Molecular evolution of rodent insulins

Several trees of amino acid sequences of rodent insulins were derived with the maximum-parsimony procedure. Possible orthologous and paralogous relationships were investigated. Except for a recent gene duplication in the ancestor of rat and mouse, there are no strong arguments for other paralogous relationships. Therefore, a tree in agreement with other biological data is the most reasonable one. According to this tree, the capacity to form zinc-binding hexamers was lost once in the ancestor of the hystricomorph rodents, followed by moderately increased evolutionary rates in the lineages to African porcupine and chinchilla but highly increased rates in at least three independent lines to other taxa of this suborder: guinea pig, cuis, and Octodontoidea (coypu and casiragua).      

Water repellency and feather structure of the Blue Swallow Hirundo atrocaerulea

Rijke, A.M., Jesser, W.A., Evans, S.W & Bouwman, H. 2000. Water repellency and feather structure of the Blue Swallow Hirundo atrocaerulea. Ostrich 71 (1 & 2): 143–145.

The Blue Swallow is an endangered species in southern Africa and is probably the most endangered passerine. It is restricted to escarpments with grasslands above 1 000 m where mists are frequent. It appears to forage on the wing even in thick mist raising the question of feather wettability in relation to its adaptation. Extensive physical and behaviourial adaptations are known to occur in a wide variety of birds to deal with the problem of shedding water continuously. To study the water repellency and resistance to water penetration of Blue Swallow feathers, we have examined the microscopic structure of head, back, throat, breast and abdominal feathers as well as remiges and tail feathers by transmission light microscopy. The width (2R) and separation (2D) of rami and barbules have been measured and were used to calculate the parameter (R + D)/R that serves as an indicator ofwater shedding potential. For the remiges and tail feathers the values of the (R+D)/R range from 5 to 10 which is comparable to values for other terrestrial birds. However, for body feathers the range is from 10 (head) and 35 (abdomen)-higher than previously observed for any other bird including Swifts, Apodidae. Blue Swallow feathers are thus the most effective feather yet discovered at repelling water drops. The water repellency is highest in those feathers that are relatively shielded From the direct impact of small water drops (throat, breast, abdomen, back). By contrast, the flight feathers must possess a relatively large resistance to water penetration to avoid becoming waterlogged and this is coupled to low (R+D)/R values. Values for the barbules lay between 2 and 6—the same as found for other bird families—supporting an earlier conclusion that they have little direct effect in repelling water.     

Global trends and uncertainties in terrestrial denitrification and N2O emissions

Soil nitrogen (N) budgets are used in a global, distributed flow-path model with 0.5° × 0.5° resolution, representing denitrification and N₂O emissions from soils, groundwater and riparian zones for the period 1900–2000 and scenarios for the period 2000–2050 based on the Millennium Ecosystem Assessment. Total agricultural and natural N inputs from N fertilizers, animal manure, biological N₂ fixation and atmospheric N deposition increased from 155 to 345 Tg N yr⁻¹ (Tg = teragram; 1 Tg = 10¹² g) between 1900 and 2000. Depending on the scenario, inputs are estimated to further increase to 408–510 Tg N yr⁻¹ by 2050. In the period 1900–2000, the soil N budget surplus (inputs minus withdrawal by plants) increased from 118 to 202 Tg yr⁻¹, and this may remain stable or further increase to 275 Tg yr⁻¹ by 2050, depending on the scenario. N₂ production from denitrification increased from 52 to 96 Tg yr⁻¹ between 1900 and 2000, and N₂O–N emissions from 10 to 12 Tg N yr⁻¹. The scenarios foresee a further increase to 142 Tg N₂–N and 16 Tg N₂O–N yr⁻¹ by 2050. Our results indicate that riparian buffer zones are an important source of N₂O contributing an estimated 0.9 Tg N₂O–N yr⁻¹ in 2000. Soils are key sites for denitrification and are much more important than groundwater and riparian zones in controlling the N flow to rivers and the oceans.     

Pesticide levels in stork and spoonbill eggs from the Okavango Delta,Botswana

Motalaotte, S. & Bouwman, H. 2000. Pesticide levels in stork and spoonbill eggs from the Okavango Delta, Botswana. Ostrich 71 (1&2):344.

