CandidaDB: a genome database for Candida albicans pathogenomics.

CandidaDB is a database dedicated to the genome of the most prevalent systemic fungal pathogen of humans, Candida albicans. CandidaDB is based on an annotation of the Stanford Genome Technology Center C.albicans genome sequence data by the European Galar Fungail Consortium. CandidaDB Release 2.0 (June 2004) contains information pertaining to Assembly 19 of the genome of C.albicans strain SC5314. The current release contains 6244 annotated entries corresponding to 130 tRNA genes and 5917 protein-coding genes. For these, it provides tentative functional assignments along with numerous pre-run analyses that can assist the researcher in the evaluation of gene function for the purpose of specific or large-scale analysis. CandidaDB is based on GenoList, a generic relational data schema and a World Wide Web interface that has been adapted to the handling of eukaryotic genomes. The interface allows users to browse easily through genome data and retrieve information. CandidaDB also provides more elaborate tools, such as pattern searching, that are tightly connected to the overall browsing system. As the C.albicans genome is diploid and still incompletely assembled, CandidaDB provides tools to browse the genome by individual supercontigs and to examine information about allelic sequences obtained from complementary contigs. CandidaDB is accessible at http://genolist.pasteur.fr/CandidaDB.

Cloning and characterisation of a gene from Plasmodium vivax and P. knowlesi: homology with valine-tRNA synthetase.

We have previously described a lambdagt11 clone detected by immune screening with a monoclonal antibody (mAb) A12. This mAb is capable of completely blocking Plasmodium vivax transmission in the mosquito vector. An epitope recognised by A12 was mapped to six amino acids (aa) within the translated sequence of this clone. Here, we describe the complete sequence of the gene within which we mapped this epitope. Surprisingly, the translated sequence of the full-length open reading frame shows homology with that of valine-tRNA synthetases (Val-tRS) from other organisms. DNA cross-hybridisation with several of these species was observed by Southern blot. In addition, the corresponding gene has been obtained from the closely related simian malaria parasite, P. knowlesi. The two aa sequences show 66% identity and yet are very divergent from other Val-tRS sequences, apart from conserved blocks related to functional activity. Multiple sequence alignments reflect this dichotomy, as do predicted differences in antigenicity.

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: 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: 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: 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.

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: 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: 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.

Tempo of neurogenesis and synaptogenesis in the primate cingulate mesocortex: comparison with the neocortex.

In the neocortex, the onset of the rapid phase (phase 3) of synaptogenesis occurs after the end of neurogenesis. However, we still do not know whether or not these two developmental events are causally related. The present study compares the time-course and tempo of neurogenesis and synaptogenesis in the anterior cingulate cortex (area 24 of Brodmann) and in the primary visual cortex (area 17) in a series of pre- and postnatal rhesus monkeys. Autoradiographic analysis of animals fetally injected with 3H-thymidine showed that all neurons destined for area 24 are generated by embryonic day 70, which is 30 days earlier than in area 17. The rapid phase of synaptogenesis in area 24 starts during the third embryonic month and continues at the same rate through the remainder of gestation and the first 2 months after birth, as has been seen in neocortical areas examined previously. Statistical analysis of the linear portions of the rapid phase indicates that, although neurogenesis in area 24 is completed 1 month earlier than in area 17, the rapid phase of synaptogenesis occurs 41 days later. Moreover, the tempo of synaptic accretion was remarkably similar to that in motor, somatosensory, visual, or associational areas. All were grouped within the same time window of about 40 days, centered at birth. After the second postnatal month, synaptic density in area 24 remains at a high level until sexual maturity. This work shows that the rapid phase of synaptogenesis in the cingulate mesocortex is not linked temporally to the end of neurogenesis. We suggest that it is regulated by the same genetic or humoral factors that control synaptogenesis in the phylogenetically newer neocortical areas.

Molecular characterization of the heat shock protein 90 gene of the human malaria parasite Plasmodium falciparum.

We report here the nucleotide sequence of hsp90 (heat shock protein 90) of Plasmodium falciparum. Computer analysis of the deduced protein sequence revealed an unusually large region of charged amino acids when compared to hsp90 from other species. This region shows striking homology to the calcium binding domain of calreticulin, the major calcium binding protein of endoplasmic reticulum. Phylogenetic tree analysis indicates that P. falciparum hsp90 is more closely related to hsp90 from plants than to hsp90 from vertebrates or other parasites. The malaria hsp90 is an ATP binding protein encoded by a single gene constitutively expressed in both asexual (trophozoite) and sexual (gametocyte) stage parasites. The hsp90 protein is homologous to a previously identified 90-kDa antigen strongly recognised by both sera from vaccinated monkeys and monoclonal antibody XIV/7.

