Conserved Gene Clusters in Bacterial Genomes Provide Further Support for the Primacy of RNA

An approximation to the ∼4-Mbp basic genome shared by 32 strains ofEscherichia colirepresenting six evolutionary groups has been derived and analyzed computationally. A multiple alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ∼90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single base-pair mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome pairs have one or two recombinant transfers of length ∼40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kilobase pairs. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. Most recombinant transfers seem likely to be due to generalized transduction by coevolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.

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Discovery of Cyanobacterial Natural Products Containing Fatty Acid Residues

10.26434/chemrxiv.13100564.v1 ◽

2020 ◽

Author(s):

Sandra A. C. Figueiredo ◽

Marco Preto ◽

Gabriela Moreira ◽

Teresa P. Martins ◽

Kathleen Abt ◽

...

Keyword(s):

Natural Products ◽

Fatty Acid ◽

Isotope Labeling ◽

Gene Clusters ◽

New Drugs ◽

Beta Oxidation ◽

Bacterial Genomes ◽

Biosynthetic Gene Clusters ◽

Apparent Lack ◽

Massive Sequencing

Natural products have an important role in several human activities, most notably as sources of new drugs. In recent years, massive sequencing and annotation of bacterial genomes has revealed an unexpectedly large number of secondary metabolite biosynthetic gene clusters whose products are yet to be discovered. For example, cyanobacterial genomes contain a large number of gene clusters that likely incorporate fatty acid-derived moieties, but for most cases we lack the knowledge and tools to effectively predict or detect the encoded natural products. Here, we exploit the apparent lack of a functional beta-oxidation pathway in cyanobacteria to achieve efficient stable-isotope labeling of their fatty acid-derived lipidome. We show that supplementation of cyanobacterial cultures with deuterated fatty acids can be used to easily detect natural product signatures in individual strains. The utility of this strategy is demonstrated in two cultured cyanobacteria by uncovering analogues of the multidrug-resistance reverting hapalosin, and novel, cytotoxic, lactylate-nocuolin A hybrids – the nocuolactylates.

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The resistome of common human pathogens

10.1101/140194 ◽

2017 ◽

Cited By ~ 4

Author(s):

Christian Munck ◽

Mostafa M. Hashim Ellabaan ◽

Michael Schantz Klausen ◽

Morten O.A. Sommer

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Bacterial Pathogens ◽

Antibiotic Resistance Genes ◽

Gene Clusters ◽

Species Level ◽

Natural Environments ◽

Human Pathogens ◽

Bacterial Genomes ◽

Risk Ranking

AbstractGenes capable of conferring resistance to clinically used antibiotics have been found in many different natural environments. However, a concise overview of the resistance genes found in common human bacterial pathogens is lacking, which complicates risk ranking of environmental reservoirs. Here, we present an analysis of potential antibiotic resistance genes in the 17 most common bacterial pathogens isolated from humans. We analyzed more than 20,000 bacterial genomes and defined a clinical resistome as the set of resistance genes found across these genomes. Using this database, we uncovered the co-occurrence frequencies of the resistance gene clusters within each species enabling identification of co-dissemination and co-selection patterns. The resistance genes identified in this study represent the subset of the environmental resistome that is clinically relevant and the dataset and approach provides a baseline for further investigations into the abundance of clinically relevant resistance genes across different environments. To facilitate an easy overview the data is presented at the species level at www.resistome.biosustain.dtu.dk.

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Horizontal gene transfer of a unique nif island drives convergent evolution of free-living N2-fixing Bradyrhizobium

10.1101/2021.02.03.429501 ◽

2021 ◽

Author(s):

Jinjin Tao ◽

Sishuo Wang ◽

Tianhua Liao ◽

Haiwei Luo

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Agricultural Research ◽

Current Knowledge ◽

Gene Clusters ◽

Soil Samples ◽

Genomic Context ◽

Free Living ◽

Phylogenomic Analyses ◽

Conserved Gene

SummaryThe alphaproteobacterial genus Bradyrhizobium has been best known as N2-fixing members that nodulate legumes, supported by the nif and nod gene clusters. Recent environmental surveys show that Bradyrhizobium represents one of the most abundant free-living bacterial lineages in the world’s soils. However, our understanding of Bradyrhizobium comes largely from symbiotic members, biasing the current knowledge of their ecology and evolution. Here, we report the genomes of 88 Bradyrhizobium strains derived from diverse soil samples, including both nif-carrying and non-nif-carrying free-living (nod free) members. Phylogenomic analyses of these and 252 publicly available Bradyrhizobium genomes indicate that nif-carrying free-living members independently evolved from symbiotic ancestors (carrying both nif and nod) multiple times. Intriguingly, the nif phylogeny shows that all nif-carrying free-living members comprise a cluster which branches off earlier than most symbiotic lineages. These results indicate that horizontal gene transfer (HGT) promotes nif expansion among the free-living Bradyrhizobium and that the free-living nif cluster represents a more ancestral version compared to that in symbiotic lineages. Further evidence for this rampant HGT is that the nif in free-living members consistently co-locate with several important genes involved in coping with oxygen tension which are missing from symbiotic members, and that while in free-living Bradyrhizobium nif and the co-locating genes show a highly conserved gene order, they each have distinct genomic context. Given the dominance of Bradyrhizobium in world’s soils, our findings have implications for global nitrogen cycles and agricultural research.

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Chapter 10 Using Phosphopantetheinyl Transferases for Enzyme Posttranslational Activation, Site Specific Protein Labeling and Identification of Natural Product Biosynthetic Gene Clusters from Bacterial Genomes

Complex Enzymes in Microbial Natural Product Biosynthesis, Part A: Overview Articles and Peptides - Methods in Enzymology ◽

10.1016/s0076-6879(09)04810-1 ◽

2009 ◽

pp. 255-275 ◽

Cited By ~ 18

Author(s):

Murat Sunbul ◽

Keya Zhang ◽

Jun Yin

Keyword(s):

Natural Product ◽

Gene Clusters ◽

Specific Protein ◽

Protein Labeling ◽

Biosynthetic Gene ◽

Bacterial Genomes ◽

Biosynthetic Gene Clusters ◽

Site Specific ◽

Phosphopantetheinyl Transferases ◽

Activation Site

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Short inversions and conserved gene clusters

Proceedings of the 2002 ACM symposium on Applied computing - SAC '02 ◽

10.1145/508791.508825 ◽

2002 ◽

Cited By ~ 1

Author(s):

David Sankoff

Keyword(s):

Gene Clusters ◽

Conserved Gene

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Bakterielle Mechanismen der marinen Polysaccharidverwertung

BIOspektrum ◽

10.1007/s12268-020-1489-9 ◽

2020 ◽

Vol 26 (7) ◽

pp. 800-802

Author(s):

Thomas Schweder ◽

Uwe Bornscheuer ◽

Jan-Hendrik Hehemann ◽

Rudolf Amann

Keyword(s):

Algal Biomass ◽

Major Part ◽

Gene Clusters ◽

Carbohydrate Active Enzymes ◽

High Productivity ◽

Rapid Turnover ◽

Conserved Gene ◽

Complex Polymer

AbstractThe oceans have been compared to a “global heterotrophic digester”. This is due to the high productivity of microalgae and the rapid turnover of the produced biomass by microbes. A major part of the algal biomass consists of diverse polysaccharides which belong to the most complex polymer structures in nature. These marine sugars are decomposed by specialized bacteria, mainly of the phyla Bacteroidetes and Gammaproteobacteria, which possess dedicated conserved gene clusters encoding a remarkable diversity of carbohydrate-active enzymes.

