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PubMed1992

Identifying genes involved in the variability of genetic fatness in the growing chicken.

A precise knowledge of the genome involved in the expression of a quantitative trait could provide a useful tool in breeding programs; molecular genetic methods are capable of yielding this kind of information. An experimental procedure is presented here for identifying genes whose expression is related to weight variability of abdominal adipose tissue in the growing chicken. Quantitative traits are the result of metabolic pathways exhibiting some major regulation stages that are controlled genetically. These steps involve genes that may act as "major genes". With regard to chicken fat metabolism, most fatty acids are synthesized in the liver and incorporated into very low density lipoprotein (VLDL) particles before their secretion into the plasma. Accordingly, the present study focused on the expression of liver genes. The mRNA of lipogenic enzymes (acetyl-coenzyme-A carboxylase, fatty acid synthase, malic enzyme, and delta 9-desaturase) were analyzed. Also studied were apoprotein (apo)A1, apoVLDL-II, and apoB mRNA from 9-wk-old male chickens from two lines selected for high and low abdominal fat pads. Significant differences for apoA1 mRNA levels occurred between fat and lean birds. Moreover, the total quantity of mRNA provided an accurate estimation of the abdominal fat pad (r = .74 with P < .05).

Adipose Tissue↗
PubMed1998

Genetic analysis of meiotic recombination in humans by use of sperm typing: reduced recombination within a heterozygous paracentric inversion of chromosome 9q32-q34.3.

To investigate patterns of genetic recombination within a heterozygous paracentric inversion of chromosome 9 (46XY inv[9] [q32q34.3]), we performed sperm typing using a series of polymorphic microsatellite markers spanning the inversion region. For comparison, two donors with cytogenetically normal chromosomes 9, one of whom was heterozygous for a pericentric chromosome 2 inversion (46XY inv[2] [p11q13]), were also tested. Linkage analysis was performed by use of the multilocus linkage-analysis program SPERM, and also CRI-MAP, which was adapted for sperm-typing data. Analysis of the controls generated a marker order in agreement with previously published data and revealed no significant interchromosomal effects of the inv(2) on recombination on chromosome 9. FISH employing cosmids containing appropriate chromosome 9 markers was used to localize the inversion breakpoint of inv(9). Analysis of inv(9) sperm was performed by use of a set of microsatellite markers that mapped centromeric to, telomeric to, and within the inversion breakpoints. Three distinct patterns of recombination across the region were observed. Proximal to the centromeric breakpoint, recombination was similar to normal levels. Distal to the telomeric breakpoint, there was an increase in recombination found in the inversion patient. Finally, within the inversion, recombination was dramatically reduced, but several apparent double recombinants were found. A putative model explaining these data is proposed.

Adult↗
PubMed1999

Complexities in the analysis of cryptic taxa within the genus Anopheles.

Grassi's discovery one hundred years ago brought to light the puzzle of anophelism without malaria in Europe. With the discovery of the European Anopheles maculipennis complex the puzzle was solved but the 'species problem' has not gone away. Meaningful epidemiologic studies and effective vector control programs depend upon efficient methods for discriminating among the major vectors, lesser vectors and non-vectors of ubiquitous anopheline sibling species complexes. We now have a variety of techniques for identifying cryptic species, ranging from crossing studies through morphological, cytogenetic, allozyme and repetitive DNA-based strategies. However, cytogenetic and molecular data can also be used to infer evolutionary relationships among cryptic taxa. This approach has been crucial to understanding the biology of the vector, and may illuminate the speciation process and the human impact upon this process. Nevertheless, the analysis of cryptic taxa has proven unexpectedly complex. Studies of An. funestus and An. gambiae reveal conflicts among classes of markers and between different genomic locations. The data are consistent with a model of speciation in which gene flow may still occur in parts of the genome, and they suggest that caution should be exercised in the interpretation of results from small numbers of loci, only one type of marker, and markers located in specific genomic regions such as chromosomal inversions.

Animals↗
PubMed1977

Genetic control of ethanol action on the central nervous system. An EEG study in twins.

