Comparative genomics and evolutionary biology

Spectrum of Light as a Determinant of Plant Functioning: A Historical Perspective

The significance of the spectral composition of light for growth and other physiological functions of plants moved to the focus of "plant science" soon after the discovery of photosynthesis, if not earlier. The research in this field recently intensified due to the explosive development of computer-controlled systems for artificial illumination and documenting photosynthetic activity. The progress is also substantiated by recent insights into the molecular mechanisms of photo-regulation of assorted physiological functions in plants mediated by photoreceptors and other pigment systems. The spectral balance of solar radiation can vary significantly, affecting the functioning and development of plants. Its effects are evident on the macroscale (e.g., in individual plants growing under the forest canopy) as well as on the meso- or microscale (e.g., mutual shading of leaf cell layers and chloroplasts). The diversity of the observable effects of light spectrum variation arises through (i) the triggering of different photoreceptors, (ii) the non-uniform efficiency of spectral components in driving photosynthesis, and (iii) a variable depth of penetration of spectral components into the leaf. We depict the effects of these factors using the spectral dependence of chloroplast photorelocation movements interlinked with the changes in light penetration into (light capture by) the leaf and the photosynthetic capacity. In this review, we unfold the history of the research on the photocontrol effects and put it in the broader context of photosynthesis efficiency and photoprotection under stress caused by a high intensity of light.

Expansion of the BPI family by duplication on human chromosome 20: characterization of the RY gene cluster in 20q11.21 encoding olfactory transporters/antimicrobial-like peptides

Antimicrobial peptides provide a defense system against microorganisms. One class of these molecules binds lipophilic substrates and is therefore directed against gram-negative bacteria. This family includes proteins related to bactericidal/permeability-increasing protein (BPI). We characterized an approximately 100-kb cluster of three human genes named RYSR, RYA3, and RY2G5 that are related to the BPI family. The RY cluster maps to 20q11.21, >5 Mb upstream of the BPI cluster. The RY and BPI genes have similar exon structures, indicating that they were derived by duplication from a common ancestor. We identified mouse BPI-related and RY orthologues in syntenic regions, indicating that the gene family expanded before mouse and human diverged. Expression analyses show that RYs are strongly expressed in the olfactory epithelium, suggesting that they also could act as odorant transporters or detoxification agents in the olfactory system. Together, these data show how mammals diversified their antimicrobial defenses/olfactory pathways through a duplication-driven adaptive selection process.

Death-associated protein 4 binds MST1 and augments MST1-induced apoptosis

The protein kinase MST1 is proapoptotic when overexpressed in an active form, however, its physiologic regulation and cellular targets are unknown. An overexpressed inactive MST1 mutant associates in COS-7 cells with an endogenous 761-amino acid polypeptide known as "death-associated protein 4" (DAP4). The DAPs are a functionally heterogeneous array of polypeptides previously isolated by Kimchi and colleagues (Kimchi, A. (1998) Biochim. Biophys. Acta 1377, F13-F33 in a screen for elements involved in the interferon gamma-induced apoptosis of HeLa cells. DAP4, which is encoded by a member of a vertebrate-only gene family, contains no identifiable domains, but is identical over its amino-terminal 488 amino acids to p52(rIPK), a putative modulator of protein kinase R. DAP4 is a widely expressed, constitutively nuclear polypeptide that homodimerizes through its amino terminus and binds MST1 through its carboxyl-terminal segment. MST1 is predominantly cytoplasmic, but cycles continuously through the nucleus, as evidenced by its rapid accumulation in the nucleus after addition of the Crm1 inhibitor, leptomycin B. Overexpression of DAP4 does not cause apoptosis, however, coexpression of DAP4 with a submaximal amount of MST1 enhances MST1-induced apoptosis in a dose-dependent fashion. DAP4 is not significantly phosphorylated by MST1 nor does it alter MST1 kinase activity in vivo or in vitro. MST1-induced apoptosis is suppressed by a dominant interfering mutant of p53. MST1 is unable to directly phosphorylate p53, however, DAP4 binds endogenous and recombinant p53. DAP4 may promote MST1-induced apoptosis by enabling colocalization of MST with p53.

Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine

We have sequenced to high levels of accuracy 714-kb and 233-kb regions of the mouse and bovine X-inactivation centers (Xic), respectively, centered on the Xist gene. This has provided the basis for a fully annotated comparative analysis of the mouse Xic with the 2.3-Mb orthologous region in human and has allowed a three-way species comparison of the core central region, including the Xist gene. These comparisons have revealed conserved genes, both coding and noncoding, conserved CpG islands and, more surprisingly, conserved pseudogenes. The distribution of repeated elements, especially LINE repeats, in the mouse Xic region when compared to the rest of the genome does not support the hypothesis of a role for these repeat elements in the spreading of X inactivation. Interestingly, an asymmetric distribution of LINE elements on the two DNA strands was observed in the three species, not only within introns but also in intergenic regions. This feature is suggestive of important transcriptional activity within these intergenic regions. In silico prediction followed by experimental analysis has allowed four new genes, Cnbp2, Ftx, Jpx, and Ppnx, to be identified and novel, widespread, complex, and apparently noncoding transcriptional activity to be characterized in a region 5' of Xist that was recently shown to attract histone modification early after the onset of X inactivation.

Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: the Plantae/Fungi/Metazoa trichotomy revisited

We investigated the basal phylogeny of eukaryotes through analyses of sequences from the ADP-ATP mitochondrial carrier, a transmembrane protein that is stable in function across eukaryote kingdoms. The ADP-ATP data strongly suggest the grouping of Plantae and Fungi to the exclusion of Metazoa. We implemented several procedures to avoid pervasive analytical artifacts such as erroneous alignment, random rooting, long branch attraction, and misidentification of noisy characters. The quest of an eukaryote tree that would be largely consistent across multiple loci might be essentially illusory because of differential lineage sorting, horizontal gene transfer, and the chimeric nature of early eukaryotes. Better understanding of these evolutionary parameters, requiring separate phylogenetic analyses of multiple independent loci, is fundamental for resolution of the modes of emergence and evolution of the major eukaryote lineages.

Functional genomics and the study of development, variation and evolution

It has rarely been possible to connect the developmental and evolutionary branches of genetics, particularly with regard to the precise changes in the molecular control of development that are responsible for phenotypic variation and evolution. Making such connections will require a high-resolution molecular description of the genetic networks that underlie development and an understanding of their responses to genetic and environmental variation. Functional genomics approaches to development and evolution promise to accelerate the research necessary to accomplish these goals.

Genome sequences and evolutionary biology, a two-way interaction

Complete genome sequences are accumulating rapidly, culminating with the announcement of the human genome sequence in February 2001. In addition to cataloguing the diversity of genes and other sequences, genome sequences will provide the first detailed and complete data on gene families and genome organization, including data on evolutionary changes. Reciprocally, evolutionary biology will make important contributions to the efforts to understand functions of genes and other sequences in genomes. Large-scale, detailed and unbiased comparisons between species will illuminate the evolution of genes and genomes, and population genetics methods will enable detection of functionally important genes or sequences, including sequences that have been involved in adaptive changes.

Current awareness

In order to keep subscribers up-to-date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly-published material on comparative and functional genomics. Each bibliography is divided into 16 sections. 1 Reviews & symposia; 2 General; 3 Large-scale sequencing and mapping; 4 Genome evolution; 5 Comparative genomics; 6 Gene families and regulons; 7 Pharmacogenomics; 8 Large-scale mutagenesis programmes; 9 Functional complementation; 10 Transcriptomics; 11 Proteomics; 12 Protein structural genomics; 13 Metabolomics; 14 Genomic approaches to development; 15 Technological advances; 16 Bioinformatics. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted