scholarly journals Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Kaleb Abram ◽  
Zulema Udaondo ◽  
Carissa Bleker ◽  
Visanu Wanchai ◽  
Trudy M. Wassenaar ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Phylogenetic Tree ◽  
Single Copy ◽  
Gene Gain ◽  
E Coli ◽  
Sequence Read Archive ◽  
Gain Loss ◽  
Lines Of Evidence ◽  
Core Genes ◽  
Genome Dataset

AbstractIn this study, more than one hundred thousand Escherichia coli and Shigella genomes were examined and classified. This is, to our knowledge, the largest E. coli genome dataset analyzed to date. A Mash-based analysis of a cleaned set of 10,667 E. coli genomes from GenBank revealed 14 distinct phylogroups. A representative genome or medoid identified for each phylogroup was used as a proxy to classify 95,525 unassembled genomes from the Sequence Read Archive (SRA). We find that most of the sequenced E. coli genomes belong to four phylogroups (A, C, B1 and E2(O157)). Authenticity of the 14 phylogroups is supported by several different lines of evidence: phylogroup-specific core genes, a phylogenetic tree constructed with 2613 single copy core genes, and differences in the rates of gene gain/loss/duplication. The methodology used in this work is able to reproduce known phylogroups, as well as to identify previously uncharacterized phylogroups in E. coli species.

scholarly journals What can we learn from over 100,000 Escherichia coli genomes?

2019 ◽  
Author(s):  
Kaleb Abram ◽  
Zulema Udaondo ◽  
Carissa Bleker ◽  
Visanu Wanchai ◽  
Trudy M. Wassenaar ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Single Copy ◽  
Gene Gain ◽  
E Coli ◽  
Phylogenetic Profiles ◽  
Genomic Studies ◽  
Gain Loss

ABSTRACTThe explosion of microbial genome sequences in public databases allows for large-scale population genomic studies of bacterial species, such as Escherichia coli. In this study, we examine and classify more than one hundred thousand E. coli and Shigella genomes. After removing outliers, a semi-automated Mash-based analysis of 10,667 assembled genomes reveals 14 distinct phylogroups. A representative genome or medoid identified for each phylogroup serves as a proxy to classify more than 95,000 unassembled genomes. This analysis shows that most sequenced E. coli genomes belong to 4 phylogroups (A, C, B1 and E2(O157)). Authenticity of the 14 phylogroups described is supported by pangenomic and phylogenetic analyses, which show differences in gene preservation between phylogroups. A phylogenetic tree constructed with 2,613 single copy core genes along with a matrix of phylogenetic profiles is used to confirm that the 14 phylogroups change at different rates of gene gain/loss/duplication. The methodology used in this work is able to identify previously uncharacterized phylogroups in E. coli species. Some of these new phylogroups harbor clonal strains that have undergone a process of genomic adaptation to the acquisition of new genomic elements related to virulence or antibiotic resistance. This is, to our knowledge, the largest E. coli genome dataset analyzed to date and provides valuable insights into the population structure of the species.

scholarly journals A Genomic Survey of Signalling in the Myxococcaceae

2020 ◽  
Vol 8 (11) ◽  
pp. 1739
Author(s):  
David E. Whitworth ◽  
Allison Zwarycz
Keyword(s):  
Core Genome ◽  
Gene Gain ◽  
Fruiting Body Formation ◽  
Two Component System ◽  
Genome Sequences ◽  
The Core ◽  
Accessory Genes ◽  
Two Component ◽  
Gain Loss ◽  
Core Genes

As prokaryotes diverge by evolution, essential ‘core’ genes required for conserved phenotypes are preferentially retained, while inessential ‘accessory’ genes are lost or diversify. We used the recently expanded number of myxobacterial genome sequences to investigate the conservation of their signalling proteins, focusing on two sister genera (Myxococcus and Corallococcus), and on a species within each genus (Myxococcus xanthus and Corallococcus exiguus). Four new C. exiguus genome sequences are also described here. Despite accessory genes accounting for substantial proportions of each myxobacterial genome, signalling proteins were found to be enriched in the core genome, with two-component system genes almost exclusively so. We also investigated the conservation of signalling proteins in three myxobacterial behaviours. The linear carotenogenesis pathway was entirely conserved, with no gene gain/loss observed. However, the modular fruiting body formation network was found to be evolutionarily plastic, with dispensable components in all modules (including components required for fruiting in the model myxobacterium M. xanthus DK1622). Quorum signalling (QS) is thought to be absent from most myxobacteria, however, they generally appear to be able to produce CAI-I (cholerae autoinducer-1), to sense other QS molecules, and to disrupt the QS of other organisms, potentially important abilities during predation of other prokaryotes.