The purpose of the investigation is to claify the genetic contribution to the interindividual variability of ethanol action on the central nervous system. The 52 adult male healthy twin pairs (26 MZ, 26 DZ) got 1.2 ml/kg ethanol p.o. under standardized conditions; furthermore, 13 non-twin subjects were repeatedly subjected to the same procedure in order to test the intraindividual variability. The EEG was recorded before and 60, 120, 180, and 240 min after alcohol intake. The EEGs were off-line analyzed by means of a computer program for time domain analysis. As was already known, on the average alcohol led to a better synchronisation of the EEG, i.e., the number of beta-waves decreased whereas the number of alpha- and theta-waves increased. The extent of the alcohol effect on the EEG varied enormously between individuals; however, the EEGs of MZ twins proved to react indentically to alcohol loading, whereas the EEGs of DZ twins became mor dissimilar during the course of the experiment. The low-voltage EEG presumably is resistant to alchohol; furthermore, it is supposed that there exists a special beta-prone EEG-type which is also genetic in origin. The identical EEG reaction of MZ twins to alcohol loading could not be attributed to more similar blood alcohol concentrations. It is hypothesized that the differences in the extent of the alcohol effect on the EEG between individuals might reflect differences in the sensitivity of the ascending reticular activating system. In the literature it has frequently been reported that alcoholics have preferentially brain wave patterns which are poorly synchronized. These findings are discussed in the light of the present results.

Adult↗
PubMed1996

A multicentre inter-rater reliability study using the OPCRIT computerized diagnostic system.

We examined the reliability of the OPCRIT system from ratings produced by 30 USA and European clinicians involved in molecular genetic research. The OPCRIT system facilitates a polydiagnostic approach to research on severe psychiatric disorders. OPCRIT comprises a 90-item checklist of signs and symptoms and a suite of computer programs, which together generate diagnoses according to the operational criteria of 12 major classificatory systems (e.g. DSM-III, DSM-III-R, RDC, ICD-10). Thirty summaries of actual cases ranging in signs and symptoms, taken from independent sources, were rated by participants from research centres across Europe and the USA using the OPCRIT system. Each rating was then compared to a standard rating using a kappa statistic. Good levels of reliability were observed within all classifications (e.g. DSM-III-R, kappa = 0.73, RDC, kappa = 0.71; ICD-10, kappa = 0.70) and a similar pattern of ratings was found in both the European and USA samples. We conclude that the OPCRIT system, is both flexible and practicable retaining the 'top-down' advantage of operational definitions as well as the 'bottom-up' potential offered by well defined signs, symptoms and other component items. Within the limitations of an international, multicentre design this study shows that the OPCRIT system affords good reliability with raters from a variety of geographical and theoretical backgrounds.

Diagnosis, Computer-Assisted↗
PubMed2005

Serotonin gene polymorphisms and bipolar I disorder: focus on the serotonin transporter.

The pathogenesis of bipolar disorder may involve, at least in part, aberrations in serotonergic neurotransmission. Hence, serotonergic genes are attractive targets for association studies of bipolar disorder. We have reviewed the literature in this field. It is difficult to synthesize results as only one polymorphism per gene was typically investigated in relatively small samples. Nevertheless, suggestive associations are available for the 5HT2A receptor and the serotonin transporter genes. With the availability of extensive polymorphism data and high throughput genotyping techniques, comprehensive evaluation of these genes using adequately powered samples is warranted. We also report on our investigations of the serotonin transporter, SLC6A4 (17q11.1-q12). An insertion/deletion polymorphism (5HTTLPR) in the promoter region of this gene has been investigated intensively. However, the results have been inconsistent. We reasoned that other polymorphism/s may contribute to the associations and the inconsistencies may be due to variations in linkage disequilibrium (LD) patterns between samples. Therefore, we conducted LD analyses, as well as association and linkage using 12 polymorphisms, including 5HTTLPR. We evaluated two samples. The first sample consisted of 135 US Caucasian nuclear families having a proband with bipolar I disorder (BDI, DSM IV criteria) and available parents. For case-control analyses, the patients from these families were compared with cord blood samples from local Caucasian live births (n = 182). Our second, independent sample was recruited through the Systematic Treatment Enhancement Program for Bipolar Disorder (STEP-BD, 545 cases, 548 controls). No significant associations were detected at the individual polymorphism or haplotype level using the case-control or family-based analyses. Our analyses do not support association between SLC6A4 and BDI families. Further studies using sub-groups of BDI are worthwhile.

Bipolar Disorder↗
PubMed2003

The effect of GJB2 allele variants on performance after cochlear implantation.

