Evolution of genome size: new approaches to an old problem

Eukaryotic genomes come in a wide variety of sizes. Haploid DNA contents (C values) range > 80,000-fold without an apparent correlation with either the complexity of the organism or the number of genes. This puzzling observation, the C-value paradox, has remained a mystery for almost half a century, despite much progress in the elucidation of the structure and function of genomes. Here I argue that new approaches focussing on the genetic mechanisms that generate genome-size differences could shed much light on the evolution of genome size.     

The role of hormones in apical dominance. New approaches to an old problem in plant development

The role of hormones in apical dominance has been under investigation with traditional 'spray and weigh' methods for nearly 5 decades. Even though the precision of hormone content analyses in tissue has greatly improved in recent years, there have been no significant breakthroughs in our understanding of the action mechanism of this classical developmental response. Auxin appears to inhibit axillary bud outgrowth whereas cytokinins will often promote it. Conclusive evidence for a direct role of these or other hormones in apical dominance has not been forthcoming. However, promising new tools and approaches recently have begun to be utilized. The manipulation of endogenous hormone levels via the use of transgenic plants transformed with bacterial genes ( iaaM and ipt from Agrobacterium tumefaciens and iaaL from Pseudomonas syringae pv. savastanoi ) has demonstrated powerful effects of auxin and cytokinin on axillary bud outgrowth. Also, possible auxin and cytokinin involvement of rolB and C genes from Agrobacterium rhizogenes whose activity is associated with reduced apical dominance in dicotyledons has received considerable attention. The characterization of unique mRNAs and proteins in non-growing and growing lateral buds before and after apical dominance release is helping to lay the groundwork for the elucidation of signal transduction and cell cycle regulation in this response. The use of auxin-deficient, and auxin/ethylene-resistant mutants has provided another approach for analyzing the role of these hormones. The presumed eventual employment of molecular assay systems (SAUR/GH3 promoters fused with GUS reporter gene) which are presently being developed for analyzing auxin localized in lateral buds will hopefully provide a critical test for the direct auxin inhibition hypothesis.     

Relation between growth and replication in bacteria

The control of chromosome replication in bacteria depends on the cell growth; a round of replication is initiated when the cell mass (or protein) per replication origin has reached a certain critical level. Relative values of this “initiation mass” have previously been estimated from the evaluation of experiments involving age fractionation of radioactively labelled bacterial cultures. Here a theoretical analysis is presented which permits a simple and accurate method to determine this initiation mass from a few parameters easily observable with exponential cultures, without the need for age fractionation.     

Metabolic control: a new solution to an old problem

The phenomenon whereby the presence of oxygen regulates the rate of glucose metabolism was first described by Louis Pasteur. A novel mechanism has now been discovered, involving the AMP-activated protein kinase cascade, that can account for the Pasteur effect in ischaemic heart muscle.     

Adhesion of ectomycorrhizal bacteria to plant cells: an in vitro evidence

Defensins are a family of host defence peptides that play an important role in the innate immunity of mammalian and avian species. In humans, four beta-defensins have been isolated so far, corresponding to the products of the genes DEFB1 (h-BD1, GenBank accession number NM_005218); DEFB4 (h-Bd2, NM_004942.2), DEFB103 (h-BD3, NM_018661); and DEFB104 (hBD4, NM_080389) mapping on chromosome 8p23.22. We have localized beta-defensin genes on metaphasic chromosomes of great apes and several non-human primate species to determine their physical mapping. Using fluorescent in situ hybridization and BAC probes containing the four beta-defensin genes, we have mapped the homologous regions to the beta-defensin genes on chromosome 8p23-p.22 in non-human primates, while no signals were detected on prosimians chromosomes.     

The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea

The Archaeon Methanosarcina mazei and related species are of great ecological importance as they are the only organisms fermenting acetate, methylamines and methanol to methane, carbon dioxide and ammonia (in case of methylamines). Since acetate is the precursor of 60% of the methane produced on earth these organisms contribute significantly to the production of this greenhouse gas, e.g. in rice paddies. The 4,096,345 base pairs circular chromosome of M. mazei is more than twice as large as the genomes of the methanogenic Archaea currently completely sequenced (Bult et al., 1996; Smith et al., 1997). 3,371 open reading frames (ORFs) were identified. Based on currently available sequence data 376 of these ORFs are Methanosarcina-specific and 1,043 ORFs find their closest homologue in the bacterial domain. 544 of these ORFs reach significant similarity values only in the bacterial domain. They include 56 of the 102 transposases, and proteins involved in gluconeogenesis, proline biosynthesis, transport processes, DNA-repair, environmental sensing, gene regulation, and stress response. Striking examples are the occurrence of the bacterial GroEL/GroES chaperone system and the presence of tetrahydrofolate-dependent enzymes. These findings might indicate that lateral gene transfer has played an important evolutionary role in forging the physiology of this metabolically versatile methanogen.     

New findings on evolution of metal homeostasis genes: evidence from comparative genome analysis of bacteria and archaea

In order to examine the natural history of metal homeostasis genes in prokaryotes, open reading frames with homology to characterized P(IB)-type ATPases from the genomes of 188 bacteria and 22 archaea were investigated. Major findings were as follows. First, a high diversity in N-terminal metal binding motifs was observed. These motifs were distributed throughout bacterial and archaeal lineages, suggesting multiple loss and acquisition events. Second, the CopA locus separated into two distinct phylogenetic clusters, CopA1, which contained ATPases with documented Cu(I) influx activity, and CopA2, which contained both efflux and influx transporters and spanned the entire diversity of the bacterial domain, suggesting that CopA2 is the ancestral locus. Finally, phylogentic incongruences between 16S rRNA and P(IB)-type ATPase gene trees identified at least 14 instances of lateral gene transfer (LGT) that had occurred among diverse microbes. Results from bootstrapped supported nodes indicated that (i) a majority of the transfers occurred among proteobacteria, most likely due to the phylogenetic relatedness of these organisms, and (ii) gram-positive bacteria with low moles percent G+C were often involved in instances of LGT. These results, together with our earlier work on the occurrence of LGT in subsurface bacteria (J. M. Coombs and T. Barkay, Appl. Environ. Microbiol. 70:1698-1707, 2004), indicate that LGT has had a minor role in the evolution of P(IB)-type ATPases, unlike other genes that specify survival in metal-stressed environments. This study demonstrates how examination of a specific locus across microbial genomes can contribute to the understanding of phenotypes that are critical to the interactions of microbes with their environment.     

Biofilms: new ideas for an old problem

Microbial cells, under moist conditions, are able to adhere to surfaces and to form structured communities embedded in a matrix of extracellular polymeric substances (EPS). In industrial environments, biofilms can cause heat and mass transfer limitations whilst in medical facilities they can be a source of contamination and proliferation of infections. Biofilm formation is related to the pathogenicity of some bacterial strains and cells in biofilms are usually resistant to antimicrobials agents, which increases the interest in new and sound methods for their prevention and destruction.     

Predicting the height of fossil plant remains: an allometric approach to an old problem

Interspecific correlations between plant height and basal stem diameter (the allometry of height) and between stem length distal to where diameter is measured (the allometry of stem taper) were determined for a total of 265 species with self-supporting stems and for the shoots of five conifers and 15 angiosperm vine species. The allometric equations obtained for these data are proposed as a method to predict the heights of fossil plants for which basal stem diameters are either known or inferred, and to predict the missing lengths of fragmented stems based on the most proximal stem diameters observed.