Low achromatic contrast sensitivity in birds: a common attribute shared by many phylogenetic orders

Vision is an important sensory modality in birds, which can outperform other vertebrates in some visual abilities. However, sensitivity to achromatic contrasts - the ability to discern luminance difference between two objects or an object and its background - has been shown to be lower in birds compared with other vertebrates. We conducted a comparative study to evaluate the achromatic contrast sensitivity of 32 bird species from 12 orders using the optocollic reflex technique. We then performed an analysis to test for potential variability in contrast sensitivity depending on the corneal diameter to the axial length ratio, a proxy of the retinal image brightness. To account for potential influences of evolutionary relatedness, we included phylogeny in our analyses. We found a low achromatic contrast sensitivity for all avian species studied compared with other vertebrates (except small mammals), with high variability between species. This variability is partly related to phylogeny but appears to be independent of image brightness.

Anomalous binocular vision in African Harrier-Hawks

An animal's visual field is the three-dimensional space around its head from which it can extract visual information at any instant1. Bird visual fields vary markedly between species, and this variation is likely to be driven primarily by foraging ecology1,2,3. The binocular visual field is the region in which the visual fields of the two eyes overlap; thus, objects in the binocular field are imaged by both eyes simultaneously. The binocular field plays a pivotal role in the detection of symmetrical optic flow-fields, providing almost instantaneous information on the direction of travel and the time to contact a target towards which the head or feet is travelling; thus, information from the binocular field is crucial in guiding key foraging behaviours2,3. Here, we demonstrate an unusual visual field and binocular extent above the head in African Harrier-Hawks, also known as Gymnogenes (Polyboroides typus) compared to 18 other members of the Accipitridae4,5. We argue that the observed visual field can be attributed to the unusual and specific foraging behaviour of African Harrier-Hawks.

Binocular field configuration in owls: the role of foraging ecology

The binocular field of vision differs widely in birds depending on ecological traits such as foraging. Owls (Strigiformes) have been considered to have a unique binocular field, but whether it is related to foraging has remained unknown. While taking into account allometry and phylogeny, we hypothesized that both daily activity cycle and diet determine the size and shape of the binocular field in owls. Here, we compared the binocular field configuration of 23 species of owls. While we found no effect of allometry and phylogeny, ecological traits strongly influence the binocular field shape and size. Binocular field shape of owls significantly differed from that of diurnal raptors. Among owls, binocular field shape was relatively conserved, but binocular field size differed among species depending on ecological traits, with larger binocular fields in species living in dense habitat and foraging on invertebrates. Our results suggest that (i) binocular field shape is associated with the time of foraging in the daily cycle (owls versus diurnal raptors) and (ii) that binocular field size differs between closely related owl species even though the general shape is conserved, possibly because the field of view is partially restricted by feathers, in a trade-off with auditory localization.

Binocular vision and foraging in ducks, geese and swans (Anatidae)

Wide variation in visual field configuration across avian species is hypothesized to be driven primarily by foraging ecology and predator detection. While some studies of selected taxa have identified relationships between foraging ecology and binocular field characteristics in particular species, few have accounted for the relevance of shared ancestry. We conducted a large-scale, comparative analysis across 39 Anatidae species to investigate the relationship between the foraging ecology traits of diet or behaviour and binocular field parameters, while controlling for phylogeny. We used phylogenetic models to examine correlations between traits and binocular field characteristics, using unidimensional and morphometric approaches. We found that foraging behaviour influenced three parameters of binocular field size: maximum binocular field width, vertical binocular field extent, and angular separation between the eye-bill projection and the direction of maximum binocular field width. Foraging behaviour and body mass each influenced two descriptors of binocular field shape. Phylogenetic relatedness had minimal influence on binocular field size and shape, apart from vertical binocular field extent. Binocular field differences are associated with specific foraging behaviours, as related to the perceptual challenges of obtaining different food items from aquatic and terrestrial environments.

Retinal topography in two species of flamingo (Phoenicopteriformes: Phoenicopteridae)

In this study, we assessed eye morphology and retinal topography in two flamingo species, the Caribbean flamingo (Phoenicopterus ruber) and the Chilean flamingo (P. chilensis). Eye morphology is similar in both species and cornea size relative to eye size (C:A ratio) is intermediate between those previously reported for diurnal and nocturnal birds. Using stereology and retinal whole mounts, we estimate that the total number of Nissl-stained neurons in the retinal ganglion cell (RGC) layer in the Caribbean and Chilean flamingo is ~1.70 and 1.38 million, respectively. Both species have a well-defined visual streak with a peak neuron density of between 13,000 and 16,000 cells mm^-2 located in a small central area. Neurons in the high-density regions are smaller and more homogeneous compared to those in medium- and low-density regions. Peak anatomical spatial resolving power in both species is approximately 10-11 cycles/deg. En-face images of the fundus in live Caribbean flamingos acquired using spectral domain optical coherence tomography (SD-OCT) revealed a thin, dark band running nasotemporally just dorsal to the pecten, which aligned with the visual streak in the retinal topography maps. Cross-sectional images (B-scans) obtained with SD-OCT showed that this dark band corresponds with an area of retinal thickening compared to adjacent areas. Neither the retinal whole mounts, nor the SD-OCT imaging revealed any evidence of a central fovea in either species. Overall, we suggest that eye morphology and retinal topography in flamingos reflects their cathemeral activity pattern and the physical nature of the habitats in which they live.