OBJECTIVES/HYPOTHESIS: It has been hypothesized that etiology of hearing loss may serve as an independent variable in performance after cochlear implantation. To test this hypothesis, the authors identified pediatric cochlear implant recipients with gap junction protein beta2 (GJB2)-related deafness. The study examines performance outcomes associated with GJB2 deafness-causing allele variants. STUDY DESIGN: Pediatric cochlear implant patients were screened for GJB2 allele variants; statistical comparisons were made with prospectively obtained performance measures. METHODS: From 181 children who participated in a nationwide cochlear implant research program, 122 children were identified with congenital nonsyndromic sensorineural hearing loss and invited to participate. Screening for GJB2 allele variants was completed for 55 children. The children were homogeneous with respect to age (8 or 9 y) and age at implant (before age 5 y). All patients have previously undergone a prospective regimented battery of performance measures. RESULTS: Performance measures were compared between 22 children with and 33 children without mutations to determine whether GJB2 status was a significant predictor of cochlear implant outcomes. Reading and cognitive outcomes were significantly dependent on connexin status. The group of children who tested positive for GJB2-related deafness scored significantly higher on a nonverbal cognitive measure, Block Design, and on a measure of reading comprehension. CONCLUSION: The isolated insult to the cochlea created by GJB2 allele variants allows for preservation of central cognitive function. Better reading performance is seen in children with GJB2-related deafness.

Alleles↗
PubMed2000

Estimating divergence times in the presence of an overdispersed molecular clock.

Molecular loci that fail relative-rate tests are said to be "overdispersed." Traditional molecular-clock approaches to estimating divergence times do not take this into account. In this study, a method was developed to estimate divergence times using loci that may be overdispersed. The approach was to replace the traditional Poisson process assumption with a more general stationary process assumption. A probability model was developed, and an accompanying computer program was written to find maximum-likelihood estimates of divergence times under both the Poisson process and the stationary process assumptions. In simulation, it was shown that confidence intervals under the traditional Poisson assumptions often vastly underestimate the true confidence limits for overdispersed loci. Both models were applied to two data sets: one from land plants, the other from the higher metazoans. In both cases, the traditional Poisson process model could be rejected with high confidence. Maximum-likelihood analysis of the metazoan data set under the more general stationary process suggested that their radiation occurred well over a billion years ago, but confidence intervals were extremely wide. It was also shown that a model consistent with a Cambrian (or nearly Cambrian) origination of the animal phyla, although significantly less likely than a much older divergence, fitted the data well. It is argued that without an a priori understanding of the variance in the time between substitutions, molecular data sets may be incapable of ever establishing the age of the metazoan radiation.

Animals↗
PubMed1987

Behavioral and cytogenetic analysis of the cacophony courtship song mutant and interacting genetic variants in Drosophila melanogaster.

The courtship song of a Drosophila melanogaster male consists of tone pulses interspersed with humming sounds. An X chromosomal mutation, cacophony (cac), causes the production of polycyclic pulses readily distinguishable from those in wild type, which are mono- or bicyclic. Yet, courtship hums and flight wing beats are normal in this mutant, suggesting a specific role of the cac gene in the neural program underlying one particular feature of the fly's wing vibrations. A precise cytogenetic localization of cac is presented; this was obtained by uncovering the song abnormality with deletions that are missing all or the distal part of region 11A; the flies tested were diplo-X adults that had been turned into males by the transformer mutation. Duplications including distal 11A covered cac. The possibility of behavioral specificity for cac's effects was examined by screening a variety of sexual and nonsexual behaviors; these experiments included tests of flies in which the mutation was uncovered by a small deletion. We conclude that cac causes only a limited array of well-defined defects: longer and louder tone pulses in the song and depressed locomotor activity. Further complementation tests involving cac and other closely linked genetic variants--the night-blind-A (nbA) visual mutation, l(1)L13 lethal mutations, and a series of X chromosomal breakpoints--suggested complex interactions among these factors: the breakpoints uncover all three types of mutations; cac and nbA appear to be alleles of l(1)L13, whereas the two behavioral mutations complement each other.

Animals↗
PubMed2000

Conserved structural features in class I major fimbrial subunits (Pilin) in gram-negative bacteria. Molecular basis of classification in seven subfamilies and identification of intrasubfamily sequence signature motifs which might Be implicated in quaternary structure.

