Genomic channeling in bacterial cell division

The bacterial dcw cluster is a group of genes involved in cell division and peptidoglycan synthesis. Comparison of the cluster across several bacterial genomes shows that its gene content and its gene order are conserved in distant bacterial lineages and, moreover, that, being most conserved in rod-shaped bacteria, the degree of conservation relates to bacterial morphology. We propose a model in which the selective pressure to maintain the cluster arises from the need to efficiently coordinate the processes of elongation and septation in rod-shaped bacteria. Gene order in the dcw cluster would be conserved as a result of mechanisms comprising: (i) a limited amount of peptidoglycan precursors required both for septation and elongation of the wall; (ii) co-translational assembly of the protein complexes involved in cell division and in the synthesis of the peptidoglycan precursors; and (iii) alternation in the cellular localization of the assembled complexes to participate either in the synthesis of the septal peptidoglycan and division, or in the synthesis of the lateral wall. The name genomic channeling is proposed for this model as it involves a genomic arrangement that could facilitate the assembly of specific protein complexes and their subsequent conveyance to specific locations in the crowded cytoplasm and the envelope.     

Apolipoprotein A-II, genetic variation on chromosome 1q21-q24, and disease susceptibility

PURPOSE OF REVIEW: Apolipoprotein (apo) A-II is the second most abundant HDL apolipoprotein; however its function remains largely unknown. Owing to the lack of consequences of apoA-II deficiency in humans, it has long been considered an apolipoprotein of minor importance. Overexpression of apoA-II in transgenic mice, however, causes combined hyperlipidemia and, in some cases, insulin resistance. This, and the location of the apoA-II gene in chromosome 1q23, a hot region in the search for genes associated with familial combined hyperlipidemia, insulin resistance and type 2 diabetes mellitus, has greatly increased interest in this protein. RECENT FINDINGS: ApoA-II is biochemically and genetically linked to familial combined hyperlipidemia. Given that the chromosome 1q21-q24 region is associated with insulin resistance or type 2 diabetes, this region is a now a focus of interest in the study of these complex, often overlapping diseases. However, no polymorphisms that increase apoA-II levels have been identified to date in humans. Other nonstructural loci may regulate apoA-II plasma concentration. Further, plasma apoA-II concentration is increased by saturated fat intake. Several reports have added to our understanding of the relationship between apoA-II mutations and amyloidosis both in humans and mice. SUMMARY: An increased plasma concentration of apoA-II might contribute to familial combined hyperlipidemia or type 2 diabetes mellitus expression, which emphasizes the need to understand its function and metabolism. Genetic studies in well characterized patients and genomic and proteomic approaches in cell and mouse models may help to achieve this understanding.     

Endemic species of grasses in Mexico: a phytogeographic approach

The Poaceae family includes approximately 700 genera and 10000 species, and Mexico is considered one of its most important centers of diversity and endemism. A total of 256 taxa (including 16 subspecific taxonomic units), belonging to 65 genera, are endemic to Mexico. Some of them are close relatives of important crops, while others are used in different ways all over the country. The aim of this paper is to discuss the distribution patterns at state level of the Mexican endemic species of Poaceae. Using cluster strategies, the states are classified according to their floristic similarities. Later, hotspots of endemism are identified, in order to discuss their role in conservation strategies. To evaluate the importance of each state in the conservation of the Mexican endemic Poaceae, two iterative complementarity methods were also used. Our results show that the largest concentration of endemic taxa occurs in a few states, such as Jalisco, Mexico, Michoacán, Durango, Oaxaca, Veracruz, San Luis Potosi, Chiapas, Chihuahua, Puebla, and Coahuila. The results also show that there are some patterns in the relationship to its endemism that seem to reflect important diversification trends in the family. Accordingly, 31% of the grass genera of Mexico have at least one endemic species, and 16.7% of the genera have only one endemic species. In contrast, six genera contribute 47.2% of the total number of grass endemics in Mexico. The Chloridoideae contributes 42.9% of the total grass endemic species of Mexico, whereas the Panicoideae includes 24.6%, and the Pooideae 19.8%. Thus, these three subfamilies contribute about 87% of the species endemism. On the basis of the habitat and distribution patterns of these subfamilies, two main areas of endemicity can be identified. The first area is located in warm habitats, whereas the second is related to temperate and high regions. The cluster analyses indicate the occurrence of four state groups whose phytogeographical explanation is discussed on the basis of a floristic regionalization of Mexico. The results also indicate the need to establish a relatively high number of sites and states for the conservation of 256 endemic taxa. The elevated number of sites required to conserve the Mexican endemic Poaceae is mainly due to the fact that many taxa have a restricted distribution pattern. On the basis of the patterns obtained, a few proposals are presented for undertaking the establishment of conservation priorities of these taxa.     

