Cloning and characterization of the rat cytochrome P450 4F5 (CYP4F5) gene

The analysis of a non-redundant set of human proteins, for which both the crystallographic structures and the corresponding gene sequences are available, show that bases at third codon position are non-uniformly distributed along the coding sequences. Significant compositional differences are found by comparing the gene regions corresponding to the different secondary structures of the proteins. Inter-and intra-structure differences were most pronounced in the GC-richest genes. These results are not compatible with any proposed hypotheses based on a neutral process of formation/maintenance of the high GC₃ levels of the genes localized in the GC-richest isochores of the human genome.     

A simple quantitative model of the molecular clock

Summary We present the ideas, and their motivation, at the basis of a simple model of nucleic acid evolution: thestationary Markov process, or Markov clock. After a brief review of its relevant mathematical properties, the Markov clock is applied to nucleotide sequences from mitochondrial and nuclear genes of different species. Particular emphasis is given to the necessity of carrying out a correct statistical analysis, which allows us to check quantitatively the applicability of our model. We find evidence that the Markov clock ticks in many different processes, and that its limitations can be understood in terms of a simple idea that we call the base-drift hypothesis. This hypothesis correlates the deviations from the stationarity of the Markov process to the evolutionary distanced _AB ^(P) of two species A and B, relative to the processP. We conclude by discussing the implications of our findings for future work.     

DNA进化马尔可夫过程模型的评价与推广

本文对ＤＮＡ序列进化过程中核苷酸替代的随机模型进行了评价,对替代速率在时间和空间上不恒定的情形进行了考察和推广。Ｌａｎａｖｅ等（１９８４）曾提出一个模型,宣称对替代的模式未做任何假定,但事实上我们证明它假定替代过程是可逆的。运用２－ｐ、４－ｐ和６－ｐ模型进行的计算表明替代速度在位点间的差异会造成估计的替代数严重偏低,并且替代数越大,偏差也越大。替代模式在位点间的差异也会造成估计值偏低,但偏差不严重     

Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds

At a resolution of 850 bands, human chromosomes comprise two subsets of bands, the GC-richest H3⁺ and the GC-poorest L1⁺ bands, accounting for about 17 and 26%, respectively, of all bands. The former are a subset of the R bands and the latter are a subset of the G bands. These bands showed the highest and the lowest gene densities, respectively, as well as a number of other distinct features. Here we report that human and chicken interphase nuclei are characterized by the following features. (1) The gene-richest/GC-richest chromosomal regions are predominantly distributed in internal locations, whereas the gene-poorest/GC-poorest DNA regions are close to the nuclear envelope. (2) The interphase chromosomes seem to be characterized by a polar arrangement, because the gene-richest/GC-richest bands and the gene-poorest/GC-poorest bands are predominantly located in the distal and proximal regions, respectively, of chromosomes, and because interphase chromosomes are extremely long. While this polar arrangement is evident in the larger chromosomes, it is not displayed by the chicken microchromosomes and by some small human chromosomes, namely by chromosomes that are almost only composed by GC-rich or by GC-poor DNA. (3) The gene-richest chromosomal regions display a much more spread-out conformation compared to the gene-poorest regions in human nuclei. This finding has interesting implications for the formation of GC-rich isochores of warm-blooded vertebrates.     

DNA turnover and the molecular clock

Summary Many detailed studies on the mechanisms by which different components of eukaryotic nuclear genomes have diverged reveal that the majority of sequences are seemingly not passively accumulating base substitutions in a clocklike manner solely determined by laws of diffusion at the population level. It appears that variation in the rates, units, biases, and gradients of several DNA turnover mechanisms are contributing to the course of DNA divergence. Turnover mechanisms have the potential to retard, maintain, or accelerate the rate of DNA differentiation between populations. Furthermore, examples are known of coding and noncoding DNA subject to the simultaneous operation of several turnover mechanisms leading to complex patterns of fine-scale restructuring and divergence, generally uninterpretable using selection and/or neutral drift arguments in isolation. Constancy in the rate of divergence, where observed over defined periods of time, could be a reflection of constancy in the rates and units of turnover. However, a consideration of the generally large disparity between rates of turnover and mutation reveals that DNA clocks, which would be independently driven by turnover in separate genomic components, would tend to be episodic. The utility of any given DNA sequence for measuring time and species relationships, like individual proteins, is proportional to the extent to which all contributing forces to the evolution of the sequence, internal and external, are understood.     