Inter-individual differences in foveal shape in a scavenging raptor, the black kite Milvus migrans

Birds, and especially raptors, are believed to forage mainly using visual cues. Indeed, raptors (scavengers and predators) have the highest visual acuity known to date. However, scavengers and predators differ in their visual systems such as in their foveal configuration. While the function of the foveal shape remains unknown, individual variation has never been quantified in birds. In this study, we examined whether foveal shape differs among individuals in relation to eye size, sex, age, eye (left or right) and genetic proximity in a scavenging raptor, the black kite Milvus migrans. We assessed foveal shape in 47 individuals using spectral domain optical coherence tomography (OCT) and geometric morphometric analysis. We found that foveal depth was significantly related to eye size. While foveal width also increased with eye size, it was strongly related to age; younger individuals had a wider fovea with a more pronounced rim. We found no relationship between foveal shape and genetic proximity, suggesting that foveal shape is not a hereditary trait. Our study revealed that the shape of the fovea is directly linked to eye size and that the physical structure of the fovea may develop during the entire life of black kites.

How fast can raptors see?

Birds, and especially raptors, are highly visual animals. Some of them have the highest spatial resolving power known in the animal kingdom, allowing prey detection at distance. While many raptors visually track fast-moving and manoeuvrable prey, requiring high temporal resolution, this aspect of their visual system has never been studied before. In this study, we estimated how fast raptors can see, by measuring the flicker fusion frequency of three species with different lifestyles. We found that flicker fusion frequency differed among species, being at least 129 Hz in the peregrine falcon, Falco peregrinus, 102 Hz in the saker falcon, Falco cherrug, and 81 Hz in the Harris's hawk, Parabuteo unicinctus We suggest a potential link between fast vision and hunting strategy, with high temporal resolution in the fast-flying falcons that chase fast-moving, manoeuvrable prey and a lower resolution in the Harris's hawk, which flies more slowly and targets slower prey.

Olfaction in raptors

Raptors from the orders Accipitriformes and Falconiformes have been considered to rely principally on vision. Historically, this assumption has led scientists to discount any possible sense of smell in these birds, until work on cathartid vultures indicated that these species at least rely on olfaction to find carrion. In this review I provide evidence that raptors in general have functional olfactory systems that they may use in a range of different contexts. Anatomical studies show that raptors have well-developed olfactory bulbs that are within the range of other bird species. Furthermore, all raptors studied have multiple functional olfactory genes, with, for instance, 283 olfactory genes in the Oriental honey buzzard, Pernis orientalis, of which 81.5% are functional. It has also been shown that some raptors species may functionally use olfactory cues to forage and, potentially, for communication. While further research is required, the available evidence suggests that olfaction may be a more important sensory modality in these birds than previously thought.

Sight or smell: which senses do scavenging raptors use to find food?

Raptors are usually considered to be mainly visually dependent, and the use of other sensory modalities has rarely been studied in these birds. Here, we investigated experimentally which senses (vision and/or olfaction) Turkey vultures (Cathartes aura) and Southern caracaras (Caracara plancus) use to find hidden food. First, two identical stainless-steel perforated balls, one containing a putrefied piece of meat and the other an odorless control, were presented to birds in binary choice experiments. Both species interacted more with the smelling ball than with the control, suggesting that they were attracted by the odor of the hidden meat. In a second experiment, individuals were accustomed to eat in one specifically colored ball (blue or green). In the test phase, the meat was hidden in the opposite color with respect to the one each bird had become accustomed to. Vultures still interacted more with the smelly ball disregarding the color, while caracaras interacted equally with the two balls. The prevalence of olfaction in Turkey vultures may partly explain why they are the first raptors to find carcasses in tropical forests. In contrast, caracaras forage on the ground opportunistically, a strategy where both olfaction and sight may be involved. Our experiments suggest that both species are able to use olfactory cues for foraging. However, olfaction could be the predominant sense in Turkey vultures while olfaction and sight could play an equivalent role in Southern caracaras.

High resolution of colour vision, but low contrast sensitivity in a diurnal raptor

Animals are thought to use achromatic signals to detect small (or distant) objects and chromatic signals for large (or nearby) objects. While the spatial resolution of the achromatic channel has been widely studied, the spatial resolution of the chromatic channel has rarely been estimated. Using an operant conditioning method, we determined (i) the achromatic contrast sensitivity function and (ii) the spatial resolution of the chromatic channel of a diurnal raptor, the Harris's hawk Parabuteo unicinctus The maximal spatial resolution for achromatic gratings was 62.3 c deg-1, but the contrast sensitivity was relatively low (10.8-12.7). The spatial resolution for isoluminant red-green gratings was 21.6 c deg-1-lower than that of the achromatic channel, but the highest found in the animal kingdom to date. Our study reveals that Harris's hawks have high spatial resolving power for both achromatic and chromatic vision, suggesting the importance of colour vision for foraging. By contrast, similar to other bird species, Harris's hawks have low contrast sensitivity possibly suggesting a trade-off with chromatic sensitivity. The result is interesting in the light of the recent finding that double cones-thought to mediate high-resolution vision in birds-are absent in the central fovea of raptors.