scholarly journals Analysis of Serial Isolates of mcr-1-Positive Escherichia coli Reveals a Highly Active ISApl1 Transposon

2017 ◽  
Vol 61 (5) ◽  
Author(s):  
Erik Snesrud ◽  
Ana C. Ong ◽  
Brendan Corey ◽  
Yoon I. Kwak ◽  
Robert Clifford ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Stress Responses ◽  
Single Copy ◽  
The United States ◽  
Content Type ◽  
E Coli ◽  
Highly Active ◽  
Copy Numbers ◽  
Genes Encoding

ABSTRACT The emergence of a transferable colistin resistance gene (mcr-1) is of global concern. The insertion sequence ISApl1 is a key component in the mobilization of this gene, but its role remains poorly understood. Six Escherichia coli isolates were cultured from the same patient over the course of 1 month in Germany and the United States after a brief hospitalization in Bahrain for an unconnected illness. Four carried mcr-1 as determined by real-time PCR, but two were negative. Two additional mcr-1-negative E. coli isolates were collected during follow-up surveillance 9 months later. All isolates were analyzed by whole-genome sequencing (WGS). WGS revealed that the six initial isolates were composed of two distinct strains: an initial ST-617 E. coli strain harboring mcr-1 and a second, unrelated, mcr-1-negative ST-32 E. coli strain that emerged 2 weeks after hospitalization. Follow-up swabs taken 9 months later were negative for the ST-617 strain, but the mcr-1-negative ST-32 strain was still present. mcr-1 was associated with a single copy of ISApl1, located on a 64.5-kb IncI2 plasmid that shared >95% homology with other mcr-1 IncI2 plasmids. ISApl1 copy numbers ranged from 2 for the first isolate to 6 for the final isolate, but ISApl1 movement was independent of mcr-1. Some movement was accompanied by gene disruption, including the loss of genes encoding proteins involved in stress responses, arginine catabolism, and l-arabinose utilization. These data represent the first comprehensive analysis of ISApl1 movement in serial clinical isolates and reveal that, under certain conditions, ISApl1 is a highly active IS element whose movement may be detrimental to the host cell.

scholarly journals Identification and Characterization of a New Lipoprotein, NlpI, in Escherichia coli K-12

1999 ◽  
Vol 181 (14) ◽  
pp. 4318-4325 ◽  
Author(s):  
Masaru Ohara ◽  
Henry C. Wu ◽  
Krishnan Sankaran ◽  
Paul D. Rick
Keyword(s):  
Escherichia Coli ◽  
Direct Consequence ◽  
Insertion Mutant ◽  
Polynucleotide Phosphorylase ◽  
Wild Type ◽  
E Coli ◽  
K 12 ◽  
Identification And Characterization ◽  
Lines Of Evidence

ABSTRACT We report here the identification of a new lipoprotein, NlpI, inEscherichia coli K-12. The NlpI structural gene (nlpI) is located between the genes pnp(polynucleotide phosphorylase) and deaD (RNA helicase) at 71 min on the E. coli chromosome. The nlpI gene encodes a putative polypeptide of approximately 34 kDa, and multiple lines of evidence clearly demonstrate that NlpI is indeed a lipoprotein. An nlpI::cm mutation rendered growth of the cells osmotically sensitive, and incubation of the insertion mutant at an elevated temperature resulted in the formation of filaments. The altered phenotype of the mutant was a direct consequence of the mutation in nlpI, since it was complemented by the wild-type nlpI gene alone. Overexpression of the unaltered nlpI gene in wild-type cells resulted in the loss of the rod morphology and the formation of single prolate ellipsoids and pairs of prolate ellipsoids joined by partial constrictions. NlpI may be important for an as-yet-undefined step in the overall process of cell division.

scholarly journals Reconstruction of ancestral genomes in presence of gene gain and loss.

2016 ◽  
Author(s):  
Pavel Avdeyev ◽  
Shuai Jiang ◽  
Sergey Aganezov ◽  
Fei Hu ◽  
Max A. Alekseyev
Keyword(s):  
Software Tool ◽  
Single Copy ◽  
Genome Rearrangements ◽  
Superior Performance ◽  
Gene Gain ◽  
Gene Duplications ◽  
Genomic Changes ◽  
Breakpoint Reuse ◽  
Gain Loss ◽  
The Given