Ecotourism in the Okavango Delta is one of the major sources of foreign revenue for the Republic of Botswana. Promoting this region is therefore vital to sustainable development. One of the concerns was the past use of organochlorine pesticides to combat tsetse fly. This study looked at the levels and possible risk this use poses to Marabou storks and African Spoonbills, as well as some other birds, from this region. One particular breeding colony also experienced a decline in breeding success, the cause of which is unknown. DDE was present in almost all the eggs and blood sampled, while DDD, DDT and Dieldrin were also found in many. These pesticides are therefore present in the food chain and should be closely monitored to determine any temporal trends.     

Arginine deficiency in preconfluent intestinal Caco-2 cells modulates expression of proteins involved in proliferation, apoptosis, and heat shock response

Arginine is classified as a conditionally essential amino acid required exogenously during catabolic disease states and periods of rapid growth, both characterized by increased arginine utilization. Arginine plays an important role in the intestine, where it is extensively metabolized, and enhances its immune-supportive function and mucosal repair. Cell proliferation is important for the latter process. This study aimed for a better molecular insight in the response to arginine deprivation/supplementation of preconfluent and 5-day-confluent, differentiated Caco-2 intestinal cells. The potential of citrulline to counteract the effects of arginine deprivation was investigated in preconfluent cells. 2-DE combined with MALDI-TOF-MS and the antibody microarray technology were applied. Evidence is provided that arginine deficiency modulates the protein expression profiles of preconfluent Caco-2 cells differently than that of postconfluent differentiated cells. In preconfluent cells, certain proteins changed in direct response to arginine deficiency, whereas other proteins did not, but instead responded during the recovery phase after an arginine/citrulline resupplementation. The protein changes suggest that arginine deprivation decreases cell proliferation and heat shock protein expression, and enhances the cells susceptibility to apoptosis. These processes are critical for proper cell function, and hence a state of arginine deficiency can be detrimental for intestinal cells which proliferate actively in vivo.     

Comparative proteomic analysis of cell lines and scrapings of the human intestinal epithelium

Background

The homologues of human disease genes are expected to contribute to better understanding of physiological and pathogenic processes. We made use of the present availability of vertebrate genomic sequences, and we have conducted the most comprehensive comparative genomic analysis of the prion protein gene PRNP and its homologues, shadow of prion protein gene SPRN and doppel gene PRND, and prion testis-specific gene PRNT so far.

Results

While the SPRN and PRNP homologues are present in all vertebrates, PRND is known in tetrapods, and PRNT is present in primates. PRNT could be viewed as a TE-associated gene. Using human as the base sequence for genomic sequence comparisons (VISTA), we annotated numerous potential cis-elements. The conserved regions in SPRNs harbour the potential Sp1 sites in promoters (mammals, birds), C-rich intron splicing enhancers and PTB intron splicing silencers in introns (mammals, birds), and hsa-miR-34a sites in 3'-UTRs (eutherians). We showed the conserved PRNP upstream regions, which may be potential enhancers or silencers (primates, dog). In the PRNP 3'-UTRs, there are conserved cytoplasmic polyadenylation element sites (mammals, birds). The PRND core promoters include highly conserved CCAAT, CArG and TATA boxes (mammals). We deduced 42 new protein primary structures, and performed the first phylogenetic analysis of all vertebrate prion genes. Using the protein alignment which included 122 sequences, we constructed the neighbour-joining tree which showed four major clusters, including shadoos, shadoo2s and prion protein-likes (cluster 1), fish prion proteins (cluster 2), tetrapode prion proteins (cluster 3) and doppels (cluster 4). We showed that the entire prion protein conformationally plastic region is well conserved between eutherian prion proteins and shadoos (18–25% identity and 28–34% similarity), and there could be a potential structural compatibility between shadoos and the left-handed parallel beta-helical fold.

Conclusion

It is likely that the conserved genomic elements identified in this analysis represent bona fide cis-elements. However, this idea needs to be confirmed by functional assays in transgenic systems.     