Visual field shape and foraging ecology in diurnal raptors

Birds, particularly raptors, are believed to forage primarily using visual cues. However, raptor foraging tactics are highly diverse — from chasing mobile prey to scavenging — which may reflect adaptations of their visual systems. To investigate this, we studied the visual field configuration of 15 species of diurnal Accipitriformes that differ in such tactics, first focusing on the binocular field and blind area by using a single traits approach, and then exploring the shape of the binocular field with morphometric approaches. While the maximum binocular field width did not differ in species of different foraging tactics, the overall shape of their binocular fields did. In particular, raptors chasing terrestrial prey (ground predators) had a more protruding binocular field and a wider blind area above the head than did raptors chasing aerial or aquatic prey and obligate scavengers. Ground predators that forage on mammals from above have a wide but short bill — which increases ingestion rate — and large suborbital ridge to avoid sun glare. This may explain the protruding binocular field and the wide blind area above the head. By contrast, species from the two other groups have long but narrow bills used to pluck, flake or tear food and may need large visual coverage (and reduced suborbital ridges) to increase their foraging efficiency (e.g. using large visual coverage to follow the escaping prey in three dimensions or detect conspecifics). We propose that binocular field shape is associated with bill and suborbital ridge shape and, ultimately, foraging strategies.

Eye Size, Fovea, and Foraging Ecology in Accipitriform Raptors

Birds with larger eyes are predicted to have higher spatial resolution because of their larger retinal image. Raptors are well known for their acute vision, mediated by their deep central fovea. Because foraging strategies may demand specific visual adaptations, eye size and fovea may differ between species with different foraging ecology. We tested whether predators (actively hunting mobile prey) and carrion eaters (eating dead prey) from the order Accipitriformes differ in eye size, foveal depth, and retinal thickness using spectral domain optical coherence tomography and comparative phylogenetic methods. We found that (1) all studied predators (except one) had a central and a temporal fovea, but all carrion eaters had only the central fovea; (2) eye size scaled with body mass both in predators and carrion eaters; (3) predators had larger eyes relative to body mass and a thicker retina at the edge of the fovea than carrion eaters, but there was no difference in the depth of the central fovea between the groups. Finally, we found that (4) larger eyes generally had a deeper central fovea. These results suggest that the visual system of raptors within the order Accipitriformes may be highly adapted to the foraging strategy, except for the foveal depth, which seems mostly dependent upon the eye size.

Visual abilities in two raptors with different ecology

Differences in visual capabilities are known to reflect differences in foraging behaviour even among closely related species. Among birds, the foraging of diurnal raptors is assumed to be guided mainly by vision but their foraging tactics include both scavenging upon immobile prey and the aerial pursuit of highly mobile prey. We studied how visual capabilities differ between two diurnal raptor species of similar size: Harris's hawks, Parabuteo unicinctus, which take mobile prey, and black kites, Milvus migrans, which are primarily carrion eaters. We measured visual acuity, foveal characteristics and visual fields in both species. Visual acuity was determined using a behavioural training technique; foveal characteristics were determined using ultra-high resolution spectral-domain optical coherence tomography (OCT); and visual field parameters were determined using an ophthalmoscopic reflex technique. We found that these two raptors differ in their visual capacities. Harris's hawks have a visual acuity slightly higher than that of black kites. Among the five Harris's hawks tested, individuals with higher estimated visual acuity made more horizontal head movements before making a decision. This may reflect an increase in the use of monocular vision. Harris's hawks have two foveas (one central and one temporal), while black kites have only one central fovea and a temporal area. Black kites have a wider visual field than Harris's hawks. This may facilitate the detection of conspecifics when they are scavenging. These differences in the visual capabilities of these two raptors may reflect differences in the perceptual demands of their foraging behaviours.

Differential evolution of the Saccharomyces cerevisiae DUP240 paralogs and implication of recombination in phylogeny

Multigene families are observed in all genomes sequenced so far and are the reflection of key evolutionary mechanisms. The DUP240 family, identified in Saccharomyces cerevisiae strain S288C, is composed of 10 paralogs: seven are organized as two tandem repeats and three are solo ORFs. To investigate the evolution of the three solo paralogs, YAR023c, YCR007c and YHL044w, we performed a comparative analysis between 15 S.cerevisiae strains. These three ORFs are present in all strains and the conservation of synteny indicates that they are not frequently involved in chromosomal reshaping, in contrast to the DUP240 ORFs organized in tandem repeats. Our analysis of nucleotide and amino acid variations indicates that YAR023c and YHL044w fix mutations more easily than YCR007c, although they all belong to the same multigene family. This comparative analysis was also conducted with five arbitrarily chosen Ascomycetes-specific genes and five arbitrarily chosen common genes (genes that have a homolog in at least one non-Ascomycetes organism). Ascomycetes-specific genes appear to be diverging faster than common genes in the S.cerevisiae species, a situation that was previously described between different yeast species. Our results point to the strong contribution, during DNA sequence evolution, of allelic recombination besides nucleotide substitution.

Functional study of the Saccharomyces cerevisiae Nha1p C-terminus

Saccharomyces cerevisiae cells possess an alkali metal cation antiporter encoded by the NHA1 gene. Nha1p is unique in the family of yeast Na+/H+ antiporters on account of its broad substrate specificity (Na+, Li+, K+) and its long C-terminus (56% of the whole protein). In order to study the role of the C-terminus in Nha1p function, we constructed a series of 13 truncated NHA1 versions ranging from the complete one (2958 nucleotides, 985 amino acids) down to the shortest version (1416 nucleotides, 472 amino acids), with only 41 amino acid residues after the last putative transmembrane domain. Truncated NHA1 versions were expressed in an S. cerevisiae alkali metal cation-sensitive strain (B31; ena1-4Delta nha1Delta). We found that the entire Nha1p C-terminus domain is not necessary for either the proper localization of the antiporter in the plasma membrane or the transport of all four substrates (we identified rubidium as the fourth Nha1p substrate). Partial truncation of the C-terminus of about 70 terminal amino acids improves the tolerance of cells to Na+, Li+ and Rb+ compared with cells expressing the complete Nha1p. The presence of the neighbouring part of the C-terminus (amino acids 883-928), rich in aspartate and glutamate residues, is necessary for the maintenance of maximum Nha1p activity towards sodium and lithium. In the case of potassium, the participation of the long C-terminus in the regulation of intracellular potassium content is demonstrated. We also present evidence that the Nha1p C-terminus is involved in the cell response to sudden changes in environmental osmolarity.

