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PubMed2005

The "domino theory" of gene death: gradual and mass gene extinction events in three lineages of obligate symbiotic bacterial pathogens.

During the adaptation of an organism to a parasitic lifestyle, various gene functions may be rendered superfluous due to the fact that the host may supply these needs. As a consequence, obligate symbiotic bacterial pathogens tend to undergo reductive genomic evolution through gene death (nonfunctionalization or pseudogenization) and deletion. Here, we examine the evolutionary sequence of gene-death events during the process of genome miniaturization in three bacterial species that have experienced extensive genome reduction: Mycobacterium leprae, Shigella flexneri, and Salmonella typhi. We infer that in all three lineages, the distribution of functional categories is similar in pseudogenes and genes but different from that of absent genes. Based on an analysis of evolutionary distances, we propose a two-step "domino effect" model for reductive genome evolution. The process starts with a gradual gene-by-gene-death sequence of events. Eventually, a crucial gene within a complex pathway or network is rendered nonfunctional triggering a "mass gene extinction" of the dependent genes. In contrast to published reports according to which genes belonging to certain functional categories are prone to nonfunctionalization more frequently and earlier than genes belonging to other functional categories, we could discern no characteristic regularity in the temporal order of function loss.

Bacteria↗
PubMed2004

Scale-free networks versus evolutionary drift.

Recent studies of properties of various biological networks revealed that many of them display scale-free characteristics. Since the theory of scale-free networks is applicable to evolving networks, one can hope that it provides not only a model of a biological network in its current state but also sheds some insight into the evolution of the network. In this work, we investigate the probability distributions and scaling properties underlying some models for biological networks and protein domain evolution. The analysis of evolutionary models for domain similarity networks indicates that models which include evolutionary drift are typically not scale free. Instead they adhere quite closely to the Yule distribution. This finding indicates that the direct applicability of scale-free models in understanding the evolution of biological network may not be as wide as it has been hoped for.

Computational Biology↗
PubMed1991

Cholinesterase-like domains in enzymes and structural proteins: functional and evolutionary relationships and identification of a catalytically essential aspartic acid.

Primary sequences of cholinesterases and related proteins have been systematically compared. The cholinesterase-like domain of these proteins, about 500 amino acids, may fulfill a catalytic and a structural function. We identified an aspartic acid residue that is conserved among esterases and lipases (Asp-397 in Torpedo acetylcholinesterase) but that had not been considered to be involved in the catalytic mechanism. Site-directed mutagenesis demonstrated that this residue is necessary for activity. Analysis of evolutionary relationships shows that the noncatalytic members of the family do not constitute a separate subgroup, suggesting that loss of catalytic activity occurred independently on several occasions, probably from bifunctional molecules. Cholinesterases may thus be involved in cell-cell interactions in addition to the hydrolysis of acetylcholine. This would explain their specific expression in well-defined territories during embryogenesis before the formation of cholinergic synapses and their presence in noncholinergic tissues.

Acetylcholinesterase↗
PubMed1999

An evolutionary classification of the metallo-beta-lactamase fold proteins.

All the detectable metallo-beta-lactamase fold proteins were identified in the publicly available sequence databases and complete genome sequences using iterative profile searches with the PSI-BLAST program and motif searches with position specific weight matrices. The catalytic site/mechanism and the corresponding structural elements were characterized for these proteins based on the available structure of the Bacillus zinc-dependent beta-lactamase. Based on pair-wise sequence and phylogenetic analysis an evolutionary classification for enzymes of this fold was developed and discussed in terms of implications for substrate specificity. Finally, some predicted inactive members which have been recruited for non-enzymatic functions such as microtubule binding in a cytoskeletal MAP1 are described.

Amino Acid Sequence↗
PubMed2006

Array2BIO: from microarray expression data to functional annotation of co-regulated genes.

BACKGROUND: There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility. RESULTS: Array2BIO converts raw intensities into probe expression values, automatically maps those to genes, and subsequently identifies groups of co-expressed genes using two complementary approaches: (1) comparative analysis of signal versus control and (2) clustering analysis of gene expression across different conditions. The identified genes are assigned to functional categories based on Gene Ontology classification and KEGG protein interaction pathways. Array2BIO reliably handles low-expressor genes and provides a set of statistical methods for quantifying expression levels, including Benjamini-Hochberg and Bonferroni multiple testing corrections. An automated interface with the ECR Browser provides evolutionary conservation analysis for the identified gene loci while the interconnection with Crème allows prediction of gene regulatory elements that underlie observed expression patterns. CONCLUSION: We have developed Array2BIO - a web based tool for rapid comprehensive analysis of Affymetrix microarray expression data, which also allows users to link expression data to Dcode.org comparative genomics tools and integrates a system for translating co-expression data into mechanisms of gene co-regulation. Array2BIO is publicly available at http://array2bio.dcode.org.