Synthesis and anti-HCMV activity of 1-acyl-beta-lactams and 1-acylazetidines derived from phenylalanine

Different Phe-derived 1-acyl-beta-lactams, analogous to a series of 2-azetidinones acting as HCMV serine protease inhibitors, were synthesized. Some of these compounds were modest inhibitors of the HCMV replication. Interestingly, removal of the carbonyl group of the beta-lactam ring, most likely acting as the serine trap, resulted in an azetidine derivative with anti-HCMV activity comparable to that of the reference compound ganciclovir.     

TRAF family proteins link PKR with NF-kappa B activation

The double-stranded RNA (dsRNA)-dependent protein kinase PKR activates NF-kappa B via the I kappa B kinase (IKK) complex, but little is known about additional molecules that may be involved in this pathway. Analysis of the PKR sequence enabled us to identify two putative TRAF-interacting motifs. The viability of such an interaction was further suggested by computer modeling. Here, we present evidence of the colocalization and physical interaction between PKR and TRAF family proteins in vivo, as shown by immunoprecipitation and confocal microscopy experiments. This interaction is induced upon PKR dimerization. Most importantly, we show that the binding between PKR and TRAFs is functionally relevant, as observed by the absence of NF-kappa B activity upon PKR expression in cells genetically deficient in TRAF2 and TRAF5 or after expression of TRAF dominant negative molecules. On the basis of sequence information and mutational and computer docking analyses, we favored a TRAF-PKR interaction model in which the C-terminal domain of TRAF binds to a predicted TRAF interaction motif present in the PKR kinase domain. Altogether, our data suggest that TRAF family proteins are key components located downstream of PKR that have an important role in mediating activation of NF-kappa B by the dsRNA-dependent protein kinase.     

Inhibition of B cell death causes the development of an IgA nephropathy in (New Zealand white x C57BL/6)F(1)-bcl-2 transgenic mice

Little is known about the pathogenic mechanisms of IgA nephropathy, despite being the most prevalent form of glomerulonephritis in humans. We report in this study that in (New Zealand White (NZW) x C57BL/6)F(1) mice predisposed to autoimmune diseases, the expression of a human bcl-2 (hbcl-2) transgene in B cells promotes a CD4-dependent lupus-like syndrome characterized by IgG and IgA hypergammaglobulinemia, autoantibody production, and the development of a fatal glomerulonephritis. Histopathological analysis of glomerular lesions reveals that the glomerulonephritis observed in these animals resembles that of human IgA nephropathy. The overexpression of Bcl-2 in B cells selectively enhances systemic IgA immune responses to T-dependent Ags. Significantly, serum IgA purified from (NZW x C57BL/6)F(1)-hbcl-2 transgenic mice, but not from nontransgenic littermates, shows reduced levels of galactosylation and sialylation and an increased ability to deposit in the glomeruli, as observed in human patients with IgA nephropathy. Our results indicate that defects in the regulation of B lymphocyte survival associated with aberrant IgA glycosylation may be critically involved in the pathogenesis of IgA nephropathy, and that (NZW x C57BL/6)F(1)-hbcl-2 Tg mice provide a new experimental model for this form of glomerulonephritis.     

Influence of proline residues in transmembrane helix packing

Integral membrane proteins often contain proline residues in their alpha-helical transmembrane (TM) fragments, which may strongly influence their folding and association. Pro-scanning mutagenesis of the helical domain of glycophorin A (GpA) showed that replacement of the residues located at the center abrogates helix packing while substitution of the residues forming the ending helical turns allows dimer formation. Synthetic TM peptides revealed that a point mutation of one of the residues of the dimerization motif (L75P) located at the N-terminal helical turn of the GpA TM fragment, adopts a secondary structure and oligomeric state similar to the wild-type sequence in detergents. In addition, both glycosylation mapping in biological membranes and molecular dynamics showed that the presence of a proline residue at the lipid/water interface has as an effect the extension of the helical end. Thus, helix packing can be an important factor that determines appearance of proline in TM helices. Membrane proteins might accumulate proline residues at the two ends of their TM segments in order to modulate the exposition of key amino acid residues at the interface for molecular recognition events while allowing stable association and native folding.     