Type 1 and P-pili are prototype members of Class I fimbriae produced by Gram-negative bacteria. Despite common structural characteristics, the low level of amino acid sequence conservation among the Class I major fimbrial subunits (pilins) indicates considerable evolutionary distance between members of this superfamily. We highlight here structural relatedness between Class I pilins from their two-dimensional sequence analysis using hydrophobic cluster analysis (HCA) and secondary structure predictions (PHD program). We present evidence that all members of the Class I pilin family have clear structural relatedness and suggest that classification based on phylogenetic analysis of Class I pilins into seven subfamilies correlates with differences in structural properties of the amino acid sequences. Using a sensitive alignment process (HCA), we identified 29 residues in topohydrophobic positions which probably play a prominent role in folding. The most striking aspects that distinguish the different pilin subfamilies are (i) large variation in the length of the loops connecting the structurally conserved regions and (ii) intrasubfamily sequence signature motifs located on regions predicted to be in the beta-conformation. We suggest that these "intrasubfamily sequence signature motifs" are part of interactive surfaces which participate in subunit-subunit interactions. These motifs prove highly useful in characterizing and classifying new Class I fimbriae that have not yet been described and whose sequence diverges appreciably from those of characterized groups. (After the submission of our manuscript, the experimental structure of Class I pilus subunits was published. In light of these actual pilin structures, a comparison has been made between the predicted results and the crystal structure in the Note Added in Proof.)

Amino Acid Motifs↗
PubMed2004

[Obesity and cardiovascular diseases-theoretical background and therapeutic consequences].

In the normal population, the prevalence of obesity is almost 20%. It is a condition influenced by genetic factors, so that individual behavior cannot be regarded as its sole cause. The amount of food is essentially determined by the hormone leptin, the feedback regulation of which can be disturbed by a modification of the molecule or a mutation of the receptor. A further important determinant is energy consumption, which is subject to large individual variations, which partly result from thermogenesis. With regard to the fat distribution, it is concentrated on the trunk in the android form as compared to the hips in the gynecoid form. The android form is subject to a higher incidence of cardiovascular morbidity and mortality. The indirect determination of body fat by measuring the body mass index (weight [kg]/body weight [m(2)]) is hence less reliable than measuring the waist (women > 80 cm, men > 94 cm). The effects of generalized obesity on cardiovascular function are chiefly an increase of blood volume and an eccentric left ventricular hypertrophy. This first of all results in diastolic dysfunction, which can give rise to a disturbance of systolic function in left ventricular dilatation. Concentric hypertrophy develops in the presence of arterial hypertension. This is twice as frequent in obese patients than in the normal population, which is due to increased activity of the sympathetic nervous system and stimulation of the renin-angiotensin system. A disturbance of lipid metabolism is observed four to six times more frequently. The qualitative change in LDL fraction with a raised concentration of low density LDL particles appears to be of crucial importance. With increasing fat mass, the sensitivity to insulin is lowered, so that in obesity the risk of developing diabetes mellitus type 2 is tripled. Since there has been a dramatic increase in the numbers of overweight children and adolescents (from 10.5% to 15.5% within the past five years), prevention programs should be started in good time. A reduction in calorie intake and an altered dietary composition (55% complex carbohydrates, 30% fat and 15% to 20% protein) on the one hand, and increased physical activity on the other hand continue to be the central components. The latter is especially effective when it regularly gives rise to an increased turnover of fatty acids as a result of an increased energy metabolism at moderate intensity. This leads to adaptation, i. e. an increase in the activity of lipoprotein lipase. If prevention programs and/or changes in lifestyle do not give rise to the desired weight reduction, medication is indicated in some adults. Sibutramine (Reductil and orlistate (Xenical) lead to an additional weight loss of up to 10%. However, consistent treatment of any cardiovascular risk factors present is more important. Treatment of arterial hypertension is of greatest prognostic significance, especially in concomitant diabetes mellitus. In individual cases and after thorough discussion of indication surgical options should be considered.

Adolescent↗
PubMed2006

Biodiversity and emerging diseases.

First we remind general considerations concerning biodiversity on earth and particularly the loss of genetic biodiversity that seems irreversible whether its origin is directly or indirectly linked to human activities. Urgent and considerable efforts must be made from now on to cataloge, understand, preserve, and enhance the value of biodiversity while ensuring food safety and human and animal health. Ambitious integrated and multifield research programs must be implemented in order to understand the causes and anticipate the consequences of loss of biodiversity. Such losses are a serious threat to sustainable development and to the quality of life of future generations. They have an influence on the natural balance of global biodiversity in particularly in reducing the capability of species to adapt rapidly by genetic mutations to survive in modified ecosystems. Usually, the natural immune systems of mammals (both human and animal), are highly polymorphic and able to adapt rapidly to new situations. We more specifically discuss the fact that if the genetic diversity of the affected populations is low the invading microorganisms, will suddenly expand and create epidemic outbreaks with risks of pandemic. So biodiversity appears to function as an important barrier (buffer), especially against disease-causing organisms, which can function in different ways. Finally, we discuss the importance of preserving biodiversity mainly in the wildlife ecosystems as an integrated and sustainable approach among others in order to prevent and control the emergence or reemergence of diseases in animals and humans (zoonosis). Although plants are also part of this paradigm, they fall outside our field of study.