Algorithms↗
PubMed1996

Evolution of the frequency (frq) clock locus in Ascomycete fungi.

The frequency (frq) locus of Neurospora crassa plays a key role in the organization of circadian rhythms. Similar timing systems have been found in nearly all eukaryotes as well as some prokaryotes; thus, frq may be an excellent gene with which to conduct evolutionary studies. To investigate, we used the cloned frq locus from ascomycete fungi representing two classical taxonomic classes and three orders to examine two open questions in ascomycete evolution. Class Pyrenomycetidae is represented by several species of Neurospora, Sordaria fimicola, and Chromocrea spinulosa; class Loculoascomycetidae is represented by the marine fungus Leptosphaeria australiensis. Generation of detailed restriction maps of homologs from the Neurospora species allows analysis of evolutionary relationships among these closely related species. A maximum-parsimony tree based on these restriction data suggests that Neurospora tetrasperma groups more closely with Neurospora sitophila than with Neurospora crassa using the homothallic species Neurospora galapagosensis as an outgroup. A maximum-parsimony tree derived using amino acid sequences from Neurospora crassa, Sordaria fimicola, Chromocrea spinulosa, and Leptosphaeria australiensis surprisingly suggests that Leptosphaeria austral should be classified within Pyrenomycetes rather than in a separate class. This suggestion is based on the observations that Leptosphaeria groups with Chromocrea on an evolutionary tree, is more closely related to Neurospora and Sordaria than is Chromocrea, and shares a conserved intron with Chromocrea. Together, these data show that frq is a useful gene with which to conduct evolutionary studies.

Amino Acid Sequence↗
PubMed2004

Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment.

The analysis of conservation between the human and mouse genomes resulted in the identification of a large number of conserved nongenic sequences (CNGs). The functional significance of this nongenic conservation remains unknown, however. The availability of the sequence of a third mammalian genome, the dog, allows for a large-scale analysis of evolutionary attributes of CNGs in mammals. We have aligned 1638 previously identified CNGs and 976 conserved exons (CODs) from human chromosome 21 (Hsa21) with their orthologous sequences in mouse and dog. Attributes of selective constraint, such as sequence conservation, clustering, and direction of substitutions were compared between CNGs and CODs, showing a clear distinction between the two classes. We subsequently performed a chromosome-wide analysis of CNGs by correlating selective constraint metrics with their position on the chromosome and relative to their distance from genes. We found that CNGs appear to be randomly arranged in intergenic regions, with no bias to be closer or farther from genes. Moreover, conservation and clustering of substitutions of CNGs appear to be completely independent of their distance from genes. These results suggest that the majority of CNGs are not typical of previously described regulatory elements in terms of their location. We propose models for a global role of CNGs in genome function and regulation, through long-distance cis or trans chromosomal interactions.

Animals↗
PubMed1998

Cloning of the alphaA-crystallin genes of a blind cave form and the epigean form of Astyanax fasciatus: a comparative analysis of structure, expression and evolutionary conservation.

In the present study we have analyzed the integrity and expression of the alphaA-crystallin gene, that codes for a major structural component of the lens, in a blind cave form of the teleostean fish, Astyanax fasciatus. This is the first alphaA-crystallin gene cloned from a teleostean fish. Sequence comparison of this cave-form gene with its epigean conspecific and with homologs of distantly related taxa has illustrated conservation of regulatory and coding regions. Although no crystallin proteins are produced in the lens of the cave form, and the mRNA of this gene could not be detected by in situ hybridization of different developmental stages, the promoter region of cave-fish alphaA-crystallin is functionally intact. The deduced amino-acid sequence of the alphaA-crystallin gene of the cave form differs from that of its epigean conspecific at only one position (139). This is within an important, small heat-shock protein-related region, HCR2. A comparison of the 5'-flanking regions of the A. fasciatus alphaA-crystallin gene with the chicken homolog revealed the high conservation of lens-specific regulatory sequences and further demonstrates the evolutionary conservation of this gene. 1988 Elsevier Science B.V.

