Abstract：
:The size and diversity of bacteriophage populations require methodologies to quantitatively study the landscape of phage differences. Statistical approaches are confronted with small genome sizes forbidding significant single-phage analysis, and comparative methods analyzing full phage genomes represent an alternative but they are of difficult interpretation due to lateral gene transfer, which creates a mosaic spectrum of related phage species. Based on a large-scale codon bias analysis of 116 DNA phages hosted by 11 translationally biased bacteria belonging to different phylogenetic families, we observe that phage genomes are almost always under codon selective pressure imposed by translationally biased hosts, and we propose a classification of phages with translationally biased hosts which is based on adaptation patterns. We introduce a computational method for comparing phages sharing homologous proteins, possibly accepted by different hosts. We observe that throughout phages, independently from the host, capsid genes appear to be the most affected by host translational bias. For coliphages, genes involved in virion morphogenesis, host interaction and ssDNA binding are also affected by adaptive pressure. Adaptation affects long and small phages in a significant way. We analyze in more detail the Microviridae phage space to illustrate the potentiality of the approach. The small number of directions in adaptation observed in phages grouped around phi X174 is discussed in the light of functional bias. The adaptation analysis of the set of Microviridae phages defined around phi MH2K shows that phage classification based on adaptation does not reflect bacterial phylogeny.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Carbone Adoi
10.1007/s00239-008-9068-6subject
Has Abstractpub_date
2008-03-01 00:00:00pages
210-23issue
3eissn
0022-2844issn
1432-1432journal_volume
66pub_type
杂志文章abstract：:Previously we suggested that four proteins including aldolase and triose phosphate isomerase (TPI) evolved with approximately constant rates over long periods covering the whole animal phyla. The constant rates of aldolase and TPI evolution were reexamined based on three different models for estimating evolutionary di...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006208
更新日期：1997-07-01 00:00:00
abstract：:We have sequenced the nuclear and mitochondrial small subunit rRNA genes (rns) and the mitochondrial genes coding for subunits 1 and 3 of the cytochrome oxidase (cox1 and cox3, respectively) of the chytridiomycete Allomyces macrogynus. Phylogenetic trees inferred from the derived COX1 and COX3 proteins and the nuclear...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00175824
更新日期：1995-11-01 00:00:00
abstract：:Photosynthetic eukaryotes can, according to features of their chloroplasts, be divided into two major groups: the red and the green lineage of plastid evolution. To extend the knowledge about the evolution of the red lineage we have sequenced and analyzed the chloroplast genome (cp-genome) of Cyanidium caldarium RK1, ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010101
更新日期：2000-10-01 00:00:00
abstract：:Analysis of the expanded data set of Sibley and Ahlquist (1987) on primate phylogeny using a maximum likelihood mixed model analysis of variance method shows that there is significant evidence for resolving the Homo-Pan-Gorilla trifurcation in favor of a Homo-Pan clade. The resulting tree is close to that estimated by...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02111286
更新日期：1987-01-01 00:00:00
abstract：:The entire mitochondrial DNA control region (mtDNA D-loop) was sequenced in the seven extant species of Alectoris partridges. The D-loop length is very conserved (1155 +/- 2 nucleotides), and substitution rates are lower than for the mitochondrial cytochrome b gene of the same species, on average. Comparative analyses...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006402
更新日期：1998-10-01 00:00:00
abstract：:The previously given systems-theoretic model for the synthesis of optical antipodes (AD and AL) in strongly asymmetric yield, which shows mono-bistable behaviour depending on the degree of "openess" of the chemical reaction system is reconsidered for two equal compartments (subscripts 1 and 2 on A) with coupling by di...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01732292