Since most dramatic genomic changes are caused by genome rearrangements as well as gene duplications and gain/loss events, it becomes crucial to understand their mechanisms and reconstruct ancestral genomes of the given genomes. This problem was shown to be NP-complete even in the "simplest" case of three genomes, thus calling for heuristic rather than exact algorithmic solutions. At the same time, a larger number of input genomes may actually simplify the problem in practice as it was earlier illustrated with MGRA, a state-of-the-art software tool for reconstruction of ancestral genomes of multiple genomes. One of the key obstacles for MGRA and other similar tools is presence of breakpoint reuses when the same breakpoint region is broken by several different genome rearrangements in the course of evolution. Furthermore, such tools are often limited to genomes composed of the same genes with each gene present in a single copy in every genome. This limitation makes these tools inapplicable for many biological datasets and degrades the resolution of ancestral reconstructions in diverse datasets. We address these deficiencies by extending the MGRA algorithm to genomes with unequal gene contents. The developed next-generation tool MGRA2 can handle gene gain/loss events and shares the ability of MGRA to reconstruct ancestral genomes uniquely in the case of limited breakpoint reuse. Furthermore, MGRA2 employs a number of novel heuristics to cope with higher breakpoint reuse and process datasets inaccessible for MGRA. In practical experiments, MGRA2 shows superior performance for simulated and real genomes as compared to other ancestral genomes reconstruction tools. The MGRA2 tool is distributed as an open-source software and can be downloaded from GitHub repository http://github.com/ablab/mgra/. It is also available in the form of a web-server at http://mgra.cblab.org, which makes it readily accessible for inexperienced users.

Expression of the gene for ornithine decarboxylase of Saccharomyces cerevisiae in Escherichia coli

1985 ◽  
Vol 5 (1) ◽  
pp. 161-166
Author(s):  
W A Fonzi ◽  
P S Sypherd
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Ornithine Decarboxylase ◽  
Blot Analysis ◽  
Single Copy ◽  
Decarboxylase Activity ◽  
E Coli ◽  
Ornithine Decarboxylase Activity ◽  
Reduced Frequency ◽  
Diploid Cells

Diploid cells of Saccharomyces cerevisiae homozygous for the spe1A mutation, which eliminates ornithine decarboxylase activity, were found to sporulate at a greatly reduced frequency in the absence of polyamines. Plasmids which complement the spe1A mutation were isolated by their ability to restore sporulation competence to these cells. Three distinct plasmids were isolated. Each plasmid insert overlapped the same 8.0-kilobase region, and each plasmid restored ornithine decarboxylase activity to spe1A mutants. These plasmids also conferred ornithine decarboxylase activity to Escherichia coli EWH319 from which the ornithine decarboxylase gene is deleted. The plasmid-encoded activity expressed in E. coli resembled S. cerevisiae ornithine decarboxylase in its kinetic characteristics, indicating that the yeast ornithine decarboxylase gene was cloned. Southern blot analysis suggested that ornithine decarboxylase is a single-copy gene in S. cerevisiae. A single 2.1-kilobase transcript was demonstrated by Northern blot analysis.

scholarly journals Methylation-Independent Aerotaxis Mediated by the Escherichia coli Aer Protein

2004 ◽  
Vol 186 (12) ◽  
pp. 3730-3737 ◽  
Author(s):  
Sergei I. Bibikov ◽  
Andrew C. Miller ◽  
Khoosheh K. Gosink ◽  
John S. Parkinson
Keyword(s):  
Escherichia Coli ◽  
Deleterious Effect ◽  
Behavioral Responses ◽  
Cellular Redox ◽  
E Coli ◽  
Signaling Domain ◽  
Chemotaxis Proteins ◽  
Homogeneous Chemical ◽  
Signaling Domains ◽  
Lines Of Evidence

ABSTRACT Aer is a membrane-associated protein that mediates aerotactic responses in Escherichia coli. Its C-terminal half closely resembles the signaling domains of methyl-accepting chemotaxis proteins (MCPs), which undergo reversible methylation at specific glutamic acid residues to adapt their signaling outputs to homogeneous chemical environments. MCP-mediated behaviors are dependent on two specific enzymes, CheR (methyltransferase) and CheB (methylesterase). The Aer signaling domain contains unorthodox methylation sites that do not conform to the consensus motif for CheR or CheB substrates, suggesting that Aer, unlike conventional MCPs, might be a methylation-independent transducer. Several lines of evidence supported this possibility. (i) The Aer protein was not detectably modified by either CheR or CheB. (ii) Amino acid replacements at the putative Aer methylation sites generally had no deleterious effect on Aer function. (iii) Aer promoted aerotactic migrations on semisolid media in strains that lacked all four of the E. coli MCPs. CheR and CheB function had no influence on the rate of aerotactic movements in those strains. Thus, Aer senses and signals efficiently in the absence of deamidation or methylation, methylation changes, methylation enzymes, and methyl-accepting chemotaxis proteins. We also found that chimeric transducers containing the PAS-HAMP sensing domain of Aer joined to the signaling domain and methylation sites of Tar, an orthodox MCP, exhibited both methylation-dependent and methylation-independent aerotactic behavior. The hybrid Aear transducers demonstrate that methylation independence does not emanate from the Aer signaling domain but rather may be due to transience of the cellular redox changes that are thought to trigger Aer-mediated behavioral responses.