Amino Acid Sequence↗
PubMed2007

A concept analysis of self-monitoring.

AIM: This paper reports a concept analysis delineating and clarifying the concept of self-monitoring to facilitate development and evaluation of interventions to enhance self-monitoring. BACKGROUND: The concepts of self-monitoring, self-management, self-care and symptom management are often used in similar or interchangeable ways. Clarification of the concept of self-monitoring is needed for research and theory development. METHOD: Rodgers and Knafl's evolutionary concept analysis process was used to delineate and clarify the concept. The PubMed and CINAHL databases were searched using keywords 'self-monitoring', 'self-management' and 'self-care' (with and without the hyphen) for the years 1998-2005, to update a previous study (not published). Later, searching was refined and the keyword 'self-monitoring' was paired with 'awareness' and 'self-regulation' was added. Approximately half the papers were from nursing (n = 34) and half from other disciplines (n = 32). The sample from 1998 to 2005 was further stratified by chronic condition. Definition, exemplars, usage, attributes, antecedents/consequences and implications for further study were identified. FINDINGS: Self-monitoring was composed of two complementary components (attributes): (1) awareness of bodily symptoms, sensations, daily activities, and cognitive processes and (2) measurements, recordings and observations that inform cognition or provide information for independent action or consultation with care providers. CONCLUSION: Self-monitoring may be an important concept for understanding how people self-manage chronic conditions. This concept analysis may be useful for researchers who wish to measure this dimension and to develop nursing theory in this area.

Awareness↗
PubMed2006

Evolutionary identification of a subtype specific functional site in the ligand binding domain of steroid receptors.

Nuclear receptors are ubiquitous eukaryotic ligand-activated transcription factors that modulate gene expression through varied interactions. However, the highly conserved functional sites known today seem insufficient to explain receptor specific recruitment of different coactivator and corepressor proteins and regulation of transcription. To search for new receptor-subtype specific functional sites, we applied difference evolutionary trace (difference ET) analysis to the ligand binding domain of steroid receptors, a subgroup of the nuclear receptor (NR) family. This computational approach identified a new functional site located on a surface opposite to currently known protein-protein interaction sites and distinct from the ligand binding pocket. Strikingly, the literature shows that in vivo variations at residues in the new site are linked to androgen resistance and leukemia, and our own targeted mutations to this site lower but do not eradicate transcriptional activation by estrogen receptor alpha (ERalpha), with reduced ligand binding affinity and SRC-1 interaction. Thus, these data demonstrate that this evolutionary important surface can function as an allosteric site that modulates some but not all receptor binding interactions. Evolutionary analysis further shows that this allosteric regulatory site is shared among all NRs from groups 2 (HNF4-like) and 4 (NGFIB-like), suggesting a role among many nuclear receptors. Its concave structure, hydrophobic composition, and residue variability among nuclear receptors further suggest that it would be amenable for specific drug design. This highlights the power of evolutionary information for the identification of new functional sites even in a protein family as well studied as NRs.

Allosteric Site↗
PubMed2003

Mother's mitochondria and optimal offspring sex ratio.

In certain cases, predicted by evolutionary theory of sex-allocation and confirmed by empirical evidence, animals adaptively change their progeny sex-ratio according to individual circumstances. Here we argue that a similar response of offspring sex-ratio must exist in relation to genetic variation of mothers' mitochondria, as a consequence of maternal inheritance of these organelles and of their influence on fitness resulting from their crucial role in metabolism. In fact, a mathematical analysis of evolutionary dynamics of sex-allocation mutants demonstrates that natural selection promotes an evolutionarily stable allocation policy where mothers with defective mitochondria generate only sons, while those with optimal mitochondria have female biased progenies.

Animals↗
PubMed2025

Genome-wide identification and analysis of paclobutrazol-resistance gene family in cotton and the positive role of GhPRE3 in salt stress and drought stress resistance.