Adaptation, Physiological↗
PubMed2006

Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers.

The archipelago of Indonesia has a long history of rice production across a broad range of rice-growing environments resulting in a diverse array of local Indonesian rice varieties. Although some have been incorporated into modern breeding programs, the vast majority of these landraces remain untapped. To better understand this rich source of genetic diversity we have characterized 330 rice accessions, including 246 Indonesian landraces and 63 Indonesian improved cultivars, using 30 fluorescently-labeled microsatellite markers. The landraces were selected across 21 provinces and include representatives of the classical subpopulations of cere, bulu, and gundil rices. A total of 394 alleles were detected at the 30 simple sequence repeat loci, with an average number of 13 alleles per locus across all accessions, and an average polymorphism information content value of 0.66. Genetic diversity analysis characterized the Indonesian landraces as 68% indica and 32% tropical japonica, with an indica gene diversity of 0.53 and a tropical japonica gene diversity of 0.56, and a Fst of 0.38 between the two groups. All of the improved varieties sampled were indica, and had an average gene diversity of 0.46. A set of high quality Indonesian varieties, including Rojolele, formed a separate cluster within the tropical japonicas. This germplasm presents a valuable source of diversity for future breeding and association mapping efforts.

Chromosomes, Plant↗
PubMed2006

Temporal analysis of French Bordetella pertussis isolates by comparative whole-genome hybridization.

Bordetella pertussis, a gram-negative beta-proteobacterium, is the agent of whooping cough in humans. Whooping cough remains a public health problem worldwide, despite well-implemented infant/child vaccination programs. It continues to be endemic and is observed cyclically in vaccinated populations. Classical molecular subtyping methods indicate that genome diversity among B. pertussis isolates is limited. Although the whole bacterial genome has been studied by pulsed-field gel electrophoresis, the genes implicated in the diversity have not been identified. We developed a B. pertussis whole-genome DNA microarray representing over 91% of the predicted coding sequences of the sequenced strain Tohama I. Genomic DNA from clinical isolates with various pulsed-field gel electrophoresis profile patterns was competitively hybridized with the DNA microarray and coding sequences were classified as present, absent or duplicated. Our data strongly suggest that the B. pertussis population is dynamic. In France, with highly vaccinated population, the genetic diversity is low and decreasing with time, and clonal expansion correlates with cycles of the disease. This decrease in diversity is essentially due to loss of genes and pseudogenes. The genes deleted are most of the time flanked by insertion sequences.

Bordetella pertussis↗
PubMed2001

Assessment of the total number of human transcription units.

Variation in the estimates of the number of genes encoded by the human genome (28,000-120,000) attests to the difficulty of systematically identifying human genes. Sequencing of human chromosome 22 (Chr22) provided the first comprehensive, unbiased view of an entire human chromosome, and intensive analysis of this sequence identified 545 genes and 134 pseudogenes that had similarity or identity to known proteins and/or ESTs and which were listed in the gene annotation (http://www.sanger.ac.uk/HGP/Chr22). This analysis yielded an estimate of approximately 36,000 functional expressed genes in the human genome (and 9000 pseudogenes). However, a key uncertainty in this estimate was that hundreds of additional genes beyond those annotated in the Chr22 sequence are predicted by the gene prediction program Genscan, an unknown number of which might represent additional expressed genes. To determine what fraction of these "predicted novel genes" (PNGs) represents expressed human genes, we used a sensitive RT-PCR assay to detect predicted transcripts in 17 tissues and one cell line. Our results indicate that at least 5000-9000 additional human genes which lack similarity to known genes or proteins exist in the human genome, increasing baseline gene estimates to approximately 41,000-45,000.

Chromosomes, Human, Pair 22↗
PubMed2003

Gene expression patterns associated with recurrent chromosomal translocations in acute lymphoblastic leukemia.