The Candida albicans Na(+)/H(+) antiporter exports potassium and rubidium

The Candida albicans Cnh1p belongs to the family of Na(+)/H(+) antiporters (TC 2.A.36) but it transports besides toxic sodium and lithium also rubidium and potassium. Upon heterologous expression in a Saccharomyces cerevisiae salt-sensitive strain, the Cnh1p is targeted to the plasma membrane and its transport activity results in increased tolerance of cells to external alkali metal cations. The cation efflux activity of Cnh1p in S. cerevisiae depends on the gradient of protons across the plasma membrane, and a Cnh1p-mediated K(+) efflux is involved in a cell response to sudden rise of cytoplasmic pH.

New plasmid system to select for Saccharomyces cerevisiae purine-cytosine permease affinity mutants

The FCY2 gene of Saccharomyces cerevisiae encodes a purine-cytosine permease (PCP) that mediates the active transport of purines and cytosine. A structure-function model for this PCP has been recently proposed. In this study, we developed a plasmid-based system that generated a number of affinity-mutated alleles, enabling us to define new amino acids critical for permease function.

The Zygosaccharomyces rouxii strain CBS732 contains only one copy of the HOG1 and the SOD2 genes

The osmotolerant yeast Zygosaccharomyces rouxii CBS732 contains only one copy of the ZrHOG1 and ZrSOD2-22 genes. Both genes were cloned and sequenced (Acc. Nos. AJ132606 and AJ252273, respectively) and their sequences were compared to homologous pairs of genes from Z. rouxii ATCC42981 (genes Z-HOG1, Z-HOG2, Z-SOD2, Z-SOD22). The CBS732 ZrHog1p is shorter than its ATCC42981 counterparts (380 aa residues vs. 407 and 420 aa, respectively) and is more similar to ATCC42981 Z-Hog2p than to Z-Hog1p. Also its promoter region corresponds to that one of Z-HOG2. The CBS732 ZrHOG1 promoter region is recognised by Saccharomyces cerevisiae, and the gene product (MAP kinase ZrHog1p) presence fully complements the osmosensitivity of a S. cerevisiae hog1 mutant strain. The CBS ZrSOD2-22 gene is highly similar to ATCC42981 Z-SOD2 but it contains also a segment of 15 aa residues specific for Z-SOD22. Z. rouxii ZrSod2-22 Na(+)/H(+) antiporter expressed in S. cerevisiae shows better activity toward toxic Na(+) and Li(+) cations than does S. cerevisiae's own Nha1 antiporter, and is efficient in improving the halotolerance of some S. cerevisiae wild types.

Endogenous acetylcholine facilitates epileptogenesis in immature rat neocortex

In the presence of the gamma-amino butyric acid-A (GABAA) antagonist bicuculline methiodide (50 microM), synchronous spontaneous and evoked potentials were recorded extracellularly from the deep layers of immature neocortex (postnatal days 10-31, P10-P31) in vitro. Addition of the anticholinesterase eserine (10 microM) depressed the amplitude (by 29.5+/-6.6%, n=13) and duration (by 26.3+/-4.7%, n=11) of the evoked field potentials in 13/19 slices (68%), and increased significantly the rates of occurrence of spontaneous epileptiform discharges or induced them in 9/19 slices (47%). All these effects were blocked by the muscarinic antagonist atropine (2.5 microM, n=3), suggesting that they were mediated by the activation of muscarinic receptors by endogenous acetylcholine. The cholinergic inhibitory effect is unlikely to terminate seizures, while the excitatory effect, could conceivably promote or aggravate their manifestation. In conclusion, these findings demonstrate that endogenous acetylcholine may contribute to epileptogenesis in immature neocortex.

Cloning and sequence of the LYS2 homologue gene from the osmotolerant yeast Pichia sorbitophila

We have isolated the Pichia sorbitophila LYS2 (PsLYS2) gene by complementation of a lys2 Saccharomyces cerevisiae mutant. The sequenced DNA fragment contains a putative ORF of 4197 bp and the deduced translation product shares a global identity of 66% and 58% to the Lys2 protein homologues of Candida albicans and S. cerevisiae, respectively. Analysis of PsLYS2 sequence suggests that, similarly to S. cerevisiae LYS2, it codes for a polypeptide having two separate enzymatic activities which reside in different domains of the protein, including an adenylate domain, an acyl-carrier site and a short-chain reductase domain. Several GCN4- and NIT2-binding motifs have been matched in the promotor sequence of PsLYS2. In addition, upstream of the sequenced PsLYS2 sequence, we have found the 3'-terminal half of a gene of same orientation encoding a RAD16-like protein, a genomic organization similar to that of C. albicans.

Genomic exploration of the hemiascomycetous yeasts: 3. Methods and strategies used for sequence analysis and annotation

The primary analysis of the sequences for our Hemiascomycete random sequence tag (RST) project was performed using a combination of classical methods for sequence comparison and contig assembly, and of specifically written scripts and computer visualization routines. Comparisons were performed first against DNA and protein sequences from Saccharomyces cerevisiae, then against protein sequences from other completely sequenced organisms and, finally, against protein sequences from all other organisms. Blast alignments were individually inspected to help recognize genes within our random genomic sequences despite the fact that only parts of them were available. For each yeast species, validated alignments were used to infer the proper genetic code, to determine codon usage preferences and to calculate their degree of sequence divergence with S. cerevisiae. The quality of each genomic library was monitored from contig analysis of the DNA sequences. Annotated sequences were submitted to the EMBL database, and the general annotation tables produced served as a basis for our comparative description of the evolution, redundancy and function of the Hemiascomycete genomes described in other articles of this issue.