scholarly journals Comparative Genomic Indexing Reveals the Phylogenomics of Escherichia coli Pathogens

2003 ◽  
Vol 71 (8) ◽  
pp. 4674-4683 ◽  
Author(s):  
Muna F. Anjum ◽  
Sacha Lucchini ◽  
Arthur Thompson ◽  
Jay C. D. Hinton ◽  
Martin J. Woodward
Keyword(s):  
Escherichia Coli ◽  
Diarrheal Disease ◽  
Comparative Genomic ◽  
E Coli ◽  
Food Borne ◽  
Typing Methods ◽  
K 12 ◽  
Genomic Indexing ◽  
Core Genes ◽  
Genomic Similarity

ABSTRACT The Escherichia coli O26 serogroup includes important food-borne pathogens associated with human and animal diarrheal disease. Current typing methods have revealed great genetic heterogeneity within the O26 group; the data are often inconsistent and focus only on verotoxin (VT)-positive O26 isolates. To improve current understanding of diversity within this serogroup, the genomic relatedness of VT-positive and -negative O26 strains was assessed by comparative genomic indexing. Our results clearly demonstrate that irrespective of virulence characteristics and pathotype designation, the O26 strains show greater genomic similarity to each other than to any other strain included in this study. Our data suggest that enteropathogenic and VT-expressing E. coli O26 strains represent the same clonal lineage and that VT-expressing E. coli O26 strains have gained additional virulence characteristics. Using this approach, we established the core genes which are central to the E. coli species and identified regions of variation from the E. coli K-12 chromosomal backbone.

scholarly journals Towards Single-Copy Gene Expression Systems Making Gene Cloning Physiologically Relevant: Lambda InCh, a Simple Escherichia coli Plasmid-Chromosome Shuttle System

2000 ◽  
Vol 182 (3) ◽  
pp. 842-847 ◽  
Author(s):  
Dana Boyd ◽  
David S. Weiss ◽  
Joseph C. Chen ◽  
Jon Beckwith
Keyword(s):  
Escherichia Coli ◽  
Attachment Site ◽  
Single Copy ◽  
Single Copy Gene ◽  
Expression Systems ◽  
Lambda Phage ◽  
E Coli ◽  
Copy Gene ◽  
Coli Plasmid ◽  
Shuttle System

ABSTRACT We describe a simple system for reversible, stable integration of plasmid-borne genes into the Escherichia coli chromosome. Most ordinary E. coli strains and a variety of pBR322-derived ampicillin-resistant plasmids can be used. A single genetic element, a lambda phage, is the only specialized vector required. The resultant strains have a single copy of the plasmid fragment inserted stably at the lambda attachment site on the chromosome, with nearly the entire lambda genome deleted.

Translocation trumps receptor binding in colicin entry into Escherichia coli

2012 ◽  
Vol 40 (6) ◽  
pp. 1443-1448 ◽  
Author(s):  
Karen S. Jakes
Keyword(s):  
Escherichia Coli ◽  
Outer Membrane ◽  
Receptor Binding ◽  
Single Copy ◽  
The Novel ◽  
Outer Membrane Receptor ◽  
E Coli ◽  
Colicin E1 ◽  
Colicin M ◽  
Colicin Ia

Of the steps involved in the killing of Escherichia coli by colicins, binding to a specific outer-membrane receptor was the best understood and earliest characterized. Receptor binding was believed to be an indispensable step in colicin intoxication, coming before the less well-understood step of translocation across the outer membrane to present the killing domain to its target. In the process of identifying the translocator for colicin Ia, I created chimaeric colicins, as well as a deletion missing the entire receptor-binding domain of colicin Ia. The normal pathway for colicin Ia killing was shown to require two copies of Cir: one that serves as the primary receptor and a second copy that serves as translocator. The novel Ia colicins retain the ability to kill E. coli, even in the absence of receptor binding, as long as they can translocate via their Cir translocator. Experiments to determine whether colicin M uses a second copy of its receptor, FhuA, as its translocator were hampered by precipitation of colicin M chimaeras in inclusion bodies. Nevertheless, I show that receptor binding can be bypassed for killing, as long as a translocation pathway is maintained for colicin M. These experiments suggest that colicin M, unlike colicin Ia, may normally use a single copy of FhuA as both its receptor and its translocator. Colicin E1 can kill in the absence of receptor binding, using translocation through TolC.

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