Stochastic approach to molecular interactions and computational theory of metabolic and genetic regulations

The underlying molecular mechanisms of metabolic and genetic regulations are computationally identical and can be described by a finite state Markov process. We establish a common computational model for both regulations based on the stationary distribution of the Markov process with the aim of establishing a unified, quantitative model of general biological regulations. Various existing results regarding intracellular regulations are derived including the classical Michaelis-Menten equation and its generalization to more complex allosteric enzymes in a systematic way. The notion of probability flow is introduced to distinguish the equilibrium stationary distribution from the non-equilibrium one; it plays a crucial role in the analysis of stationary state equations. A graphical criterion to guarantee the existence of an equilibrium stationary distribution is derived, which turns out to be identical to the classical Wegscheider condition. Simple graphical methods to compute the equilibrium and non-equilibrium stationary distributions are derived based crucially on the probability flow, which dramatically simplifies the classical methods still used in enzymology.     

Body mass is less important than bird order in determining the molecular rate for bird mitochondrial DNA

A negative relationship between body mass and molecular evolution rates has been suggested, and recently a correlation equation has been published based on mitochondrial genomic data of 475 bird species and their body masses. Here, we re‐analysed these data and show that the bird order as a proxy of monophyletic groups was a stronger predictor of the molecular rate than the body mass. We provide order‐specific molecular substitution rates. Only three orders (Galliformes, Gruiformes, Pelecaniformes) showed a very clear negative correlation, and specific correlation equations are given for these. The molecular rates of bird orders differed strongly at similar mean body masses, and we suggest that the previously described trend across all birds may arise as smaller species also tend to have characteristic life histories, namely faster turnover of generations, higher fecundity and shorter lifespans.     

Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata)

The phylogenetic relationships of 46 echinoids, with representatives from 13 of the 14 ordinal-level clades and about 70% of extant families commonly recognized, have been established from 3 genes (3,226 alignable bases) and 119 morphological characters. Morphological and molecular estimates are similar enough to be considered suboptimal estimates of one another, and the combined data provide a tree that, when calibrated against the fossil record, provides paleontological estimates of divergence times and completeness of their fossil record. The order of branching on the cladogram largely agrees with the stratigraphic order of first occurrences and implies that their fossil record is more than 85% complete at family level and at a resolution of 5-Myr time intervals. Molecular estimates of divergence times derived from applying both molecular clock and relaxed molecular clock models are concordant with estimates based on the fossil record in up to 70% of cases, with most concordant results obtained using Sanderson's semiparametric penalized likelihood method and a logarithmic-penalty function. There are 3 regions of the tree where molecular and fossil estimates of divergence time consistently disagree. Comparison with results obtained when molecular divergence dates are estimated from the combined (morphology + gene) tree suggests that errors in phylogenetic reconstruction explain only one of these. In another region the error most likely lies with the paleontological estimates because taxa in this region are demonstrated to have a very poor fossil record. In the third case, morphological and paleontological evidence is much stronger, and the topology for this part of the molecular tree differs from that derived from the combined data. Here the cause of the mismatch is unclear but could be methodological, arising from marked inequality of molecular rates. Overall, the level of agreement reached between these different data and methodological approaches leads us to believe that careful application of likelihood and Bayesian methods to molecular data provides realistic divergence time estimates in the majority of cases (almost 80% in this specific example), thus providing a remarkably well-calibrated phylogeny of a character-rich clade of ubiquitous marine benthic invertebrates.     

Contrasting rates of nucleotide substitution in the X-Linked and Y-Linked zinc finger genes

We have sequenced the entire exon (1,180 bp) encoding the zinc finger domain of the X-linked and Y-linked zinc finger genes (ZFX and ZFY, respectively) in the orangutan, the baboon, the squirrel monkey, and the rat; a total of 9,442 by were sequenced. The ratio of the rates of synonymous substitution in the ZFY and ZFX genes is estimated to be 2.1 in primates. This is close to the ratio of 2.3 estimated from primate ZFY and ZFX intron sequences and supports the view that the male-to-female ratio of mutation rate in humans is considerably higher than 1 but not extremely large. The ratio of synonymous substitution rates in ZFY and ZFX is estimated to be 1.3 in the rat lineage but 4.2 in the mouse lineage. The former is close to the estimate (1.4) from introns. The much higher ratio in the mouse lineage (not statistically significant) might have arisen from relaxation of selective constraints. The synonymous divergence between mouse and rat ZFX is considerably lower than that between mouse and rat autosomal genes, agreeing with previous observations and providing some evidence for stronger selective constraints on synonymous changes in X-linked genes than in autosomal genes. At the protein level ZFX has been highly conserved in all placental mammals studied while ZFY has been well conserved in primates and foxes but has evolved rapidly in mice and rats, possibly due to relaxation of functional constraints as a result of the development of X-inactivation of ZFX in rodents. The long persistence of the ZFY-ZFX gene pair in mammals provides some insight into the process of degeneration of Y-linked genes.Correspondence to: W.-H. Li     

Molecular phylogeny of the Chinese ranids inferred from nuclear and mitochondrial DNA sequences

The phylogeny of representative species of Chinese ranids was reconstructed using two nuclear (tyrosinase and rhodopsin) and two mitochondrial (12S rRNA, 16S rRNA) DNA fragments. Maximum parsimony, Bayesian, and maximum likelihood analyses were employed. In comparison with the results from nuclear and mitochondrial data, we used nuclear gene data as our preferred phylogenetic hypothesis. We proposed two families (Ranidae, Dicroglossidae) for Chinese ranids, with the exception of genus Ingerana. Within Dicroglossidae, four tribes were supported including Dicroglossini, Paini, Limnonectini, and Occidozygini. A broader sampling strategy and evidence from additional molecular markers are required to decisively evaluate the evolutionary history of Chinese ranids.     

