scholarly journals Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment

2017 ◽  
Vol 11 (10) ◽  
pp. 2258-2266 ◽  
Author(s):  
Michael Baumgartner ◽  
Stefan Roffler ◽  
Thomas Wicker ◽  
Jakob Pernthaler
Keyword(s):  
Bacterial Genome ◽  
Genome Reduction ◽  
Predation Mortality ◽  
Letting Go ◽  
Restricted Environment

scholarly journals DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jimena Solana ◽  
Emilio Garrote-Sánchez ◽  
Rosario Gil
Keyword(s):  
In Silico ◽  
Functional Annotation ◽  
Large Scale ◽  
Optimal Algorithm ◽  
Bacterial Genome ◽  
Genome Reduction ◽  
Model Organisms ◽  
Analysis Tool ◽  
Bartonella Quintana ◽  
Gene Essentiality

Abstract Background The study of gene essentiality is fundamental to understand the basic principles of life, as well as for applications in many fields. In recent decades, dozens of sets of essential genes have been determined using different experimental and bioinformatics approaches, and this information has been useful for genome reduction of model organisms. Multiple in silico strategies have been developed to predict gene essentiality, but no optimal algorithm or set of gene features has been found yet, especially for non-model organisms with incomplete functional annotation. Results We have developed DELEAT v0.1 (DELetion design by Essentiality Analysis Tool), an easy-to-use bioinformatic tool which integrates an in silico gene essentiality classifier in a pipeline allowing automatic design of large-scale deletions in any bacterial genome. The essentiality classifier consists of a novel logistic regression model based on only six gene features which are not dependent on experimental data or functional annotation. As a proof of concept, we have applied this pipeline to the determination of dispensable regions in the genome of Bartonella quintana str. Toulouse. In this already reduced genome, 35 possible deletions have been delimited, spanning 29% of the genome. Conclusions Built on in silico gene essentiality predictions, we have developed an analysis pipeline which assists researchers throughout multiple stages of bacterial genome reduction projects, and created a novel classifier which is simple, fast, and universally applicable to any bacterial organism with a GenBank annotation file.

scholarly journals Reduction of bacterial genome size and expansion resulting from obligate intracellular lifestyle and adaptation to soil habitat.

2001 ◽  
Vol 48 (2) ◽  
pp. 367-381 ◽  
Author(s):  
T Stepkowski ◽  
A B Legocki
Keyword(s):  
Genome Size ◽  
Soil Bacteria ◽  
Bacterial Genome ◽  
Housekeeping Genes ◽  
Eukaryotic Cell ◽  
Genome Reduction ◽  
Mutational Bias ◽  
Effective Population ◽  
Obligate Intracellular ◽  
Bacterial Genes

Prokaryotic organisms are exposed in the course of evolution to various impacts, resulting often in drastic changes of their genome size. Depending on circumstances, the same lineage may diverge into species having substantially reduced genomes, or such whose genomes have undergone considerable enlargement. Genome reduction is a consequence of obligate intracellular lifestyle rendering numerous genes expendable. Another consequence of intracellular lifestyle is reduction of effective population size and limited possibility of gene acquirement via lateral transfer. This causes a state of relaxed selection resulting in accumulation of mildly deleterious mutations that can not be corrected by recombination with the wild type copy. Thus, gene loss is usually irreversible. Additionally, constant environment of the eukaryotic cell renders that some bacterial genes involved in DNA repair are expandable. The loss of these genes is a probable cause of mutational bias resulting in a high A+T content. While causes of genome reduction are rather indisputable, those resulting in genome expansion seem to be less obvious. Presumably, the genome enlargement is an indirect consequence of adaptation to changing environmental conditions and requires the acquisition and integration of numerous genes. It seems that the need for a great number of capabilities is common among soil bacteria irrespective of their phylogenetic relationship. However, this would not be possible if soil bacteria lacked indigenous abilities to exchange and accumulate genetic information. The latter are considerably facilitated when housekeeping genes are physically separated from adaptive loci which are useful only in certain circumstances.

scholarly journals Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling

2015 ◽  
Vol 25 (3) ◽  
pp. 435-444 ◽  
Author(s):  
Yo Suzuki ◽  
Nacyra Assad-Garcia ◽  
Maxim Kostylev ◽  
Vladimir N. Noskov ◽  
Kim S. Wise ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Genome Reduction

Holding On… and Letting Go

ASHA Leader ◽  
2015 ◽  
Vol 20 (2) ◽  
pp. 48-53 ◽  
Author(s):  
Maggie Vescovich
Keyword(s):  
Letting Go

Review of Letting Go: A Parents' Guide to Today's College Experience.

1989 ◽  
Vol 34 (3) ◽  
pp. 297-297
Author(s):  
No authorship indicated
Keyword(s):  
College Experience ◽  
Letting Go

Letting Go of Grief Work.

2000 ◽  
Author(s):  
G. A. Bonanno ◽  
S. Kaltman
Keyword(s):  
Grief Work ◽  
Letting Go

Power, Intersubjectivity, and Letting Go

2007 ◽  
Author(s):  
Frank C. Richardson ◽  
Kathryn M. Frost
Keyword(s):  
Letting Go

scholarly journals Sequence of a Coxiella endosymbiont of the tick Amblyomma nuttalli suggests a pattern of convergent genome reduction in the Coxiella genus

2020 ◽  
Author(s):  
Tiago Nardi ◽  
Emanuela Olivieri ◽  
Edward Kariuki ◽  
Davide Sassera ◽  
Michele Castelli
Keyword(s):  
Coxiella Burnetii ◽  
Phylogenetic Analyses ◽  
Genome Reduction ◽  
Metabolic Profiles ◽  
The Novel ◽  
Bacterial Symbionts ◽  
Human Pathogen ◽  
Host Genus ◽  
Supportive Role ◽  
Genus One

Abstract Ticks require bacterial symbionts for the provision of necessary compounds that are absent in their hematophagous diet. Such symbionts are frequently vertically transmitted and, most commonly, belong to the Coxiella genus, which also includes the human pathogen Coxiella burnetii. This genus can be divided in four main clades, presenting partial but incomplete co-cladogenesis with the tick hosts. Here we report the genome sequence of a novel Coxiella, endosymbiont of the African tick Amblyomma nuttalli, and the ensuing comparative analyses. Its size (~1 Mb) is intermediate between symbionts of Rhipicephalus species and other Amblyomma species. Phylogenetic analyses show that the novel sequence is the first genome of the B clade, the only one for which no genomes were previously available. Accordingly, it allows to draw an enhanced scenario of the evolution of the genus, one of parallel genome reduction of different endosymbiont lineages, which are now at different stages of reduction from a more versatile ancestor. Gene content comparison allows to infer that the ancestor could be reminiscent of Coxiella burnetii. Interestingly, the convergent loss of mismatch repair could have been a major driver of such reductive evolution. Predicted metabolic profiles are rather homogenous among Coxiella endosymbionts, in particular vitamin biosynthesis, consistently with a host-supportive role. Concurrently, similarities among Coxiella endosymbionts according to host genus and despite phylogenetic unrelatedness hint at possible host-dependent effects.

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