Isolation from human brain of six previously unreported cDNAs related to the reverse transcriptase of human endogenous retroviruses.

cDNAs prepared from total RNA extracted from plaques of multiple sclerosis were amplified by the polymerase chain reaction. The 11-bp degenerate primers used were derived from conserved sequences of reverse transcriptase. Amplified cDNAs were fractionated according to size by electrophoresis in polyacrylamide gels under denaturing conditions. cDNAs of the proper size were cloned, grouped according to the sequence of their insert by differential hybridization, and sequenced. Six cDNAs were isolated and found to belong to new members of two groups of human endogenous retroviruses: the group related to ERV9 and that related to HERVK10 and HUMMTV. These sequences were expressed in all human organs tested, including normal white matter of brain. The approach described in this article is a powerful tool with which to isolate new members of the reverse transcriptase gene family.

Seroepidemiology, viral isolation, and molecular characterization of human T cell leukemia/lymphoma virus type I from La Réunion Island, Indian Ocean.

Data indicate the presence in the Seychelles Islands of a high level of human T cell leukemia/lymphoma virus type I (HTLV-I) endemicity as well as the presence of tropical spastic paraparesis/HTLV-I-associated myelopathy (TSP/HAM). We present here the results of an hospital survey performed since 1988 in La Réunion Island, located in the Indian Ocean southeast of the Seychelles archipelago, aimed at evaluating HTLV-I endemicity, detecting HTLV-I-associated diseases, and characterizing viral isolates. Seven individuals were found to have HTLV-I-specific antibodies in their sera. These include 3 of 257 patients from St. Pierre Hospital, 1 of them exhibiting a typical clinical feature of TSP/HAM (the first described case in this region), 1 blood donor of 3900, and 3 relatives. A further nine individuals exhibiting only "gag-encoded proteins" by Western blot (p19 and/or p24 bands) were found negative by polymerase chain reaction using LTR, pol, and tax HTLV-I specific primers. A long-term T cell line, designated Mel.J, exhibiting T cell activation markers (CD4+, CD25+, HLA-DR+), and producing HTLV-I antigens and viral particles, was established from one of the HTLV-I,-seropositive patients. The sequence of a 522-bp fragment corresponding to the carboxy terminus of gp46 and the majority of gp21 were determined for five HTLV-I-seropositive individuals, including the TSP/HAM patient. Alignment and phylogenetic comparison of these five nucleotide sequences with all the 53 other available HTLV-I env sequences demonstrated that the virus from La Réunion Island belongs to the group of the HTLV-I cosmopolitan subtype and is not related to the Melanesian HTLV-I variants.

Molecular epidemiology of HTLV type I in Japan: evidence for two distinct ancestral lineages with a particular geographical distribution.

Japan is one of the highest endemic areas of the world for human T cell leukemia-lymphoma virus type I (HTLV-I). To gain new insight as to the origin of this virus in Japan and especially in the southern islands of the archipelago, we investigated the long terminal repeat (LTR) of 67 newly isolated HTLV-I proviral DNAs from peripheral blood mononuclear cells of HTLV-I-infected individuals for their restriction fragment length polymorphism (RFLP). The specimens were from Japanese living in different geographical areas (Hokkaido, Honshu, Kyushu, or the Ryukyu Islands) of Japan (59 cases) or Americans of Japanese ancestry living in Hawaii (8 cases). The analysis of the results, together with data for the 19 previously published LTR sequences, demonstrated the existence of 2 subtypes of HTLV-I in Japan. The first, which we propose to name Japanese subtype (previously named subtype III), is more frequent (67 of 86: 78%) than the second, the cosmopolitan subtype (previously named subtype II) (19 of 86: 22%). In parallel, a fragment of 413 base pairs of the U3/R region (nucleotide 22 to 434) was cloned and sequenced from 10 of the new Japanese samples. The alignment of these sequences and their comparison and phylogenetic analysis with previously published LTR HTLV-I sequences, demonstrated clearly the existence of the two distinct molecular subtypes of HTLV-I in Japan, diverging in this LTR region by about 1.6%. Furthermore, the study of the geographical distribution of the 2 subtypes among the 80 samples from patients whose place of residence in Japan was known showed an uneven distribution. While the Japanese subtype was present in all parts of Japan, the cosmopolitan subtype seemed to cluster in the southern islands of the archipelago (i.e., Kyushu and the Ryukyu Islands) as well as in immigrants from those areas who had lived in Hawaii for decades. These new molecular data raise questions and suggest hypotheses, discussed here, concerning the origin and means of dissemination of these human retrovirus subtypes in Japan.

A new HTLV type II subtype A isolate in an HIV type 1-infected prostitute from Cameroon, Central Africa.

