An Italian functional genomic resource for <Emphasis Type="Italic">Medicago truncatula</Emphasis>

Background

Medicago truncatula is a model species for legumes. Its functional genomics have been considerably boosted in recent years due to initiatives based both in Europe and US. Collections of mutants are becoming increasingly available and this will help unravel the genetic control of important traits for many species of legumes.

Findings

Our report is on the production of three complementary mutant collections of the model species Medicago truncatula produced in Italy in the frame of a national genomic initiative. Well established strategies were used: Tnt1 mutagenesis, TILLING and activation tagging. Both forward and reverse genetics screenings proved the efficiency of the mutagenesis approaches adopted, enabling the isolation of interesting mutants which are in course of characterization. We anticipate that the reported collections will be complementary to the recently established functional genomics tools developed for Medicago truncatula both in Europe and in the United States.

     

Aquatic Plants Stimulate the Growth of and Biofilm Formation by Mycobacterium ulcerans in Axenic Culture and Harbor These Bacteria in the Environment

Mycobacterium ulcerans is the causative agent of Buruli ulcer, one of the most common mycobacterial diseases of humans. Recent studies have implicated aquatic insects in the transmission of this pathogen, but the contributions of other elements of the environment remain largely unknown. We report here that crude extracts from two green algae added to the BACTEC 7H12B culture medium halved the doubling time of M. ulcerans and promoted biofilm formation. Using the 7H12B medium, modified by the addition of the algal extract, and immunomagnetic separation, we also demonstrate that M. ulcerans is associated with aquatic plants in an area of the Ivory Coast where Buruli ulcer is endemic. Genotype analysis showed that plant-associated M. ulcerans had the same profile as isolates recovered in the same region from both aquatic insects and clinical specimens. These observations implicate aquatic plants as a reservoir of M. ulcerans and add a new potential link in the chain of transmission of M. ulcerans to humans.     

Controlled disassembly of peptide amphiphile fibres.

In this paper, the introduction of both a methionine residue and a nitrobenzyl derivative as a labile linker between the peptide part and the hydrophobic alkyl chain of a peptide amphiphile are presented. These modifications are shown not to inhibit the formation of structured assemblies that analogous peptide amphiphiles lacking the linkers are able to form. Moreover, the introduction of either labile linker allows removal of the peptide amphiphile's stabilizing hydrophobic moieties to initiate a controlled disassembly of fibre aggregates. This is achieved by either treatment with CNBr or UV irradiation, respectively. These disassembly mechanisms could be the starting point for methodology that allows further manipulation of self-assembled peptide amphiphile architectures.     

Seven Decades of Change in the Zooplankton (s.l.) of the Nile Delta Lakes (Egypt), with Particular Reference to Lake Borullus

Around the 1930s, the zooplankton (and benthos) of the Nile delta lakes, and Lake Borullus in particular, had a mixed, eutrophic facies, with marine and mesohaline elements dominant for about eight months per year, and freshwater species taking over during the four months of the Nile flood. After the Aswan dam became operational, this regime changed: a steady supply of agricultural drainage water of Nilotic origin consistently freshened the delta. Thus, except in the immediate vicinity of their outlet to the sea, the lakes became almost fresh. Only during the rare and short‐lived (one‐three weeks) occasions when Aswan closes in winter, marine water is sucked in, and along with it, a saline fauna temporarily becomes re‐established in the east and centre of lake Borullus, and presumably of the other delta lakes as well. This marine fauna remained the same over 70+ years of observations. The freshwater component, in contrast, partly nilotic, partly mediterranean, changed deeply over time. First, the fraction of species from temporary waters disappeared, as well as (among copepods and cladocerans) all large‐bodied species. Several cladocerans and copepods with a euro‐mediterranean range appeared and diluted the pre‐existing Afrotropical fauna. The abundance of small cladocerans and, especially, rotifers increased by a factor ten or more. This latter change is believed to reflect two pressures. In a first phase, a re‐arrangement of the lake's fish fauna (a top down force) occurred. Freshwater fish replaced marine diadromic species, and their predation pressure on the zooplankton preferentially removed large‐bodied prey. In a second phase, increased agricultural drainage caused eutrophication (a bottom‐up force) and larger filtrators (cladocerans, some copepods) began to be replaced by small filtrators (rotifers). (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase by Archaea through an ancient horizontal gene transfer

The Pyrococcus abyssi genome displays two genes possibly coding for S-adenosyl-l-methionine-dependent RNA(uracil, C5)-methyltransferases (PAB0719 and PAB0760). Their amino acid sequences are more closely related to Escherichia coli RumA catalysing the formation of 5-methyluridine (m(5)U)-1939 in 23S rRNA than to E. coli TrmA (tRNA methyltransferase A) methylating uridine-54 in tRNA. Comparative genomic and phylogenetic analyses show that homologues of PAB0719 and PAB0760 occur only in a few Archaea, these genes having been acquired via a single horizontal gene transfer from a bacterial donor to the common ancestor of Thermococcales and Nanoarchaea. This transfer event was followed by a duplication event in Thermococcales leading to two closely related genes. None of the gene products of the two P. abyssi paralogues catalyses in vitro the formation of m(5)U in a P. abyssi rRNA fragment homologous to the bacterial RumA substrate. Instead, PAB0719 enzyme (renamed (Pab)TrmU54) displays an identical specificity to TrmA, as it catalyses the in vitro formation of m(5)U-54 in tRNA. Thus, during evolution, at least one of the two P. abyssi RumA-type enzymes has changed of target specificity. This functional shift probably occurred in an ancestor of all Thermococcales. This study also provides new evidence in favour of a close relationship between Thermococcales and Nanoarchaea.     