Testing the relationship between morphological and molecular rates of change along phylogenies

Abstract.— Molecular evolution has been considered to be essentially a stochastic process, little influenced by the pace of phenotypic change. This assumption was challenged by a study that demonstrated an association between rates of morphological and molecular change estimated for "total-evidence" phylogenies, a finding that led some researchers to challenge molecular date estimates of major evolutionary radiations. Here we show that Omland's (1997) result is probably due to methodological bias, particularly phylogenetic nonindependence, rather than being indicative of an underlying evolutionary phenomenon. We apply three new methods specifically designed to overcome phylogenetic bias to 13 published phylogenetic datasets for vertebrate taxa, each of which includes both morphological characters and DNA sequence data. We find no evidence of an association between rates of molecular and morphological rates of change.     

Human OGG1 activity in nucleosomes is facilitated by transient unwrapping of DNA and is influenced by the local histone environment

If unrepaired, damage to genomic DNA can cause mutations and/or be cytotoxic. Single base lesions are repaired via the base excision repair (BER) pathway. The first step in BER is the recognition and removal of the nucleobase lesion by a glycosylase enzyme. For example, human oxoguanine glycosylase 1 (hOGG1) is responsible for removal of the prototypic oxidatively damaged nucleobase, 8-oxo-7,8-dihydroguanine (8-oxoG). To date, most studies of glycosylases have used free duplex DNA substrates. However, cellular DNA is packaged as repeating nucleosome units, with 145 base pair segments of DNA wrapped around histone protein octamers. Previous studies revealed inhibition of hOGG1 at the nucleosome dyad axis and in the absence of chromatin remodelers. In this study, we reveal that even in the absence of chromatin remodelers or external cofactors, hOGG1 can initiate BER at positions off the dyad axis and that this activity is facilitated by spontaneous and transient unwrapping of DNA from the histones. Additionally, we find that solution accessibility as determined by hydroxyl radical footprinting is not fully predictive of glycosylase activity and that histone tails can suppress hOGG1 activity. We therefore suggest that local nuances in the nucleosome environment and histone-DNA interactions can impact glycosylase activity.     

Light and feeding entrainment of the molecular circadian clock in a marine teleost (Sparus aurata)

Daily light and feeding cycles act as powerful synchronizers of circadian rhythmicity. Ultimately, these external cues entrain the expression of clock genes, which generate daily rhythmic behavioral and physiological responses in vertebrates. In the present study, we investigated clock genes in a marine teleost (gilthead sea bream). Partial cDNA sequences of key elements from both positive (Bmal1, Clock) and negative (Per2, Cry1) regulatory loops were cloned before studying how feeding time affects the daily rhythms of locomotor activity and clock gene expression in the central (brain) and peripheral (liver) oscillators. To this end, all fish were kept under a light-dark (LD) cycle and were divided into three experimental groups, depending on the time of their daily meal: mid-light (ML), mid-darkness (MD), or at random (RD) times. Finally, the existence of circadian control on gene expression was investigated in the absence of external cues (DD?+?RD). The behavioral results showed that seabream fed at ML or RD displayed a diurnal activity pattern (>91% of activity during the day), whereas fish fed at MD were nocturnal (89% of activity during the night). Moreover, seabream subjected to regular feeding cycles (ML and MD groups) showed food-anticipatory activity (FAA). Regardless of the mealtime, the daily rhythm of clock gene expression in the brain peaked close to the light-dark transition in the case of Bmal1 and Clock, and at the beginning of the light phase in the case of Per2 and Cry1, showing the existence of phase delay between the positive and negative elements of the molecular clock. In the liver, however, the acrophases of the daily rhythms differed depending on the feeding regime: the maximum expression of Bmal1 and Clock in the ML and RD groups was in antiphase to the expression pattern observed in the fish fed at MD. Under constant conditions (DD?+?RD), Per2 and Cry1 showed circadian rhythmicity in the brain, whereas Bmal1, Clock, and Per2 did in the liver. Our results indicate that the seabream clock gene expression is endogenously controlled and in liver it is strongly entrained by food signals, rather than by the LD cycle, and that scheduled feeding can shift the phase of the daily rhythm of clock gene expression in a peripheral organ (liver) without changing the phase of these rhythms in a central oscillator (brain), suggesting uncoupling of the light-entrainable oscillator (LEO) from the food-entrainable oscillator (FEO). These findings provide the basis and new tools for improving our knowledge of the circadian system and entraining pathways of this fish species, which is of great interest for the Mediterranean aquaculture. (Author correspondence: javisan@um.es).     

