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Kamel Jabbari

Publications and source records attributed to Kamel Jabbari.

15 recordsLinked to original sources
PubMed2007

Simple proteomic checks for detecting noncoding RNA.

Proper validation can accelerate sequence-based discovery of proteins and protein-coding genes. Databases currently contain a backlog of experimentally unverified gene models and tentative assignments of observed transcripts to coding or noncoding RNA. We present and apply a general principle, founded on base composition and the genetic code and validated here by bulk 2-D gels, that can improve the reliability of such classifications and of the algorithms or pipelines that lead to them.

Base Composition↗
PubMed2006

Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features.

The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer is the world's smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C(4) photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry.

Animals↗
PubMed2005

The evolution of introns in human duplicated genes.

In previous work [Jabbari, K., Rayko, E., Bernardi, G., 2003. The major shifts of human duplicated genes. Gene 317, 203-208], we investigated the fate of ancient duplicated genes after the compositional transitions that occurred between the genomes of cold- and warm-blooded vertebrates. We found that the majority of duplicated copies were transposed to the "ancestral genome core", the gene-dense genome compartment that underwent a GC enrichment at the compositional transitions. Here, we studied the consequences of the events just outlined on the introns of duplicated genes. We found that, while intron number was highly conserved, total intron size (the sum of intron sizes within any given gene) was smaller in the GC-rich copies compared to the GC-poor copies, especially in dispersed copies (i.e., copies located on different chromosomes or chromosome arms). GC-rich copies also showed higher densities of CpG islands and Alus, whereas GC-poor copies were characterized by higher densities of LINEs. The features of the copies that underwent the compositional transition and became GC-richer are suggestive of, or related to, functional changes.

Alu Elements↗
PubMed2005

Comparative genomics of the pennate diatom Phaeodactylum tricornutum.

Diatoms are one of the most important constituents of phytoplankton communities in aquatic environments, but in spite of this, only recently have large-scale diatom-sequencing projects been undertaken. With the genome of the centric species Thalassiosira pseudonana available since mid-2004, accumulating sequence information for a pennate model species appears a natural subsequent aim. We have generated over 12,000 expressed sequence tags (ESTs) from the pennate diatom Phaeodactylum tricornutum, and upon assembly into a nonredundant set, 5,108 sequences were obtained. Significant similarity (E < 1E-04) to entries in the GenBank nonredundant protein database, the COG profile database, and the Pfam protein domains database were detected, respectively, in 45.0%, 21.5%, and 37.1% of the nonredundant collection of sequences. This information was employed to functionally annotate the P. tricornutum nonredundant set and to create an internet-accessible queryable diatom EST database. The nonredundant collection was then compared to the putative complete proteomes of the green alga Chlamydomonas reinhardtii, the red alga Cyanidioschyzon merolae, and the centric diatom T. pseudonana. A number of intriguing differences were identified between the pennate and the centric diatoms concerning activities of relevance for general cell metabolism, e.g. genes involved in carbon-concentrating mechanisms, cytosolic acetyl-Coenzyme A production, and fructose-1,6-bisphosphate metabolism. Finally, codon usage and utilization of C and G relative to gene expression (as measured by EST redundance) were studied, and preferences for utilization of C and CpG doublets were noted among the P. tricornutum EST coding sequences.

Animals↗
PubMed2004

Comparative genomics of Anopheles gambiae and Drosophila melanogaster.

A sequence analysis of the genomes of Anopheles gambiae and Drosophila melanogaster reveals that Anopheles DNA is more heterogeneous and GC-richer than Drosophila DNA. The gene concentration across the Anopheles genome is characterized by low levels in the GC-poor part of the genome and a 3-fold increase in the GC-richest part; this gene density gradient is approximately half that of Drosophila. GC levels of introns and flanking sequences are correlated with GC(3) values (GC levels of third codon positions) of the corresponding genes with slopes much lower than unity; in other words, most introns and intergenic sequences are less GC-rich than the corresponding GC(3) values. These findings, which describe a compositional shift within Diptera, is of interest because of their parallels in the well studied major shift in vertebrates.

Animals↗
PubMed2004

Incorrectly predicted genes in rice?

Between one third and one half of the proposed rice genes appear to have no homologs in other species, including Arabidopsis. Compositional considerations, and a comparison of curated rice sequences with ex novo predictions, suggest that many or most of the putative genes without homologs may be false positive predictions, i.e., sequences that are never translated into functional proteins in vivo.

Base Composition↗
PubMed2004

Cytosine methylation and CpG, TpG (CpA) and TpA frequencies.

An analysis of dinucleotide frequencies was carried out on DNAs from insects and mammals, as well as on large DNA sequences from the genomes of Drosophila melanogaster, Anopheles gambiae, puffer fish (Takifugu rubripes), zebra fish (Danio rerio) and human. These organisms were chosen because Drosophila and Anopheles DNAs have an extremely low level of methylation, human DNA a high level and fish DNA a two-fold higher level compared to human. The results indicate that: (i) CpG deficiency and the corresponding TpG (CpA) excess show no correlation with the level of DNA methylation; indeed, genomes endowed with strikingly different levels of DNA methylation (such as those of Drosophila and human) exhibited similar TpG (CpA) levels; (ii) the correlation between GC levels of large (50 kb) DNA sequences and TpA or CpG shortage levels do not appear to be due to CpG methylation followed by deamination; (iii) CpG dinucleotides are more frequent in fishes than in mammals; interestingly, the monotreme Ornitorhinchus anatinus shows an intermediate CpG frequency. The implications of these results are discussed.