Local sex ratio affects the cost of reproduction

1.?Costs and benefits of reproduction are central to life-history theory, and the outcome of reproductive trade-offs may depend greatly on the ecological conditions in which they are estimated. In this study, we propose that costs and benefits of reproduction are modulated by social effects, and consequently that selection on reproductive rates depends on the social environment. 2.?We tested this hypothesis in a great tit Parus major population. Over 3 years, we altered parental reproductive effort via brood size manipulations (small, intermediate, large) and manipulated the local social environment via changes in the local fledgling density (decreased, increased) and the local sex ratio (female-biased, control, male-biased). 3.?We found that male-biased treatment consistently increased the subsequent local breeding densities over the 3-year study period. We also found that parents rearing small broods in these male-biased plots had increased survival rates compared with the other experimental groups. 4.?We conclude that reproductive costs are the product of an interaction between parental phenotypic quality after reproduction and the social environment: raising a small brood had long-lasting effects on some phenotypic traits of the parents and that this increased their survival chances in male-biased environment where habitat quality may have deteriorated (via increased disease/predation risk or intraspecific competition). 5.?Our results provide the first experimental evidence that local sex ratio can affect reproductive costs and thus optimal clutch size.     

Coordination of Polymerization, Chain Termination, and Export in Assembly of the Escherichia coli Lipopolysaccharide O9a Antigen in an ATP-binding Cassette Transporter-dependent Pathway