Among 332 female sex workers in Douala, Cameroon, 113 were HIV-1 seropositive, 3 were HTLV-I seropositive, and only 1 had specific anti-HTLV-II antibodies. By cocultivation with BJAB cells, an HTLV-II was isolated from the peripheral blood mononuclear cells of this 32-year-old woman coinfected by HIV-1. This new African HTLV-II isolate (PH230PCAM) belongs to the molecular subtype A, exhibiting, however, a nucleotide variability of 2.4% and 0.8%, vis-à-vis the MO prototype, in the LTR and in the gp21 env gene, respectively. These data, as well as the previous findings of another HTLV-II subtype A in a Ghanean prostitute, suggest that this viral subtype had been imported into Africa, while the HTLV-II subtype B, described in remote areas of Zaire, Gabon, and Cameroon, could be a genuine African HTLV-II, present in this continent for a long period of time.

Seroepidemiological and molecular studies of human T cell lymphotropic virus type II, subtype b, in isolated groups of Mataco and Toba Indians of northern Argentina.

We studied plasma samples from 2082 Mataco Indians living in 22 different communities in the western part of Formosa Province, northern Argentina. Samples were screened for HTLV-I/II antibodies by particle agglutination assay. All positive or borderline samples were then tested by an immunofluorescence assay (IFA) on C19 HTLV-II-producing cells. Western blot was used for confirmation of all IFA-positive plasma samples. The crude HTLV-II seroprevalence was 3.0% (62 of 2051), and 0.9% (5 of 588) in children less than 10 years old. The latter result suggests ongoing mother-to-child transmission, probably by breast feeding. There was a marked increase in HTLV-II seroprevalence with age (0.9%, 0-10 years; 1.6%, 11-20 years; 4.4%, 21-30 years; 3.4%, 31-40 years; 7.2%, 41-50 years; 5.7%, >50 years) in both male (p = 0.002) and female subjects (p = 0.00002). None of the 80 non-Indian inhabitants tested was HTLV-I/II seropositive. In a second study, among 105 Toba Indians from a village (Primavera) of the eastern part of this region, 23 were HTLV-II seropositive with a seroprevalence of 59% in those more than 40 years old. From seven of the Indians from Primavera, three others from neighboring regions (including two Tobas and one Pilaga), and one intravenous drug user (IVDU) from Rosario, DNA was extracted from peripheral blood mononuclear cells, and the gp21 transmembrane-encoding gene (590 bp) was amplified by PCR, cloned, and sequenced. LTR sequences were also obtained from the Pilaga, the IVDU, and one Toba. Molecular and phylogenetic analyses revealed that the Indians were all infected with closely related HTLV-II molecular strains belonging to the b subtype, while the IVDU was infected with an HTLV-II subtype a variant. Such data help to make a phylogenetic atlas of HTLV-II among Amerindian tribes and are crucial to gain new insights into the origin and modes of dissemination of this human retrovirus in the Americas.

ACTH/beta-endorphins and ACTH/cortisol ratios as early biological markers in HIV infection.

Three groups of male homosexuals: AIDS (n = 19), HIV seropositive (n = 15), and seronegative partners of seropositive subjects (n = 15), were compared to a heterosexual seronegative control group (n = 13). Twice daily evaluations (8 A.M. and 5 P.M.) of plasma levels of beta-endorphin, ACTH, and cortisol were done by radioimmunoassay. Seropositive subjects and their seronegative partners showed similar levels of neurohormones: 1. An elevation in the ACTH/beta-endorphin ratio in the plasma, (C = 0.69 +/- 0.84, AIDS = 0.44 +/- 0.32, S+ = 0.42 +/- 0.28, and S- = 0.42 +/- 0.5); 2. A loss of normal relationship of the coupling ACTH/total cortisol, (C = 0.00035 +/- 0.00028, AIDS = 0.00042 +/- 0.0034, S+ = 0.00074 +/- 0.00068, and S- = 0.00072 +/- 0.0008. Neuroendocrinological disorders have been observed in HIV-infected subjects and in their seronegative partners. These could be related to their sexual behavior, as well as to the HIV infection. If this last hypothesis is confirmed, the ACTH/beta-endorphin and ACTH/cortisol ratios may be seen as possible early signs of HIV infection.

The decaying genome of Mycobacterium leprae.

Everything that we need to know about Mycobacterium leprae, a close relative of the tubercle bacillus, is encrypted in its genome. Inspection of the 3.27 Mb genome sequence of an armadillo-derived Indian isolate of the leprosy bacillus identified 1,605 genes encoding proteins and 50 genes for stable RNA species. Comparison with the genome sequence of Mycobacterium tuberculosis revealed an extreme case of reductive evolution, since less than half of the genome contains functional genes while inactivated or pseudogenes are highly abundant. The level of gene duplication was approximately 34% and, on classification of the proteins into families, the largest functional groups were found to be involved in the metabolism and modification of fatty acids and polyketides, transport of metabolites, cell envelope synthesis and gene regulation. Reductive evolution, gene decay and genome downsizing have eliminated entire metabolic pathways, together with their regulatory circuits and accessory functions, particularly those involved in catabolism. This may explain the unusually long generation time and account for our inability to culture the leprosy bacillus.