Compared with other transcription factors, much less studies have been performed on paclobutrazol-resistance (PRE), a subgroup of the extensive bHLH transcription factor gene family, and the research in cotton was also limited. By utilizing the PRE genes and their conserved domains identified in Arabidopsis, a total of 23, 22, 11, and 12 PRE genes were identified from two major cultivated cotton species and their two ancestors, respectively. The cotton PRE gene family was categorized into three subgroups based on evolutionary tree analysis. Motif and intron analyses indicated that the PRE gene has remained highly conserved throughout evolution. Collinearity analysis indicated that gene duplication, particularly through fragment replication, has significantly contributed to the expansion of the cotton PRE family. An exploration of the conserved elements within the PRE gene family uncovered numerous elements associated with plant stress resistance. Additionally, cotton transcriptome and qRT-PCR analysis showed that PRE genes were associated with a variety of abiotic stresses, including salt, drought, and cold treatments. Subcellular localization experiments indicated that the GhPRE3 gene is associated with membrane proteins. Finally, we selected the GhPRE3 gene for a VIGS experiment, which revealed that under salt stress and drought stress conditions, the wilting of leaves in the GhPRE3-silenced plants was significantly more severe than that observed in the control group, with T-AOC levels notably lower and MDA levels significantly higher. Overexpression of GhPRE3 enhanced seed germination and root development in transgenic Arabidopsis thaliana under salt stress and drought stresses. This suggests that GhPRE3 plays a positive regulatory role in cotton tolerance to salt and drought stressed, providing a reference for molecular genetic breeding of cotton with salt and drought tolerance.

Gossypium↗
PubMed1991

Identification of nucleotide substitutions necessary for trans-activation of mariner transposable elements in Drosophila: analysis of naturally occurring elements.

Six copies of the mariner element from the genomes of Drosophila mauritiana and Drosophila simulans were chosen at random for DNA sequencing and functional analysis and compared with the highly active element Mos1 and the inactive element peach. All elements were 1286 base pairs in length, but among them there were 18 nucleotide differences. As assayed in Drosophila melanogaster, three of the elements were apparently nonfunctional, two were marginally functional, and one had moderate activity that could be greatly increased depending on the position of the element in the genome. Both molecular (site-directed mutagenesis) and evolutionary (cladistic analysis) techniques were used to analyze the functional effects of nucleotide substitutions. The nucleotide sequence of the element is the primary determinant of function, though the activity level of elements is profoundly influenced by position effects. Cladistic analysis of the sequences has identified a T----A transversion at position 1203 (resulting in a Phe----Leu amino acid replacement in the putative transposase) as being primarily responsible for the low activity of the barely functional elements. Use of the sequences from the more distantly related species, Drosophila yakuba and Drosophila teissieri, as outside reference species, indicates that functional mariner elements are ancestral and argues against their origination by a novel mutation or by recombination among nonfunctional elements.

Animals↗
PubMed1992

A partial phylogenetic analysis of the "flavobacter-bacteroides" phylum: basis for taxonomic restructuring.

On the basis of small subunit rRNA sequence analyses five major subgroups within the flavobacteria-bacteroides phylum have been defined. These are tentatively designated the cytophaga subgroup (comprising largely Cytophaga species), the flavobacter subgroup (comprising the true flavobacteria and the polyphyletic genus Weeksella), the bacteroides subgroup (comprising the bacteroides and certain cytophaga-like bacteria), the sphingobacter subgroup (which contains the known sphingolipid-producing members of the phylum), and the saprospira subgroup (comprising particular species of Flexibacter, Flavobacterium, Haliscomenobacter, and, of course, the genus Saprospira). These groupings are given not only by evolutionary distance analysis, but can be defined and distinguished on the basis of a simple small subunit rRNA signatures.

Bacteroides↗
PubMed2026

Genome-wide characterization of the tomato PERK gene family and its expression profiling under abiotic stresses.

UNLABELLED: This study presents the first systematic genome-wide characterization of the proline-rich extensin-like receptor kinases (PERK) gene family in tomato (Solanum lycopersicum) and their transcriptional responses under abiotic stresses. Using the latest SL4.0/ITAG4.0 genome assembly, we identified six SlPERK genes, all harboring the conserved Ser/Thr protein kinase domain. Evolutionary and structural analyses revealed strong purifying selection (Ka/Ks&#x2009;<&#x2009;1), distinct exon-intron organizations, and the presence of stress- and hormone-responsive cis-regulatory elements in their promoters. Furthermore, post-transcriptional regulation by 57 miRNAs and complex protein-protein interaction networks were predicted. To validate their stress-responsive roles, two tomato cultivars (GMOTL-1 and Roma) were subjected to cold, heat, and salinity treatments. Quantitative RT-PCR analysis revealed cultivar-specific expression dynamics: SlPERK4 exhibited strong transient induction under cold and heat stress, while SlPERK6 was highly responsive to salinity. Notably, the GMOTL-1 cultivar displayed significantly higher and broader stress-responsive expression profiles compared to Roma, indicating a potential role of these SlPERK genes in cultivar-specific stress tolerance. These findings provide a comprehensive genomic resource and establish a critical foundation for the functional validation and molecular breeding for stress-resilience tomato cultivars. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s13205-026-05044-y.