Crystal structure of the RIM2 C2A-domain at 1.4 A resolution

RIMs are large proteins that contain two C2-domains and are localized at presynaptic active zones, where neurotransmitters are released. RIMs play key roles in synaptic vesicle priming and regulation of presynaptic plasticity. A mutation in the RIM1 C2A-domain has been implicated in autosomal dominant cone-rod dystrophy (CORD7). The RIM C2A-domain does not contain the full complement of aspartate residues that commonly mediate Ca2+ binding at the top loops of C2-domains, and has been reported to interact with SNAP-25 and synaptotagmin 1, two proteins from the Ca2+-dependent membrane fusion machinery. Here we have used NMR spectroscopy and X-ray crystallography to analyze the structure and biochemical properties of the RIM2 C2A-domain, which is closely related to the RIM1 C2A-domain. We find that the RIM2 C2A-domain does not bind Ca2+. Moreover, little binding of the RIM2 C2A-domain to SNAP-25 and to the C2-domains of synaptotagmin 1 was detected by NMR experiments, suggesting that as yet unidentified interactions of the RIM C2A-domain mediate its function. The crystal structure of the RIM2 C2A-domain using data to 1.4 A resolution reveals a beta-sandwich that resembles those observed for other C2-domains, but exhibits a unique dipolar distribution of electrostatic charges whereby one edge of the beta-sandwich is highly positive and the other edge is highly negative. The location of the mutation site implicated in CORD7 at the bottom of the domain and the pattern of sequence conservation suggest that, in contrast to most C2-domains, the RIM C2A-domains may function through Ca2+-independent interactions involving their bottom face.     

Phosphorylation modulates the alpha-helical structure and polymerization of a peptide from the third tau microtubule-binding repeat

Paired helical filaments (PHFs) isolated from patients with Alzheimer's disease (AD) mainly consist of the microtubule-associated protein tau in a hyperphosphorylated form. It has been found that PHFs are the first example of pathological protein aggregation associated with formation of alpha-helices [Biochemistry (2002) 41, 7150-5]. In an effort to investigate the interplay between phosphorylation and the putative role of short regions of alpha-helix in the polymerization of tau, we have focused on the region of tau encompassing residues 317 to 335. This region is able to form protein fibrils in vitro and has two serines that are often found phosphorylated in PHFs. Using trifluoroethanol as an indicator of the alpha-helix, we find that the stability of the alpha-helix conformation is enhanced by phosphorylation. Circular dichroism data show that the phosphorylated peptide in water presents a content in alpha-helix similar to the unphosphorylated peptide at 40% of trifluoroethanol. Phosphorylation also stimulates the effect of juglone in promoting the in vitro polymerization. Furthermore, Fourier transformed infrared spectroscopy of samples of phosphorylated peptide polymerized with juglone renders a spectrum with maxima at approximately 1665 and approximately 1675 cm(-1), which are suggestive of a mixture of turns and alpha-helix conformations. Our results provide a direct mechanistic connection between phosphorylation and polymerization in tau. The connection between phosphorylation and polymerization appears to involve formation of alpha-helix structure.     

Molecular associations and surface-active properties of short- and long-N-acyl chain ceramides

The behaviour of N-hexadecanoylsphingosine (Cer16), N-hexanoylsphingosine (Cer6) and N-acetylsphingosine (Cer2) in aqueous media and in lipid-water systems, monolayers and bilayers has been comparatively examined using Langmuir balance and fluorescence techniques. Cer16 behaves as an insoluble non-swelling amphiphile, not partitioning into the air-water interface, thus not modifying the surface pressure of the aqueous solutions into which it is included. By contrast both Cer6 and Cer2 behave as soluble amphiphiles, up to approx. 100 microM. At low concentrations, they become oriented at the air-water interface, increasing surface pressure in a dose-dependent way up to ca. 5 microM bulk concentration. At higher concentrations, the excess ceramide forms micelles, critical micellar concentrations of both Cer6 and Cer2 being in the 5-6 microM range. When the air-water interface is occupied by a phospholipid, 6Cer2 and Cer6 become inserted in the phospholipid monolayer, causing a further increase in surface pressure. This increase is dose dependent, and reaches a plateau at ca. 2 microM ceramide bulk concentration. Both Cer2 and Cer6 become inserted in phospholipid monolayers with initial surface pressures of up to 43 and 46 mN m(-1), respectively, which ensures their capacity to become inserted into cell membranes whose monolayers are estimated to support a surface pressure of about 30 mN m(-1). Both Cer2 and Cer6, but not Cer16, had detergent-like properties, such as giving rise to phospholipid-ceramide mixed micelles, when added to phospholipid monolayers or bilayers. The short-chain ceramides form large aggregates and precipitate at concentrations above approx. 100 microM. These results are relevant in cell physiology studies in which short- and long-chain ceramides are sometimes used as equivalent molecules, in spite of their different biophysical behaviour.