The Escherichia coli O9a O-polysaccharide (O-PS) is a prototype for O-PS synthesis and export by the ATP-binding cassette transporter-dependent pathway. Comparable systems are widespread in Gram-negative bacteria. The polymannose O9a O-PS is assembled on a polyisoprenoid lipid intermediate by mannosyltransferases located at the cytoplasmic membrane, and the final polysaccharide chain length is determined by the chain terminating dual kinase/methyltransferase, WbdD. The WbdD protein is tethered to the membrane via a C-terminal region containing amphipathic helices located between residues 601 and 669. Here, we establish that the C-terminal domain of WbdD plays an additional pivotal role in assembly of the O-PS by forming a complex with the chain-extending mannosyltransferase, WbdA. Membrane preparations from a ΔwbdD mutant had severely diminished mannosyltransferase activity in vitro, and no significant amounts of the WbdA protein are targeted to the membrane fraction. Expression of a polypeptide comprising the WbdD C-terminal region was sufficient to restore both proper localization of WbdA and mannosyltransferase activity. In contrast to WbdA, the other required mannosyltransferases (WbdBC) are targeted to the membrane independent of WbdD. A bacterial two-hybrid system confirmed the interaction of WbdD and WbdA and identified two regions in the C terminus of WbdD that contributed to the interaction. Therefore, in the O9a assembly export system, the WbdD protein orchestrates the critical localization and coordination of activities involved in O-PS chain extension and termination at the cytoplasmic membrane.Lipopolysaccharide (LPS)³ is a glycolipid unique to the outer membranes of Gram-negative bacteria. LPS has three structural domains in most bacteria (1). Hydrophobic lipid A is a major component of the outer leaflet of the outer membrane. A short core oligosaccharide (OS) serves as a linker between lipid A and a repeat unit polymer termed the O-polysaccharide (O-PS; O-antigen). The structure of lipid A is conserved among Gram-negative bacteria, whereas limited variability is observed among the core OSs of a given species. For example, five closely related core oligosaccharides have been described for Escherichia coli (2). In contrast, the O-PS structures vary extensively within species. O-PS structural variations include differences in the number and type of sugars in the repeat unit and the nature of the glycosidic linkages within and between repeat units. O-PS variations provide the basis for the O-antigen serotyping system, and there are over 180 O-antigen serogroups proposed for E. coli (3, 4).Lipid A-core OS and O-PS are synthesized independently at the cytoplasmic membrane and are subsequently linked together in the periplasm (reviewed in Ref. 1). O-PS assembly is initiated by transfer of a sugar-1-phosphate from a nucleotide sugar precursor to the 55-carbon lipid acceptor, undecaprenol phosphate. In the majority of E. coli serotypes, the initiating reaction is performed by the GlcNAc:Und-P GlcNAc-1-P transferase, WecA (5, 6). WecA is an integral membrane protein and is also essential for initiating synthesis of the enterobacterial common antigen (7). In E. coli, elongation and export of the undecaprenol-PP-linked intermediate proceeds through one of two fundamentally different O-PS assembly pathways. These pathways have been termed Wzy (polymerase)-dependent and ATP-binding cassette (ABC) transporter-dependent biosynthesis, respectively (reviewed in Ref. 1). In Wzy-dependent O-PS biosynthesis, single repeat units are assembled on the undecaprenol-PP-linked intermediate at the cytoplasmic face of the inner membrane. The lipid-linked repeat units are subsequently reoriented to the periplasm where they are assembled into polysaccharide by a process involving Wzy and a chain length regulator, Wzz. In contrast, in the ABC transporter-dependent pathway, the O-PS is elongated on the undecaprenol-PP-linked intermediate in the cytoplasm by sequential glycosyl transfer. Depending on the system, chain extension is terminated by the addition of a nonreducing terminal residue or by interaction with the ABC transporter (8). Full-length O-PS chains are then translocated across the inner membrane by the ABC transporter. The two O-PS assembly pathways converge at a ligation reaction, which transfers the O-PS from undecaprenol-PP to lipid A-core OS at the periplasmic face of the inner membrane. Once assembled, LPS molecules are shuttled to the outer membrane through a process involving the LptABCDE complex (reviewed in Ref. 9).The polymannose O-PS of E. coli O9a provides a model system for ABC transporter-dependent O-PS biosynthesis. The E. coli O9a PS biosynthesis gene cluster (see Fig. 1A) encodes three GDP-mannose-dependent mannosyltransferases (WbdA, WbdB, and WbdC) that assemble the O-PS on undecaprenol-PP-GlcNAc (10). Structural studies identify terminal capping residues in a number of O-PSs synthesized by the ABC transporter-dependent pathway (11). It has been proposed that the addition of a capping residue to the nonreducing end of the undecaprenol-PP-linked PS serves to regulate O-PS chain length by terminating elongation. In the case of the O9a PS, termination involves methylation and phosphorylation. The chain length of the O9a PS is strictly controlled by the activity of WbdD, and O-PS-substituted LPS molecules expressed on the cell surface exhibit a narrow size distribution. The E. coli O9a WbdD protein contains putative kinase and methyltransferase domains, and these activities have been confirmed in biochemical studies (12). In addition to the role in O-PS chain regulation, methyl and/or phosphoryl modification is required for binding of the O9a PS to the nucleotide-binding component (Wzt) of the ABC transporter (13, 14), a crucial initial step in O-PS export. Unmodified O9a PS does not bind to Wzt, and a wbdD mutant accumulates unmodified polysaccharide in the cytoplasm.Open in a separate windowFIGURE 1.Structure and biosynthesis of the E. coli O9a PS and schematic showing WbdD and mutant derivatives. A, the structure of the O9a PS shows the adaptor region, repeat unit, and terminating residues. The nonreducing end of the O-PS is capped by methylation and phosphorylation, but the nature of the linkage between capping residues and the repeat unit is unknown (11, 12). The O9a-PS biosynthesis and export genes are shown together with the functions of the encoded proteins. B, a linear representation of the wild-type WbdD protein from CWG634 is shown in context with the genomic wbdD mutations in CWG635 and CWG900. The methyltransferase (MTase) and kinase domains are shown within WbdD and have been described previously (12). In CWG635, the chromosomal wbdD ORF was disrupted by replacing a 500-bp SmaI restriction fragment with the aacC1 cassette. A potential ribosomal-binding site, initiation codon, and stop codon are shown and together define an ORF encoding amino acids 501–708 of WbdD. In CWG900, the entire wbdD ORF has been removed from the chromosome. C, a schematic of the truncated WbdD polypeptide derivatives encoded by plasmids used in this study. The numbers shown above the polypeptides refer to amino acid positions in the native WbdD protein. Each polypeptide contained either an N-terminal His₆ tag or the T25 fragment of B. pertussis adenylate cyclase (see plasmids in 15, 16). However, the variability of specific assembly proteins among different biosynthetic systems precludes development of a generalized model for a polysaccharide assembly complex. Here we present data revealing the mechanisms that target the O9a mannosyltransferases to the cytoplasmic membrane and identify essential protein-protein interactions within the biosynthesis complex.