Heterogeneity of Genome and Proteome Content in Bacteria, Archaea, and Eukaryotes

Karlin, Samuel; Brocchieri, Luciano; Trent, Jonathan D.; Blaisdell, B. Edwin; Mrázek, Jan

doi:10.1006/tpbi.2002.1606

Cited by 42 publications

(30 citation statements)

References 80 publications

(84 reference statements)

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“…Alignment-free analysis has been used previously to compare amino acid compositions in whole genome and proteome datasets [2] [3]. In this study, we focus on a set of homolog protein data from a relatively narrow range of closely related species belonging to the group Vibrios of gamma proteobacteria -a strategy also adopted by [4].…”

Section: Biological Motivationmentioning

confidence: 99%

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Extracting Molecular Diversity Between Populations Through Sequence Alignments

Thorvaldsen¹,

Flå²,

Willassen

2005

Biological and Medical Data Analysis

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Abstract. The use of sequence alignments for establishing protein homology relationships has an extensive tradition in the field of bioinformatics, and there is an increasing desire for more statistical methods in the data analysis. We present statistical methods and algorithms that are useful when the protein alignments can be divided into two populations based on known features or traits. The algorithms are considered valuable for discovering differences between populations at a molecular level. The approach is illustrated with examples from real biological data sets, and we present experimental results in applying our work on bacterial populations of Vibrio, where the populations are defined by optimal growth temperature, T opt .Keywords: sequence analysis; structural analysis; physicochemical properties; extremophiles; Fisher's exact test; Wilcoxon test. Biological MotivationExtreme environments are those that fall outside the limited range in which we, and most other eukaryotes can survive, and are inhabited by the extremophiles. Among extremophiles, which include thermophiles, psychrophiles, acidophiles, alkalophiles, halophiles, barophiles and xerophiles, those who live and prefer low temperatures are the largest and least studied group. Psycrophilic organisms are living at temperatures close to the freezing point of water. It is of great interest to understand how these organisms can function at "the limits of life" [1].Living at extreme temperatures requires a multiplicity of crucial adaptations including preservation of membrane stability and maintenance of enzymatic activities at appropriate levels. At these temperatures a number of physiological factors are changed; the solubility of gases is not the same, the viscosity of water changes several folds as temperature is changed towards the extreme areas, for example.The number of characterized cold or heat adapted proteins, reported sequences and high resolution structures is growing. The Vibrios are of the species with the greatest amount of published genomes, reaching five completed genomes this year, and seven ongoing whole genome sequencing projects including the cold adapted Vibrio salmonicida.Alignment-free analysis has been used previously to compare amino acid compositions in whole genome and proteome datasets [2] [3]. In this study, we focus on a set of homolog protein data from a relatively narrow range of closely related

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Section: Biological Motivationmentioning

confidence: 99%

“…We define the difference between the sequences from population p (1) and p (2) at position j by averaging the measurements at position j within each population:…”

Section: Residue Propertiesmentioning

confidence: 99%

Extracting Molecular Diversity Between Populations Through Sequence Alignments

Thorvaldsen¹,

Flå²,

Willassen

2005

Biological and Medical Data Analysis

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“…It also has been verified, however, that they reflect adaptations to specific environmental conditions. Thus, acidic residues predominate over basic residues in halophilic prokaryotes (5)(6)(7). A variety of amino acid compositional properties further distinguish thermophilic vs. mesophilic species.…”

Section: Amino Acid Compositionmentioning

confidence: 99%

“…In relation to the size of proteins in eukaryotic, bacterial, and archaeal proteomes, various studies (4,7,(13)(14)(15) have reported that proteins in eukaryotes are significantly longer than proteins in prokaryotes and are moderately longer in bacteria than in archaea.…”

Section: Protein Lengthmentioning

confidence: 99%

“…The pH value 5.0 was chosen for its biological relevance, because it corresponds to the cytoplasmic pH maintained in E. coli when it crosses the highly acidic environment of the stomach. It is likely to be biologically relevant that although at physiological pH most of the proteins in E. coli, and in the majority of prokaryotic species (1,7,19), are negatively charged, most of them become positively charged at acidic pH. As seen in Fig.…”

Section: Measures Of Size and Chargementioning

confidence: 99%

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Environmental signatures in proteome properties

Brocchieri

2004

Proc. Natl. Acad. Sci. U.S.A.

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Prokaryotic Systematics: Theoretical Overview in the Light of Molecular Advances

Kurtböke

2014

Encyclopedia of Life Sciences

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Systematics describes the ordering of information on organisms and plays an important role in communicating information within biological sciences. Systematics seeks to reveal the phenotypic and genotypic diversity of organisms while relating this information to natural interactions and evolutionary history. Systematics may utilise a wide range of data and is not limited to the experimental methods that it may draw on in order to make sensible comparisons between organisms. Systematics requires an underlying order, and both systematics and taxonomy are strongly dependent on theory and philosophy, which are used to create this order. Systematics is a complex area, which has seen much change and progress in the last century. Developments in molecular biology have been adapted in line with the theory and philosophy and have become established in systematics. In the molecular era, accumulated data including those genomics‐derived will be the driving force behind the revalidation of currently used theories and hypotheses formulated in systematics and lead towards the establishment of a ‘genomic taxonomy’. Key Concepts: Systematics seeks to discover phenotypic and genotypic diversity of organisms. Taxonomy, the theory and practice of identifying, describing, naming and classifying organisms. Current systematists make extensive use of molecular biology and bioinformatics to study microorganisms. The basis of molecular phylogeny refers to evolutive relationship of microorganisms that can be inferred from the relationships of their genes and their genomes. Genomics explores the biology of organisms through their genetic blueprints. Metagenomics provide access to genome for prediction of the ecological role of members of microbial communities. Current comparative genomics approaches will lead towards establishment of a ‘genomic taxonomy’.

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Heterogeneity of Genome and Proteome Content in Bacteria, Archaea, and Eukaryotes

Cited by 42 publications

References 80 publications

Extracting Molecular Diversity Between Populations Through Sequence Alignments

Extracting Molecular Diversity Between Populations Through Sequence Alignments

Environmental signatures in proteome properties

Prokaryotic Systematics: Theoretical Overview in the Light of Molecular Advances

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