Abiotic stress↗
PubMed2003

[Microsatellite analysis of genetic diversity and phylogenetic relationship of eight sheep breeds in Xinjiang].

To reveal the genetic diversity and syseighttemic relationship of main sheep breeds in north Xingjiang, the genetic polymorphisms of 10 microsatellites in 8 sheep breeds and one first filial generation (F1) in north Xinjiang were studied by means of PCR, polyacrylamide gel electrophoresis and silver staining. Number of alleles, average effective number of alleles (E) and average rates of homozygote of each breeds were counted. According to allele frequencies of ten microsatellites, polymorphism information content (PIC), mean heterozygosity (h) and genetic distances were calculated for each breeds. By using the Neighbor-joining method of Molecular Evolutionary Genetics Analysis software, a dendrogram was obtained based on genetic distances. Another dendrogram was obtained by Maximum Likelihood method in PHYLIP (3.6) software. The bootstrap values were evaluated for each crunode of the dendrogram by means of bootstrap test. The systemic relationship was analyzed as well. The results showed that 8 of 10 microsatellite loci were highly polymorphic, but BM1824 and MAF65 were low and medium polymorphic respectively, so the 8 microsatellite loci were effective markers for analysis of genetic relationship among sheep breeds. The average PIC (0.5631), h (0.5721) and E(2.9) of the whole population was all lower than those of other sheep breeds reported in the documents, which showed the gene polymorphisms and genetic diversity in these sheep breeds are relative rare. The genetic distances of native Aletai, Kazak and Bashibai sheeps in Xingjiang from foreign sheep breeds and cultivated breeds bearing foreign bloodline are relatively large. Consequently, they clustered in two groups. The phylogenetic relationship between different sheep breeds was in accordance with their resource, breeding history, differentiation and localities.

Algorithms↗
PubMed2006

Genome-wide searching of single-nucleotide polymorphisms among eight distantly and closely related rice cultivars (Oryza sativa L.) and a wild accession (Oryza rufipogon Griff.).

We searched the genomes of eight rice cultivars (Oryza sativa L. ssp. japonica and ssp. indica) and a wild rice accession (Oryza rufipogon Griffith) for nucleotide polymorphisms, and identified 7805 polymorphic loci, including single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels), in predicted intergenic regions. Polymorphisms are useful as DNA markers for genetic analysis or positional cloning with segregating populations of crosses. Pairwise comparison between cultivars and a neighbor-joining tree calculated from SNPs agreed very well with relationships between rice strains predicted from pedigree data or calculated with other DNA markers such as p-SINE1 and simple sequence repeats (SSRs), suggesting that whole-genome SNP information can be used for analysis of evolutionary relationships. Using multiple SNPs to identify alleles, we drew a map to illustrate the alleles shared among the eight cultivars and the accession. The map revealed that most of the genome is mono- or di-allelic among japonica cultivars, whereas alleles well conserved among modern japonica paddy rice cultivars were often shared with indica cultivars or wild rice, suggesting that the genome structure of modern cultivars is composed of chromosomal segments from various genetic backgrounds. Use of allele-sharing analysis and association analysis were also tested and are discussed.

Alleles↗
PubMed1999

Reconstructing the complex evolutionary history of hepatitis B virus.

A detailed analysis of the evolutionary history of hepatitis B virus (HBV) was undertaken using 39 mammalian hepadnaviruses for which complete genome sequences were available, including representatives of all six human genotypes, as well as a large sample of small S gene sequences. Phylogenetic trees of these data were ambiguous, supporting no single place of origin for HBV, and depended heavily on the underlying model of DNA substitution. In some instances genotype F, predominant in the Americas, was the first to diverge, suggesting that the virus arose in the New World. In other trees, however, sequences from genotype B, prevalent in East Asia, were the most divergent. An attempt was also made to determine the rate of nucleotide substitution in the C open reading frame and then to date the origin of HBV. However, no relationship between time and number of substitutions was found in two independent data sets, indicating that a reliable molecular clock does not exist for these data. Both the pattern and the rate of nucleotide substitution are therefore complex phenomena in HBV and hinder any attempt to reconstruct the past spread of this virus.

Americas↗