Genomic exploration of the hemiascomycetous yeasts: 8. Zygosaccharomyces rouxii

This paper reports the genomic analysis of strain CBS732 of Zygosaccharomyces rouxii, a homothallic diploid yeast. We explored the sequences of 4934 random sequencing tags of about 1 kb in size and compared them to the Saccharomyces cerevisiae gene products. Approximately 2250 nuclear genes, 57 tRNAs, the rDNA locus, the endogenous pSR1 plasmid and 15 mitochondrial genes were identified. According to 18S and 25S rRNA cladograms and to synteny analysis, Z. rouxii could be placed among the S. cerevisiae sensu lato yeasts.

Genomic exploration of the hemiascomycetous yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae

We have analyzed the evolution of chromosome maps of Hemiascomycetes by comparing gene order and orientation of the 13 yeast species partially sequenced in this program with the genome map of Saccharomyces cerevisiae. From the analysis of nearly 8000 situations in which two distinct genes having homologs in S. cerevisiae could be identified on the sequenced inserts of another yeast species, we have quantified the loss of synteny, the frequency of single gene deletion and the occurrence of gene inversion. Traces of ancestral duplications in the genome of S. cerevisiae could be identified from the comparison with the other species that do not entirely coincide with those identified from the comparison of S. cerevisiae with itself. From such duplications and from the correlation observed between gene inversion and loss of synteny, a model is proposed for the molecular evolution of Hemiascomycetes. This model, which can possibly be extended to other eukaryotes, is based on the reiteration of events of duplication of chromosome segments, creating transient merodiploids that are subsequently resolved by single gene deletion events.

Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes-specific genes

Comparisons of the 6213 predicted Saccharomyces cerevisiae open reading frame (ORF) products with sequences from organisms of other biological phyla differentiate genes commonly conserved in evolution from 'maverick' genes which have no homologue in phyla other than the Ascomycetes. We show that a majority of the 'maverick' genes have homologues among other yeast species and thus define a set of 1892 genes that, from sequence comparisons, appear 'Ascomycetes-specific'. We estimate, retrospectively, that the S. cerevisiae genome contains 5651 actual protein-coding genes, 50 of which were identified for the first time in this work, and that the present public databases contain 612 predicted ORFs that are not real genes. Interestingly, the sequences of the 'Ascomycetes-specific' genes tend to diverge more rapidly in evolution than that of other genes. Half of the 'Ascomycetes-specific' genes are functionally characterized in S. cerevisiae, and a few functional categories are over-represented in them.

Genomic exploration of the hemiascomycetous yeasts: 21. Comparative functional classification of genes

We explored the biological diversity of hemiascomycetous yeasts using a set of 22000 newly identified genes in 13 species through BLASTX searches. Genes without clear homologue in Saccharomyces cerevisiae appeared to be conserved in several species, suggesting that they were recently lost by S. cerevisiae. They often identified well-known species-specific traits. Cases of gene acquisition through horizontal transfer appeared to occur very rarely if at all. All identified genes were ascribed to functional classes. Functional classes were differently represented among species. Species classification by functional clustering roughly paralleled rDNA phylogeny. Unequal distribution of rapidly evolving, ascomycete-specific, genes among species and functions was shown to contribute strongly to this clustering. A few cases of gene family amplification were documented, but no general correlation could be observed between functional differentiation of yeast species and variations of gene family sizes. Yeast biological diversity seems thus to result from limited species-specific gene losses or duplications, and for a large part from rapid evolution of genes and regulatory factors dedicated to specific functions.

Genomic exploration of the hemiascomycetous yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae

We have evaluated the degree of gene redundancy in the nuclear genomes of 13 hemiascomycetous yeast species. Saccharomyces cerevisiae singletons and gene families appear generally conserved in these species as singletons and families of similar size, respectively. Variations of the number of homologues with respect to that expected affect from 7 to less than 24% of each genome. Since S. cerevisiae homologues represent the majority of the genes identified in the genomes studied, the overall degree of gene redundancy seems conserved across all species. This is best explained by a dynamic equilibrium resulting from numerous events of gene duplication and deletion rather than by a massive duplication event occurring in some lineages and not in others.

Genomic exploration of the hemiascomycetous yeasts: 15. Pichia sorbitophila

This paper reports the genomic analysis of the strain CBS7064 of Pichia sorbitophila, a homothallic diploid yeast. We sequenced 4829 random sequence tags of about 1 kb and compared them to the Saccharomyces cerevisiae gene products. Approximately 1300 nuclear genes, 22 tRNAs, the rDNA locus, and six mitochondrial genes have been identified. The analysis of the rDNA genes has permitted to classify this organism close to the Candida species. Accession numbers from AL414896 to AL419724 at EMBL databank.

Genomic exploration of the hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies

The identification of molecular evolutionary mechanisms in eukaryotes is approached by a comparative genomics study of a homogeneous group of species classified as Hemiascomycetes. This group includes Saccharomyces cerevisiae, the first eukaryotic genome entirely sequenced, back in 1996. A random sequencing analysis has been performed on 13 different species sharing a small genome size and a low frequency of introns. Detailed information is provided in the 20 following papers. Additional tables available on websites describe the ca. 20000 newly identified genes. This wealth of data, so far unique among eukaryotes, allowed us to examine the conservation of chromosome maps, to identify the 'yeast-specific' genes, and to review the distribution of gene families into functional classes. This project conducted by a network of seven French laboratories has been designated 'Génolevures'.

Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited

Since its completion more than 4 years ago, the sequence of Saccharomyces cerevisiae has been extensively used and studied. The original sequence has received a few corrections, and the identification of genes has been completed, thanks in particular to transcriptome analyses and to specialized studies on introns, tRNA genes, transposons or multigene families. In order to undertake the extensive comparative sequence analysis of this program, we have entirely revisited the S. cerevisiae sequence using the same criteria for all 16 chromosomes and taking into account publicly available annotations for genes and elements that cannot be predicted. Comparison with the other yeast species of this program indicates the existence of 50 novel genes in segments previously considered as 'intergenic' and suggests extensions for 26 of the previously annotated genes.

Organization of specific genomic regions of Zygosaccharomyces rouxii and Pichia sorbitophila: comparison with Saccharomyces cerevisiae

The genomes of Zygosaccharomyces rouxii and Pichia sorbitophila were partially explored. The genome of Z. rouxii CBS 732 consists of seven chromosomes with an approximate size of 1.0-2.75 Mb, 12.8 Mb in total. Five of the chromosomes were labelled with specific probes. Three Z. rouxii genomic DNA fragments were sequenced; all 10 ORFs found were without introns and they have homologues in S. cerevisiae. Gene order comparison revealed that the organization is partially conserved in both species. The genome of P. sorbitophila CBS 7064 consists of seven chromosomes with an approximate size of 1.0-2.9 Mb, 13.9 Mb in total. Three of the chromosomes were labelled with specific probes. The sequencing of a 5.2 kb genomic DNA fragment revealed three ORFs, but no conservation of their organization was found, although all of them have their respective homologues in S. cerevisiae. According to our results, the presence of two overlapping ORFs in S. cerevisiae (YJL107c-YJL108c) could be interpreted as the result of a frameshift mutation.

Involvement of very short DNA tandem repeats and the influence of the RAD52 gene on the occurrence of deletions in Saccharomyces cerevisiae

Chromosomal rearrangements, such as deletions, duplications, or Ty transposition, are rare events. We devised a method to select for such events as Ura(+) revertants of a particular ura2 mutant. Among 133 Ura(+) revertants, 14 were identified as the result of a deletion in URA2. Of seven classes of deletions, six had very short regions of identity at their junctions (from 7 to 13 bp long). This strongly suggests a nonhomologous recombination mechanism for the formation of these deletions. The total Ura(+) reversion rate was increased 4.2-fold in a rad52Delta strain compared to the wild type, and the deletion rate was significantly increased. All the deletions selected in the rad52Delta context had microhomologies at their junctions. We propose two mechanisms to explain the occurrence of these deletions and discuss the role of microhomology stretches in the formation of fusion proteins.

Isolation and characterization of the TIM10 homologue from the yeast Pichia sorbitophila: a putative component of the mitochondrial protein import system

The Saccharomyces cerevisiae TIM10 gene encodes one of the few essential mitochondrial proteins that are required for the import of nuclear-encoded precursor proteins from the cytosol and their subsequent sorting into the different mitochondrial compartments. We have isolated and characterized a putative homologue of TIM10 from the halotolerant yeast Pichia sorbitophila. The Pichia TIM10 gene encodes a protein of 90 amino acids with 66% identity to S. cerevisiae Tim10p. It was capable of suppressing the temperature sensitivity of tim10-1 mutant in S. cerevisiae, suggesting that Pichia TIM10 is both a functional and structural homologue of S. cerevisiae TIM10. The putative Pichia TIM10 gene product contains all the four conserved cysteine residues and the two CX(3)C motifs typical of the Tim family proteins in the mitochondrial intermembrane space. Using anti-Tim10p serum, Western blots detected a protein of about 10 kDa, suggesting that the Pichia Tim10p is a mitochondrial protein. The results suggest that mitochondrial import and sorting systems might be also strongly conserved in other fungi. The coding sequence of the P. sorbitophila TIM10 has been deposited in the EMBL Nucleotide Sequence Database under Accession No. AJ243940.

The ORF YBL042 of Saccharomyces cerevisiae encodes a uridine permease

The purpose of this work was to identify the function of an open reading frame called YBL042, found during the systematic sequencing of Saccharomyces cerevisiae's chromosome II. The YBL042 gene product shows 70% similarity with the uracil permease and the allantoin permease encoded by FUR4 and DAL4, respectively. The mutation constructed by disruption of this ORF is allelic to the FUI1 gene previously described as encoding the uridine permease but not cloned yet. A strain carrying the disrupted allele and a fui1 mutant exhibit the same phenotype as they do not grow on a medium containing uridine as the sole source of pyrimidines and as they are resistant to 10(-3) M 5-fluorouridine (5FUI), a toxic analog of uridine. Even though the FUI1 gene has a multicopy suppressor effect on uracil transport, its product does not seem to be involved in this transport, in contrast to the FUR4 gene product which is involved in uridine transport. Moreover, the FUI1 gene product does not play any role in allantoin transport.