5-Methylcytosine↗
PubMed2004

Body temperature and evolutionary genomics of vertebrates: a lesson from the genomes of Takifugu rubripes and Tetraodon nigroviridis.

In this paper, we provide evidence for the body temperature effect on the formation of GC-rich isochores, by analysing genomic sequences from two puffer fishes living at different temperatures. The higher body temperature of Tetraodon nigroviridis compared to Takifugu rubripes (DeltaT approximately 15 degrees C) appears to be the cause of a higher compositional heterogeneity of the former due to the formation of GC-rich regions. Such an effect does not only concern large DNA segments but also coding sequences.

Adaptation, Physiological↗
PubMed2004

Compositional gene landscapes in vertebrates.

The existence of a well conserved linear relationship between GC levels of genes' second and third codon positions (GC2, GC3) prompted us to focus on the landscape, or joint distribution, spanned by these two variables. In human, well curated coding sequences now cover at least 15%-30% of the estimated total gene set. Our analysis of the landscape defined by this gene set revealed not only the well documented linear crest, but also the presence of several peaks and valleys along that crest, a property that was also indicated in two other warm-blooded vertebrates represented by large gene databases, that is, mouse and chicken. GC2 is the sum of eight amino acid frequencies, whereas GC3 is linearly related to the GC level of the chromosomal region containing the gene. The landscapes therefore portray relations between proteins and the DNA environments of the genes that encode them.

Animals↗
PubMed2003

The correlation between GC3 and hydropathy in human genes.

A positive correlation holds between the GC level of third codon positions of human genes (GC(3)) and hydropathy of the encoded proteins. This correlation may appear counterintuitive, since it links a physical property of proteins to the base composition of 'synonymous' sites. We here establish the nontriviality of the correlation, which has recently been contested. In particular, the correlation cannot simply be a consequence of an analogous correlation for first and second codon positions, since no such correlation exists. More generally, for any explanation via two chained correlations, the intermediate property would need to be strongly correlated with hydrophobicity and/or GC(3).

Amino Acids↗
PubMed2003

GC3 heterogeneity and body temperature in vertebrates.

A recent paper by Belle et al. (J. Mol. Evol. 55 (2002) 356) reported an analysis of mean GC(3) (the GC level of third codon positions) and standard deviations of GC(3) of vertebrate genomes as related to body temperature, and concluded that "the thermal stability hypothesis does not appear to explain the general patterns of composition", apparently contradicting a previous working hypothesis from our laboratory. We have analyzed the data of Belle et al. and find that their data not only do not contradict the thermal stability hypothesis, but if anything support it.

Adaptation, Physiological↗
PubMed2003

The major shifts of human duplicated genes.

Since many gene duplications in the human genome are ancient duplications going back to the origin of vertebrates, the question may be asked about the fate of such duplicated genes at the compositional genome transitions that occurred between cold- and warm-blooded vertebrates. Indeed, at that transition, about half of the (GC-poor) genes of cold-blooded vertebrates (the genes of the gene-dense "ancestral genome core") underwent a GC enrichment to become the genes of the "genome core" of warm-blooded vertebrates. Since the compositional distribution of the human duplicated genes investigated (1111 pairs) mimics the general distribution of human genes (about 50% GC(3)-poor and 50% GC(3)-rich genes, the border being at 60% GC(3)), we considered two possibilities, namely that the compositional transition affected either (i) about half of the copies on a random basis, or (ii) preferentially only one copy of the duplicated genes. The two possibilities could be distinguished if each copy is put into one of two subsets according to its GC(3) level. Indeed, in the first case, the two distributions would be similar, whereas in the second case, the two distributions would be different, one copy having maintained the ancestral GC-poor composition, and one copy having undergone the compositional change. Using this approach, we could show that, by far and large, one copy of the duplicated genes preferentially underwent the GC enrichment. This result implies that this copy, which had possibly acquired a different function and/or regulation, was preferentially translocated into the gene-dense compartment of the genome, the "ancestral genome core", namely the "gene space" which underwent the compositional transition at the emergence of warm-blooded vertebrates.

Adaptation, Physiological↗
PubMed2003

Compositional features of eukaryotic genomes for checking predicted genes.

Gene prediction relies on the identification of characteristic features of coding sequences that distinguish them from non-coding DNA. The recent large-scale sequencing of entire genomes from higher eukaryotes, in conjunction with currently used gene prediction algorithms, has provided an abundance of putative genes that can now be analysed for their compositional properties. Strong, systematic differences still exist, in several species, between the compositional properties of sets of ex novo predicted genes and genes that have been experimentally detected and/or verified. This is particularly evident in the estimated gene set (>45,000 genes) of the recently sequenced rice genome, where roughly half the predicted genes are compositionally unusual and have no known orthologues in the dicot Arabidopsis. In a few cases such differences might suggest a bias in experimental gene-finding protocols, but the quasi-random nature of the compositionally aberrant predicted genes is a strong indication that many, if not most, of them are false positives. It therefore appears that some important features of coding regions have not yet been taken into account in existing gene prediction programs. Statistical base compositional properties of curated gene data sets from vertebrates, which we briefly review here, should therefore provide a useful benchmark for fine-tuning probabilistic gene models and model parameters that are currently in use.

Animals↗