We obtained a global view of gene expression in both cell lines and pediatric acute lymphoblastic leukemia (ALL) samples that harbor one of several selected chromosomal abnormalities. When the cell lines were studied alone, we found that these chromosomal abnormalities were associated with the predominant variation in transcriptional programs across the set of cell lines studied. When cell lines and clinical samples were studied together, we found that each chromosomal abnormality (TEL/AML1, BCR/ABL, or MLL abnormalities) was associated with a characteristic gene expression signature that was shared by both cell lines and clinical samples. However, BCR/ABL was associated with a much more heterogeneous pattern of expression than were TEL/AML1 and MLL abnormalities. This observation has important implications for the study of BCR/ABL ALL. In addition, we systematically identified genes whose expression was associated with TEL/AML1, BCR/ABL, or MLL abnormalities in both clinical samples and cell lines. Although some of these genes have previously been described, many have not previously been reported to be associated with one of these chromosomal abnormalities. Notably, we found that the erythropoietin receptor (EPOR) is consistently highly expressed in TEL/AML1 ALL compared with BCR/ABL or MLL.

Adolescent↗
PubMed2005

High frequency of the IVS2-2A>G DNA sequence variation in SLC26A5, encoding the cochlear motor protein prestin, precludes its involvement in hereditary hearing loss.

BACKGROUND: Cochlear outer hair cells change their length in response to variations in membrane potential. This capability, called electromotility, is believed to enable the sensitivity and frequency selectivity of the mammalian cochlea. Prestin is a transmembrane protein required for electromotility. Homozygous prestin knockout mice are profoundly hearing impaired. In humans, a single nucleotide change in SLC26A5, encoding prestin, has been reported in association with hearing loss. This DNA sequence variation, IVS2-2A>G, occurs in the exon 3 splice acceptor site and is expected to abolish splicing of exon 3. METHODS: To further explore the relationship between hearing loss and the IVS2-2A>G transition, and assess allele frequency, genomic DNA from hearing impaired and control subjects was analyzed by DNA sequencing. SLC26A5 genomic DNA sequences from human, chimp, rat, mouse, zebrafish and fruit fly were aligned and compared for evolutionary conservation of the exon 3 splice acceptor site. Alternative splice acceptor sites within intron 2 of human SLC26A5 were sought using a splice site prediction program from the Berkeley Drosophila Genome Project. RESULTS: The IVS2-2A>G variant was found in a heterozygous state in 4 of 74 hearing impaired subjects of Hispanic, Caucasian or uncertain ethnicity and 4 of 150 Hispanic or Caucasian controls (p = 0.45). The IVS2-2A>G variant was not found in 106 subjects of Asian or African American descent. No homozygous subjects were identified (n = 330). Sequence alignment of SLC26A5 orthologs demonstrated that the A nucleotide at position IVS2-2 is invariant among several eukaryotic species. Sequence analysis also revealed five potential alternative splice acceptor sites in intron 2 of human SLC26A5. CONCLUSION: These data suggest that the IVS2-2A>G variant may not occur more frequently in hearing impaired subjects than in controls. The identification of five potential alternative splice acceptor sites in intron 2 of human SLC26A5 suggests a potential mechanism by which expression of prestin might be maintained in cells carrying the SLC26A5 IVS2-2A>G DNA sequence variation. Additional studies are needed to evaluate the effect of the IVS2-2A>G transition on splicing of SLC26A5 transcripts and characterize the hearing status of individuals homozygous for the IVS2-2A>G variant.

Adenine↗
PubMed1986

Examination of protein sequence homologies: III. Ribosomal protein YS25 from Saccharomyces cerevisiae and its counterparts from Schizosaccharomyces pombe, rat liver, and Escherichia coli.

The sequences of the ribosomal proteins YS25, SP-S28, RL-S21, and Ec-S6, from Saccharomyces cerevisiae, Schizosaccharomyces pombe, rat liver, and Escherichia coli, respectively, have been examined using a computer program that searches for homologous tertiary structures. Matrices of comparisons among the eukaryotic sequences show that they match each other sequentially without any internal gaps. The average values of the correlation coefficients obtained from the comparison matrices are higher for the first halves of the sequences than for the latter halves. This result suggests that the first halves of the sequences may represent a more important domain than the latter halves. The comparison matrices between the eukaryotic and bacterial sequences of ribosomal proteins, however, do not show sequentially arranged homology, though there are six well-matching segments arranged in different orders in the two types of sequences. This implies that the eukaryotic sequences of the ribosomal protein were reconstituted by two internal transpositions and six deletions of 4-12 residues each from the ancestral sequence during the divergence between bacterial and eukaryotic genes. These findings may give insight into structural and quantitative studies of evolutionary divergence between eukaryotes and prokaryotes.

Amino Acid Sequence↗