The characterization of two new clusters of duplicated genes suggests a 'Lego' organization of the yeast Saccharomyces cerevisiae chromosomes

The systematic sequencing of 42,485 bp of yeast chromosome VII (nucleotides 377948 to 420432) has revealed the presence of 27 putative open reading frames (ORFs) coding for proteins of at least 100 amino acids. The degree of redundancy observed is elevated since five of the 27 ORFs are duplications of a previously identified gene. These duplicated copies may be classified in two types of cluster organization. The first type includes genes sharing a significant level of identity in the amino acid sequences of their predicted protein product. They are recovered on two different chromosomes, transcribed in the same orientation and the distance between them is conserved. The second type of cluster is based on one gene unit tandemly repeated. This duplication is itself repeated elsewhere in the genome. The level of nucleic acid identity is high within the coding sequence and the non-coding region between the two repeats. In addition, the basic gene unit is recovered many times in the genome and is a component of a multigene family of unknown function. These organizations in clusters of genes suggest a 'Lego organization' of the yeast chromosomes, as recently proposed for the genome of plants (Moore, 1995). The sequence is deposited in the Yeast Genome Databank under Accession Number from Z72562 to Z72586.

Analysis of 21.7 kb DNA sequence from the left arm of chromosome VII reveals 11 open reading frames: two correspond to new genes

The DNA sequence of a fragment of 21731 bp (nucleotides 87408 to 109138) located on the left arm of chromosome VII from Saccharomyces cerevisiae S288C has been determined using a random cloning strategy followed by an oligonucleotide-directed sequencing. This fragment contains eight complete genes previously sequenced (CLG1, SKI8, VAM7, YPT32, MIG2, SIP2, SPT16 and CHC1), the 5' part of POX1 and two other complete unidentified open reading frames of more than 100 amino acids.

Delta sequence of Ty1 transposon can initiate transcription of the distal part of the URA2 gene complex in Saccharomyces cerevisiae

Expression of a silent aspartate transcarbamylase (ATCase) domain can occur by insertion of a Tyl retrotransposon within the coding sequence of a mutated ura2 allele. This unusual type of Ty-mediated gene activation is possible as the URA2 gene product is a multifunctional protein containing the carbamoyl phosphate synthetase (CPSase), the ATCase and a cryptic dihydroorotase (DHOase) domain. The region in which transcription of the corresponding allele is initiated was determined by RT-PCR experiments. Expression is initiated by a sequence located in the delta element of the Tyl and not by a sequence of the URA2 gene itself. This situation differs with the Ty-mediated gene activation described thus far, in which the transposon substitutes only the 5' regulatory sequences and in which the normal transcription start point is used. The corresponding protein carries both the DHOase-like domain and the ATCase domain, suggesting that the DHOase-like domain is at least involved in the architecture of the protein and necessary to render the ATCase domain functional.

Characterization of the NHA1 gene encoding a Na+/H+-antiporter of the yeast Saccharomyces cerevisiae

The NHA1 gene (2958 nt) encoding a putative Na(+)/H(+) antiporter (986 aa) in Saccharomyces cerevisiae was cloned by selection based on increased NaCl tolerance. The putative protein is highly similar to sodium/proton antiporters from Schizosaccharomyces pombe (gene sod2), and Zygosaccharomyces rouxii (gene Z-SOD2). Overexpression of the NHA1 gene results in higher and partially pH-dependent tolerance to sodium and lithium; its disruption leads to an increased sensitivity towards these ions.

Cloning of Arabidopsis thaliana glutathione synthetase (GSH2) by functional complementation of a yeast gsh2 mutant

Glutathione (L-gamma-glutamyl-L-cysteinylglycine, GSH) plays an important role in the protection of plants against various types of stress caused by reactive oxygen species, gazeous pollutants, heavy metals and xenobiotics. A cDNA fragment containing the entire coding unit for glutathione synthetase (GSH2) of Arabidopsis thaliana was cloned by complementation of the methylglyoxal sensitivity of a gsh2 mutant of the yeast Saccharomyces cerevisiae. The cDNA encodes a protein of 478 amino acids (deduced Mr: 53783), bearing clear sequence similarities to GSH2 products from frog embryos (Xenopus laevis), rat kidney (Rattus norvegicus) and from the fission yeast (Schizosaccharomyces pombe). A highly conserved glycine-rich domain close to the carboxy-terminus was found in the GSH2 product and appears to be typical for eukaryotic glutathione synthetases. The Mr is similar to those of soluble animal enzymes, suggesting that the Arabidopsis gene also codes for a cytosolic protein. Genomic DNA-blot analysis indicates the presence of a single GSH2 gene. The yeast gsh2 mutant becomes resistant to methylglyoxal and cadmium after transformation with the plasmid bearing the Arabidopsis GSH2 cDNA. Moreover, this increased resistance is correlated to the restoration of GSH content from below detectability in mutants to about 50% of the wild-type levels in transformed cells.

As in Saccharomyces cerevisiae, aspartate transcarbamoylase is assembled on a multifunctional protein including a dihydroorotase-like cryptic domain in Schizosaccharomyces pombe

The organisation of the URA1 gene of Schizosaccharomyces pombe was determined from the entire cDNA cloned by the transformation of an ATCase-deficient strain of Saccharomyces cerevisiae. The URA1 gene encodes the bifunctional protein GLNase/CPSase-ATCase which catalyses the first two steps of the pyrimidine biosynthesis pathway. The complete nucleotide sequence of the URA1 cDNA was elucidated and the deduced amino-acid sequence was used to define four domains in the protein; three functional domains, corresponding to GLNase (glutamine amidotransferase), CPSase (carbamoylphosphate synthetase) and ATCase (aspartate transcarbamoylase) activities, and one cryptic DHOase (dihydroorotase) domain. Genetic investigations confirmed that both GLNase/CPSase and ATCase activities are carried out by the same polypeptide. They are also both feedback-inhibited by UTP (uridine triphosphate). Its organization and regulation indicate that the S. pombe URA1 gene product appears very similar to the S. cerevisiae URA2 gene product.