Differentiation trees,a junk DNA molecular clock,and the evolution of neoteny in salamanders

Obligate neotenic salamanders die if forced to metamorphose. We suggest that this can be explained by assuming: 1) their “excess” DNA is “junk” DNA; 2) the “adult” specifying portion of the DNA becomes junk DNA and is available for repeated duplication. This suggests a “new” junk DNA molecular clock. We obtain remarkable agreement in “predicting” the amount of DNA per nucleus in present day non-obligate neotene salamanders from this molecular clock. These observatons are consistent with the idea that the development of these animals is describable in terms of differentiation trees whose branches (gene cascades) corresponding to adult somatic tissues accumulate deleterious mutations over evolutionary time. We show that the amount of DNA per nucleus increases linearly with the phylogenetic age of salamander families. The lack of constraints by natural selection, on unused adult branches, may account for the large amount of so-called “junk DNA” in obligate neotenic salamanders. The effects of this excess DNA, via increased cell size, suggest a positive feedback, ecophysiological explanation for such junk DNA: adaptation to cool water environments is enhanced by the lower metabolism associated with more DNA, larger cells and slower developmental time.     

The MADS-box floral homeotic gene lineages predate the origin of seed plants: Phylogenetic and molecular clock estimates

Flower development in angiosperms is controlled in part by floral homeotic genes, many of which are members of the plant MADS-box regulatory gene family. The evolutionary history of these developmental genes was reconstructed using 74 loci from 15 dicot, three monocot, and one conifer species. Molecular clock estimates suggest that the different floral homeotic gene lineages began to diverge from one another about 450–500 mya, around the time of the origin of land plants themselves. Received: 31 January 1997 / Accepted: 9 April 1997     

Nuclear counterparts of the cytoplasmic mitochondrial 12S rRNA gene: A problem of ancient DNA and molecular phylogenies

Monkey mummy bones and teeth originating from the North Saqqara Baboon Galleries (Egypt), soft tissue from a mummified baboon in a museum collection, and nineteenth/twentieth-century skin fragments from mangabeys were used for DNA extraction and PCR amplification of part of the mitochondrial 12S rRNA gene. Sequences aligning with the 12S rRNA gene were recovered but were only distantly related to contemporary monkey mitochondrial 12S rRNA sequences. However, many of these sequences were identical or closely related to human nuclear DNA sequences resembling mitochondrial 12S rRNA (isolated from a cell line depleted in mitochondria) and therefore have to be considered contamination. Subsequently in a separate study we were able to recover genuine mitochondrial 12S rRNA sequences from many extant species of nonhuman Old World primates and sequences closely resembling the human nuclear integrations. Analysis of all sequences by the neighbor-joining (NJ) method indicated that mitochondrial DNA sequences and their nuclear counterparts can be divided into two distinct clusters. One cluster contained all temporary cytoplasmic mitochondrial DNA sequences and approximately half of the monkey nuclear mitochondriallike sequences. A second cluster contained most human nuclear sequences and the other half of monkey nuclear sequences with a separate branch leading to human and gorilla mitochondrial and nuclear sequences. Sequences recovered from ancient materials were equally divided between the two clusters. These results constitute a warning for when working with ancient DNA or performing phylogenetic analysis using mitochondrial DNA as a target sequence: Nuclear counterparts of mitochondrial genes may lead to faulty interpretation of results.Correspondence to: A.C. van der Kuyl     

Molecular systematics and diversification of the Asian scimitar babblers (Timaliidae, Aves) based on mitochondrial and nuclear DNA sequences

The Asian scimitar babblers, including the genus Pomatorhinus and Xiphirhynchus, are a small group of babblers characterized by long down-curved bills and a distribution throughout East and Southeast Asia. To infer the molecular phylogeny of this group and their divergence time, we examined sequences of multiple fragments including two entire mitochondrial genes and four nuclear introns (4352 bp in total) from multiple samples of eight of the nine recognized species of Asian scimitar babblers. The phylogeny resulting from the concatenated multi-locus dataset suggests that Pomatorhinus is paraphyletic. Due to its paraphyly, we propose dividing the traditional genus Pomatorhinus into two morphologically and genetically diagnosable genera: Pomatorhinus and Erythrogenys. Results of the molecular dating based on the conventional mitochondrial DNA divergence rate indicates that the diversification of these babblers is likely congruent with the historical climatic events. Our findings shed light on the diversification of avian species in southern Asia, a poorly studied biodiversity hotspot.