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EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes

Bioinformatics ◽

10.1093/bioinformatics/btz706 ◽

2019 ◽

Author(s):

Marina Marcet-Houben ◽

Toni Gabaldón

Keyword(s):

Secondary Metabolism ◽

Computational Prediction ◽

Gene Clusters ◽

Supplementary Information ◽

Supplementary Data ◽

Automated Inference ◽

Or Gene ◽

Conserved Gene ◽

Genome Comparisons

Abstract Motivation The evolution and role of gene clusters in eukaryotes is poorly understood. Currently, most studies and computational prediction programs limit their focus to specific types of clusters, such as those involved in secondary metabolism. Results We present EvolClust, a python-based tool for the inference of evolutionary conserved gene clusters from genome comparisons, independently of the function or gene composition of the cluster. EvolClust predicts conserved gene clusters from pairwise genome comparisons and infers families of related clusters from multiple (all versus all) genome comparisons. Availability and implementation https://github.com/Gabaldonlab/EvolClust/. Supplementary information Supplementary data are available at Bioinformatics online.

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A UNIVERSAL OPERON PREDICTOR FOR PROKARYOTIC GENOMES

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720009003984 ◽

2009 ◽

Vol 07 (01) ◽

pp. 19-38 ◽

Cited By ~ 15

Author(s):

GUOJUN LI ◽

DONGSHENG CHE ◽

YING XU

Keyword(s):

Structural Information ◽

Prokaryotic Genome ◽

Prediction Method ◽

Gene Clusters ◽

Specific Information ◽

Theoretic Approach ◽

Graph Theoretic ◽

Prokaryotic Genomes ◽

Conserved Gene ◽

Two Kingdoms

Identification of operons at the genome scale of prokaryotic organisms represents a key step in deciphering of their transcriptional regulation machinery, biological pathways, and networks. While numerous computational methods have been shown to be effective in predicting operons for well-studied organisms such as Escherichia coli K12 and Bacillus subtilis 168, these methods generally do not generalize well to genomes other than the ones used to train the methods, or closely related genomes because they rely on organism–specific information. Several methods have been explored to address this problem through utilizing only genomic structural information conserved across multiple organisms, but they all suffer from the issue of low prediction sensitivity. In this paper, we report a novel operon prediction method that is applicable to any prokaryotic genome with high prediction accuracy. The key idea of the method is to predict operons through identification of conserved gene clusters across multiple genomes and through deriving a key parameter relevant to the distribution of intergenic distances in genomes. We have implemented this method using a graph-theoretic approach, to calculate a set of maximum gene clusters in the target genome that are conserved across multiple reference genomes. Our computational results have shown that this method has higher prediction sensitivity as well as specificity than most of the published methods. We have carried out a preliminary study on operons unique to archaea and bacteria, respectively, and derived a number of interesting new insights about operons between these two kingdoms. The software and predicted operons of 365 prokaryotic genomes are available at .

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Transposable temperate phages promote the evolution of divergent social strategies inPseudomonas aeruginosapopulations

10.1101/593798 ◽

2019 ◽

Cited By ~ 1

Author(s):

Siobhán O’Brien ◽

Rolf Kümmerli ◽

Steve Paterson ◽

Craig Winstanley ◽

Michael A. Brockhurst

Keyword(s):

Experimental Evolution ◽

Gene Clusters ◽

Siderophore Production ◽

Evolutionary Divergence ◽

Social Strategies ◽

Bacterial Genomes ◽

The Social ◽

Insertional Inactivation ◽

Genes Encoding ◽

Evolutionary Trajectories

AbstractTransposable temperate phages randomly insert into bacterial genomes, providing increased supply and altered spectra of mutations available to selection, thus opening alternative evolutionary trajectories. Transposable phages accelerate bacterial adaptation to new environments, but their effect on adaptation to the social environment is unclear. Here we show, using experimental evolution ofPseudomonas aeruginosain iron-limited and iron-rich environments causing differential expression of siderophore cooperation, that transposable phages promoted divergence into extreme siderophore production phenotypes in iron-limited populations. Iron-limited populations with transposable phages evolved siderophore over-producing clones alongside siderophore non-producing cheats. Low siderophore production was associated with parallel mutations inpvdgenes, encoding pyoverdine biosynthesis, andpqsgenes, encoding quinolone signaling, while high siderophore production was associated with parallel mutations in phenazine-associated gene clusters. Notably, some of these parallel mutations were caused by phage insertional inactivation. These data suggest that transposable phages, which are widespread in microbial communities, can mediate the evolutionary divergence of social strategies.

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