽  
Zhemin Zhou ◽  
Jane Charlesworth ◽  
Laura A. Baxter
Keyword(s):  
Core Genome ◽  
Bacterial Species ◽  
Automated Identification ◽  
Bacterial Genomes ◽  
Bacterial Populations ◽  
Vertical Inheritance ◽  
Definition Of ◽  
Taxonomic Assignments ◽  
Species Specific ◽  
Sequence Types

The definition of bacterial species is traditionally a taxonomic issue while defining bacterial populations is done with population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST alleles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate the ability of HierCC to correctly assign 100,000s of genomes to the species/subspecies and population levels for Salmonella, Clostridoides, Yersinia, Vibrio and Streptococcus. HierCC assignments were more consistent with maximum-likelihood super-trees of core SNPs or presence/absence of accessory genes than classical taxonomic assignments or 95% ANI. However, neither HierCC nor ANI were uniformly consistent with classical taxonomy of Streptococcus. HierCC was also consistent with legacy eBGs/ST Complexes in Salmonella or Escherichia and revealed differences in vertical inheritance of O serogroups. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.

scholarly journals A unique mode of nucleic acid immunity performed by a single multifunctional enzyme

2019 ◽  
Author(s):  
S. M. Nayeemul Bari ◽  
Lucy Chou-Zheng ◽  
Katie Cater ◽  
Vidya Sree Dandu ◽  
Alexander Thomas ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Genetic Material ◽  
Dual Function ◽  
Bacterial Phyla ◽  
Dna And Rna ◽  
Multiple Components ◽  
Unique Mode ◽  
Phage Dna ◽  
Domains Of Life ◽  
Replication Intermediates

Organisms spanning all domains of life protect against pathogens using diverse mechanisms of nucleic acid immunity which detect and eliminate foreign genetic material1. The perpetual arms race between bacteria and their viruses (phages) has given rise to both innate and adaptive nucleic acid immunity mechanisms, including restriction-modification and CRISPR-Cas, respectively2. These sophisticated systems encode multiple components that sense and degrade phage-derived genetic material while leaving the host genome unharmed. Here, we describe a unique mode of innate immunity performed by a single protein, SERP2475, herein renamed to Nhi. We show that this enzyme protects against phages by preventing phage DNA accumulation, and in a purified system it degrades both DNA and RNA substrates. This enzyme also exhibits ATP-dependent helicase activity, and excess ATP abrogates nuclease function, suggesting a possible mechanism for its regulation. Further, using directed evolution, we isolated and characterized a collection of resistant phage mutants and found that a single-stranded DNA binding protein provides a natural means for phages to escape immunity. These observations support a model in which Nhi senses and degrades phage-specific replication intermediates. We also found that this dual-function enzyme protects against diverse phages, and its homologs are distributed across several bacterial phyla. Altogether, our findings reveal a new innate immune system with minimal composition that provides robust defense against diverse bacterial viruses.

scholarly journals Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1839 ◽  
Author(s):  
Tom O. Delmont ◽  
A. Murat Eren
Keyword(s):  
High Throughput Sequencing ◽  
Draft Genome ◽  
Cost Effective ◽  
Single Copy ◽  
Eukaryotic Genome ◽  
Sequencing Data ◽  
Bacterial Genomes ◽  
Long Read ◽  
Domains Of Life ◽  
Genome Assemblies

High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigradeHypsibius dujardini,and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome forH. dujardinisupported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today’s microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes.

scholarly journals GRINS: Genetic elements that recode assembly-line polyketide synthases and accelerate their diversification

2021 ◽  
Vol 118 (26) ◽  
pp. e2100751118 ◽  
Author(s):  
Aleksandra Nivina ◽  
Sur Herrera Paredes ◽  
Hunter B. Fraser ◽  
Chaitan Khosla
Keyword(s):  
Molecular Mechanisms ◽  
Assembly Line ◽  
Gene Families ◽  
Gene Clusters ◽  
Nucleotide Composition ◽  
Polyketide Synthases ◽  
Bacterial Genomes ◽  
Biosynthetic Gene Clusters ◽  
Bacterial Phyla ◽  
Genetic Elements

Assembly-line polyketide synthases (PKSs) are large and complex enzymatic machineries with a multimodular architecture, typically encoded in bacterial genomes by biosynthetic gene clusters. Their modularity has led to an astounding diversity of biosynthesized molecules, many with medical relevance. Thus, understanding the mechanisms that drive PKS evolution is fundamental for both functional prediction of natural PKSs as well as for the engineering of novel PKSs. Here, we describe a repetitive genetic element in assembly-line PKS genes which appears to play a role in accelerating the diversification of closely related biosynthetic clusters. We named this element GRINS: genetic repeats of intense nucleotide skews. GRINS appear to recode PKS protein regions with a biased nucleotide composition and to promote gene conversion. GRINS are present in a large number of assembly-line PKS gene clusters and are particularly widespread in the actinobacterial genus Streptomyces. While the molecular mechanisms associated with GRINS appearance, dissemination, and maintenance are unknown, the presence of GRINS in a broad range of bacterial phyla and gene families indicates that these genetic elements could play a fundamental role in protein evolution.

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