Sequence of a 9.8 kb segment of yeast chromosome II including the three genes of the MAL3 locus and three unidentified open reading frames

We report the DNA sequence of a segment located on the right arm of chromosome II from Saccharomyces cerevisiae S288C near the subtelomeric sequences. The sequence was determined using a random cloning strategy followed by an oligonucleotide-directed sequencing. The segment contains four non-overlapping open reading frames (ORFs) YBR297w, YBR298c, YBR299w and YBR301c, and two overlapping ones (YBR300c and YBR300w). Three of them--YBR297w, YBR298c and YBR299w--are the MAL3R (transcriptional regulatory protein), MAL3T (maltose permease) and MAL3S (maltase) genes of the MAL3 locus previously localized. The three other ORFs are unidentified. Another MAL locus (MALl) has been localized on chromosome VII. The Mal- phenotype of strain S288c cannot be explained by telomeric silencing.

Allosteric regulation of carbamoylphosphate synthetase-aspartate transcarbamylase multifunctional protein of Saccharomyces cerevisiae: selection, mapping and identification of missense mutations define three regions involved in feedback inhibition by UTP

The positive screening procedure previously described was used in order to select, clone and characterize mutants defective in negative feedback control by UTP of the yeast carbamoylphosphate synthetase-aspartate transcarbamylase protein (CPSase-ATCase). The selection procedure was improved by adding a general mapping method for dominant mutations in order to avoid sequencing the whole URA2 allele (7 kb). All 16 mutants obtained carry missense mutations leading to single amino acid replacements: five of them are located in the CPSase domain while the other 11 are in the ATCase domain. In these 16 mutants, ATCase is no longer inhibited by UTP although CPSase retains full sensitivity to the effector, suggesting that the regulation of the two activities involve distinct mechanisms. Amino acid replacements in the ATCase domain were located on a three-dimensional model structure of the yeast ATCase domain. They are clustered in two regions of this domain which must be directly involved in the feedback process.

Reactivation of the ATCase domain of the URA2 gene complex: a positive selection method for Ty insertions and chromosomal rearrangements in Saccharomyces cerevisiae

Genetic rearrangements such as deletions or duplications of DNA sequences are rarely detected in the yeast Saccharomyces cerevisiae. We have developed a screening system using the URA2 gene coding for the bi-functional CPSase-ATCase (carbamyl phosphate synthetase - aspartate transcarbamylase) to select positively for these kinds of events. Nonsense mutations in the CPSase region cause a complete loss of the ATCase activity because of their strong polar effect. Thirty-seven ATCase+ revertants were isolated from a strain containing three nonsense mutations in the proximal CPSase region. Genetic and structural analysis of the URA2 locus in these strains allowed us to characterize two major classes of revertants. In the first, an entire copy of a Ty transposon was found to be inserted in the CPSase coding domain. This event, which represents a new form of Ty-mediated gene activation was further analysed by mapping the Ty integration site in 26 strains. In a second class of revertants, we observed chromosomal rearrangements and, in particular, duplication of the ATCase region and its integration in a new chromosomal environment in which this sequence becomes active.

Recovery of gene function by gene duplication in Saccharomyces cerevisiae

A prototroph revertant (Rev9) selected from an ATCase- mutant of the URA2 gene containing three nonsense mutations was shown to contain two ATCase coding sequences. We cloned both ATCase coding areas to show that the duplicated locus (dl9) was the only functional one. Its size corresponded roughly to the second half of the URA2 wild-type gene. Sequence analysis of the 5' end of dl9 indicated that this duplicated sequence was inserted within the intergenic region close to the MRS3 gene and was transcribed from an unknown promoter divergently from the MRS3 gene. The event leading to the revertant strain Rev9 included a rearrangement that increased the size of chromosome X by about 60 kb. In agreement with such a rearrangement, recombination was undetectable in the vicinity of the locus dl9. Genetic mapping confirms that the MRS3 gene is 2 cM distal to the URA2 gene on the right arm of chromosome X.

Complete DNA sequence of yeast chromosome II

In the framework of the EU genome-sequencing programmes, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II (807 188 bp) has been determined. At present, this is the largest eukaryotic chromosome entirely sequenced. A total of 410 open reading frames (ORFs) were identified, covering 72% of the sequence. Similarity searches revealed that 124 ORFs (30%) correspond to genes of known function, 51 ORFs (12.5%) appear to be homologues of genes whose functions are known, 52 others (12.5%) have homologues the functions of which are not well defined and another 33 of the novel putative genes (8%) exhibit a degree of similarity which is insufficient to confidently assign function. Of the genes on chromosome II, 37-45% are thus of unpredicted function. Among the novel putative genes, we found several that are related to genes that perform differentiated functions in multicellular organisms of are involved in malignancy. In addition to a compact arrangement of potential protein coding sequences, the analysis of this chromosome confirmed general chromosome patterns but also revealed particular novel features of chromosomal organization. Alternating regional variations in average base composition correlate with variations in local gene density along chromosome II, as observed in chromosomes XI and III. We propose that functional ARS elements are preferably located in the AT-rich regions that have a spacing of approximately 110 kb. Similarly, the 13 tRNA genes and the three Ty elements of chromosome II are found in AT-rich regions. In chromosome II, the distribution of coding sequences between the two strands is biased, with a ratio of 1.3:1. An interesting aspect regarding the evolution of the eukaryotic genome is the finding that chromosome II has a high degree of internal genetic redundancy, amounting to 16% of the coding capacity.