Total synthesis and evaluation of C25-benzyloxyepothilone C for tubulin assembly and cytotoxicity against MCF-7 breast cancer cells

The total synthesis of C25-benzyloxy epothilone C is described. A sequential Suzuki–Aldol–Yamaguchi macrolactonization strategy was utilized employing a novel derivatized C8–C12 fragment. The C25-benzyloxy analog exhibited significantly reduced biological activity in microtubule assembly and cytotoxicity assays. Molecular modeling simulations indicated that excessive steric bulk in the C25 position may reduce activity by disrupting key hydrogen bonds that are crucial for epothilone binding to β-tubulin.     

The seabird paradox: dispersal, genetic structure and population dynamics in a highly mobile, but philopatric albatross species

The philopatric behaviour of albatrosses has intrigued biologists due to the high mobility of these seabirds. It is unknown how albatrosses maintain a system of fragmented populations without frequent dispersal movements, in spite of the long-term temporal heterogeneity in resource distribution at sea. We used both genetic (amplified fragment length polymorphism) and capture-mark-recapture (CMR) data to identify explicitly which among several models of population dynamics best applies to the wandering albatross (Diomedea exulans) and to test for migration-drift equilibrium. We previously documented an extremely low genetic diversity in this species. Here, we show that populations exhibit little genetic differentiation across the species' range (Theta(B) < 0.05, where Theta(B) is an F(ST) analogue). Furthermore, there was no evidence of hierarchical structure or isolation-by-distance. Wright's F(ST) between pairs of colonies were low in general and the pattern was consistent with a nonequilibrium genetic model. In contrast, CMR data collected over the last decades indicated that about one bird per cohort has dispersed among islands. Overall, F(ST) values were not indicative of contemporary dispersal as inferred from CMR data. Moreover, all genotypes grouped together in a cluster analysis, indicating that current colonies may have derived from one ancestral source that had a low genetic diversity. A metapopulation dynamics model including a recent (postglacial) colonization of several islands seems consistent with both the very low levels of genetic diversity and structure within the wandering albatross. Yet, our data suggest that several other factors including ongoing gene flow, recurrent long-distance dispersal and source-sink dynamics have contributed to different extent in shaping the genetic signature observed in this species. Our results show that an absence of genetic structuring may in itself reveal little about the true population dynamics in seabirds, but can provide insights into important processes when a comparison with other information, such as demographic data, is possible.     

Expression of K+ channels in normal and cancerous human breast

Potassium (K+) channels contribute to the regulation of cell proliferation and apoptosis and are also involved in tumor generation and malignant growth. Using immunohistochemical analysis, we investigated the expression of four K+ channels GIRK1 (G-Protein Inwardly Rectifying Potassium Channel 1), Ca2+-activated K channel (K Ca 1.1), voltage activated K+ channels (KV 1.1 and KV 1.3) and of the anti-apoptotic protein Bcl2 in normal and cancerous breast tissues and compared their expression with clinicopathological data. GIRK1 was overexpressed in carcinomatous tissues. In contrast, K V 1.1 and K V 1.3 were less expressed in cancerous tissue. The expression of Bcl-2 was similar in both tissues. As to the clinicopathological data, a correlation between K Ca 1.1 channel and estrogen receptor (ER) expression was observed. GIRK1 was overexpressed in breast carcinoma suggesting its involvement in proliferation and oncogenesis and its possible use as a putative pharmaceutical target. The correlation between K Ca 1.1 channel and ER suggests the involvement of this channel in proliferation. The loss of expression of the two channels K V 1.1 and K V 1.3 may correspond to their role in apoptosis.     

Elimination of competing hydrolysis and coupling side reactions of a cyclodextrin glucanotransferase by directed evolution

Thermoanaerobacterium thermosulfurigenes cyclodextrin glucanotransferase primarily catalyses the formation of cyclic alpha-(1,4)-linked oligosaccharides (cyclodextrins) from starch. This enzyme also possesses unusually high hydrolytic activity as a side reaction, thought to be due to partial retention of ancestral enzyme function. This side reaction is undesirable, since it produces short saccharides that are responsible for the breakdown of the cyclodextrins formed, thus limiting the yield of cyclodextrins produced. To reduce the competing hydrolysis reaction, while maintaining the cyclization activity, we applied directed evolution, introducing random mutations throughout the cgt gene by error-prone PCR. Mutations in two residues, Ser-77 and Trp-239, on the outer region of the active site, lowered the hydrolytic activity up to 15-fold with retention of cyclization activity. In contrast, mutations within the active site could not lower hydrolytic rates, indicating an evolutionary optimized role for cyclodextrin formation by residues within this region. The crystal structure of the most effective mutant, S77P, showed no alterations to the peptide backbone. However, subtle conformational changes to the side chains of active-site residues had occurred, which may explain the increased cyclization/hydrolysis ratio. This indicates that secondary effects of mutations located on the outer regions of the catalytic site are required to lower the rates of competing side reactions, while maintaining the primary catalytic function. Subsequent functional analysis of various glucanotransferases from the superfamily of glycoside hydrolases also suggests a gradual evolutionary progression of these enzymes from a common 'intermediate-like' ancestor towards specific transglycosylation activity.