更新日期：1975-10-29 00:00:00
abstract：:Cot and chemical analysis show that the haploid genome size of Thermobia domestica is 3-4x10(9) nucleotide pairs. Of this DNA 33% is single copy sequences and 67% is repetitive sequences. The repetitive sequences are predominantly 300 nucleotides in length and are interspersed among the single copy sequences in a shor...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01733135
更新日期：1980-08-01 00:00:00
abstract：:Small heat shock proteins (sHSPs), as one subclass of molecular chaperones, are important for cells to protect proteins under stress conditions. Unlike the large HSPs (represented by Hsp60 and Hsp70), sHSPs are highly divergent in both primary sequences and oligomeric status, with their evolutionary relationships bein...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0076-5
更新日期：2006-03-01 00:00:00
abstract：:The usage of synonymous codons and the frequencies of amino acids were investigated in the complete genome of the bacterium Thermotoga maritima using a multivariate statistical approach. The GC3 content of each gene was the most prominent source of variation of codon usage. Surprisingly the usage of UGU and UGC (synon...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-001-0040-y
更新日期：2002-05-01 00:00:00
abstract：:RNA polymerase III promoter is located within the coding region in all eukaryotic tRNA genes, whereas in prokaryotic tRNA genes, the promoter is located upstream of the transcription initiation site. We analyzed the nucleotide sequence context of the A and B boxes of RNA polymerase III promoters from different unicell...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2504-8
更新日期：2003-11-01 00:00:00
abstract：:We have analyzed the gene that encodes receptor tyrosine kinase (RTK) from the marine sponge Geodia cydonium, which belongs to the most ancient and simple metazoan groups, the Porifera. RTKs are enzymes found only in metazoa. The sponge gene contains two introns in the extracellular part of the protein. However, the r...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006141
更新日期：1997-03-01 00:00:00
abstract：:The kinetics of synonymous codon change and species divergence is described in a matrix formalism that is equally applicable to all levels of codon degeneracy and all levels of codon or nucleotide bias. Based on the formalism it is possible to calculate the sum of all synonymous substitution rate constants from the ob...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00186546
更新日期：1995-09-01 00:00:00
abstract：:Nucleotide sequences for the kappa-casein precursor proteins have been determined from the genomic DNAs or hair roots of the Ruminantia. The coding regions, exons 2, 3, and 4, were amplified separately via the three kinds of PCRs and then directly sequenced. The primers were designed from the sequence of bovine kappa-...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00173165
更新日期：1995-12-01 00:00:00
abstract：:Eukaryotic Nramp genes encode divalent metal ion permeases important for nutrition and resistance to microbial infection. Bacterial homologs encode proton-dependent transporters of manganese (MntH), and other divalent metal ions. Bacterial MntH were classified in three homology groups (A, B, C) and MntH C further subd...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2472-z
更新日期：2003-10-01 00:00:00
abstract：:Two protein-coding regions (cytochrome b, ATPase 8, and part of ATPase 6) from mitochondrial DNA of Cottus kessleri, Cottocomephorus grewingki, and Cottocomephorus inermis--Baikalian endemic sculpins--were amplified via polymerase chain reaction, and sequenced. Two novel primers--L8352 (5'-TAAAGATTGGTGAC TCCCAACCACC) ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00163855
更新日期：1992-01-01 00:00:00
abstract：:The codon assignment of the quasi-universal genetic code can be assumed to have resulted from the evolutionary pressures that prevailed when the code was still evolving. Here, we review studies of the structure of the genetic code based on optimization models. We also review studies that, from the structure of the cod...
journal_title：Journal of molecular evolution
pub_type： 杂志文章,评审
doi：10.1007/s00239-009-9287-5
更新日期：2009-11-01 00:00:00
abstract：:In this study, the molecular population genetics of the orangutan's alpha-2 globin (HBA2) gene were investigated in order to test for the action of natural selection. Haplotypes from 28 orangutan chromosomes were collected from a 1.46-kilobase region of the alpha-2 globin locus. While many aspects of the data were con...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0201-x
更新日期：2005-03-01 00:00:00
abstract：:An exhaustive computer-assisted analysis of the Moloney murine leukemia virus nucleotide sequence shows numerous deviations in the oligomeric distribution, suggesting three overlapping levels of a stepwise duplicative evolution. (1) The sequence fits the universal rule of TG/CT excess which has been proposed as the co...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00171820
更新日期：1992-11-01 00:00:00
abstract：:Catalyzed polymerization reactions represent a primary anabolic activity of all cells. It can be assumed that early cells carried out such reactions, in which macromolecular catalysts were encapsulated within some type of boundary membrane. In the experiments described here, we show that a template-independent RNA pol...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00160400
更新日期：1994-12-01 00:00:00
abstract：:Autosomal chorion genes s18, s15, and s19 are shown to diverge at extremely rapid rates in closely related taxa of Hawaiian Drosophila. Their nucleotide divergence rates are at least as fast as those of intergenic regions that are known to evolve more extensively between distantly related species. Their amino acid div...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02106055
更新日期：1990-11-01 00:00:00
abstract：:Evidence from a number of studies indicates that protein folding is dictated not only by factors stabilizing the native state, but also by potentially independent factors that create folding pathways. How natural selection might cope simultaneously with two independent factors was addressed in this study within the fr...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9465-0
更新日期：2011-10-01 00:00:00
abstract：:Leucine-rich repeat receptor-like kinases (LRR RLKs) comprise the largest group within the plant receptor-like kinase (RLK) superfamily, and the Arabidopsis genome alone contains over 200 LRR RLK genes. Although there is clear evidence for diverse roles played by individual LRR RLK genes in Arabidopsis growth and deve...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0187-z
更新日期：2006-11-01 00:00:00
abstract：:The amino acid sequences of 22 alpha-amylases from family 13 of glycosyl hydrolases were analyzed with the aim of revealing the evolutionary relationships between the archaeal alpha-amylases and their eubacterial and eukaryotic counterparts. Two evolutionary distance trees were constructed: (i) the first one based on ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006486
更新日期：1999-04-01 00:00:00
abstract：:The neutral theory of molecular evolution states that most mutations are deleterious or neutral. It results that the evolutionary rate of a given position in an alignment is a function of the level of constraint acting on this position. Inferring evolutionary rates from a set of aligned sequences is hence a powerful m...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9139-8
更新日期：2008-09-01 00:00:00
abstract：:DEAD-box proteins are found in all domains of life and participate in almost all cellular processes that involve RNA. The presence of DEAD and Helicase_C conserved domains distinguish these proteins. DEAD-box proteins exhibit RNA-dependent ATPase activity in vitro, and several also show RNA helicase activity. In this ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9441-8
更新日期：2011-04-01 00:00:00
abstract：:The observed and expected frequencies of occurrence of microsatellites in the yeast Saccharomyces cerevisiae were investigated. In all cases, the observed frequencies exceeded the expected ones. In contrast to predictions by Messier et al. (1996), there is no critical number of repeats beyond which the observed freque...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006474
更新日期：1999-03-01 00:00:00
abstract：:The genome organization of the Hardness locus in the tribe Triticeae constitutes an excellent model for studying the mechanisms of evolution that played a role in the preservation and potential functional innovations of duplicate genes. Here we applied the nonsynonymous-synonymous rate ratio (d ( N )/d ( S ) or omega)...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0292-z
更新日期：2006-10-01 00:00:00
abstract：:Wild-type Escherichia coli utilizes glycerol aerobically through an inducible pathway mediated by an ATP-dependent kinase and a glycerol 3-phosphate dehydrogenase which is a flavoprotein. A mutant, strain ECL424, employing a novel pathway for glycerol utilization was isolated. The novel pathway is mediated by an NAD-l...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102318
更新日期：1983-01-01 00:00:00
abstract：:The mitochondrial genetic variability in European rabbit (Oryctolagus cuniculus) populations present in Europe and North Africa from 11,000 years ago to the present day has been analyzed using ancient DNA techniques. DNA was extracted from 90 rabbit bones found in 22 archaeological sites dated between the Mesolithic a...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00163228
更新日期：1995-03-01 00:00:00
abstract：:The question of whether natural selection favors genetic stability or genetic variability is a fundamental problem in evolutionary biology. Bioinformatic analyses demonstrate that selection favors genetic stability by avoiding unstable nucleotide sequences in protein encoding DNA. Yet, such unstable sequences are main...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-010-9328-0
更新日期：2010-03-01 00:00:00
