The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies

Synthetic antibody libraries with restricted chemical diversity were used to explore the intrinsic contributions of four amino acids (Tyr, Ser, Gly and Arg) to the affinity and specificity of antigen recognition. There was no correlation between nonspecific binding and the content of Tyr, Ser or Gly in the antigen-binding site, and in fact, the most specific antibodies were those with the highest Tyr content. In contrast, Arg content was clearly correlated with increased nonspecific binding. We combined Tyr, Ser and Gly to generate highly specific synthetic antibodies with affinities in the subnanomolar range, showing that the high abundance of Tyr, Ser and Gly in natural antibody germ line sequences reflects the intrinsic capacity of these residues to work together to mediate antigen recognition. Despite being a major functional contributor to co-evolved protein-protein interfaces, we find that Arg does not contribute generally to the affinity of naïve antigen-binding sites and is detrimental to specificity. Again, this is consistent with studies of natural antibodies, which have shown that nonspecific, self-reactive antibodies are rich in Arg and other positively charged residues. Our findings suggest that the principles governing naïve molecular recognition differ from those governing co-evolved interactions. Analogous studies can be designed to explore the roles of the other amino acids in molecular recognition. Results of such studies should illuminate the basic principles underlying natural protein-protein interactions and should aid the design of synthetic binding proteins with functions beyond the scope of natural proteins.     

Developmental control of integrin expression regulates Th2 effector homing

Integrin CD18, a component of the LFA-1 complex that also includes CD11a, is essential for Th2, but not Th1, cell homing, but the explanation for this phenomenon remains obscure. In this study, we investigate the mechanism by which Th2 effector responses require the LFA-1 complex. CD11a-deficient T cells showed normal in vitro differentiation and function. However, Th2 cell-dependent allergic lung disease was markedly reduced in CD11a null mice and wild-type mice given LFA-1 inhibitors, whereas control of infection with Leishmania major, a Th1-dependent response, was enhanced. In both disease models, recruitment of IL-4-, but not IFN-gamma-secreting cells to relevant organs was impaired, as was adhesion of Th2 cells in vitro. These diverse findings were explained by the markedly reduced expression of CD29, an alternate homing integrin, on Th2, but not Th1, cells, which precludes Th2 homing in the absence of CD11a. Thus, murine Th1 and Th2 cells use distinct integrins for homing, suggesting novel opportunities for integrin-based therapeutic intervention in diverse human ailments influenced by Th2 cells.     

Diversity and Activity of Cellulose-Decomposing Bacteria,Isolated from a Sandy and a Loamy Soil after Long-Term Manure Application

The community of culturable cellulolytic bacteria was analyzed in two long-term experimental field sites on Albic Luvisol (silty sand) and Haplic Phaeozem (loam), with and without farmyard manure treatment. Against the backdrop of significant differences in soil properties, the bacterial community structure differed clearly between sites and was affected by manure application as analyzed by T-RFLP of 16S rDNA. The population densities of cellulolytic bacteria were significantly increased by manure application in Phaeozem. Cellulose decomposing potentials of 537 isolates were tested on soluble, colloidal, and crystalline cellulose. The results showed some evidence of a greater proportion of isolates with high decomposition activity in Luvisol, but no impact from manure application could be observed in both soils. Restriction analysis and sequencing of 16S rDNA of isolates revealed a rather simple community composition that was dominated by Streptomyces (67%). The composition of the RFLP groups was affected by manure application, which was most evident in Luvisol, whereas an effect of the soil type could not be found. Although abundant RFLP groups were assigned to phylogenetically different bacterial classes (Actinobacteria, Betaproteobacteria, and Gammaproteobacteria), cellulolytic activity could not consistently be differentiated. All in all, cellulolytic capabilities of the isolates were highly variable and did not map to phylogenetic affiliation.     

Role of domestication in shaping <Emphasis Type="Italic">Castanea sativa</Emphasis> genetic variation in Europe

The genetic structure of sweet chestnut (Castanea sativa Mill.) across Europe was assessed using 73 inter-simple sequence repeat markers to screen 1,768 individuals from 68 stands distributed across 29 sites in five European countries (Italy, France, Spain, Greece, and UK). At each site, trees were sampled from three distinct management types (domestication levels): naturalized stands, managed coppice, and grafted fruit orchards. In more than a third of the orchards, nonlocal genetic material (grafted clones) were evident, showing (as predicted) large differences from the other two domestication levels for most of the within-population genetic diversity parameters estimated. Randomly generated linkage disequilibrium analysis revealed weak though significant differences in two-locus allelic correlations between naturalized stands and coppice, suggesting that long-term management techniques may influence the genetic makeup of the populations. Multivariate analysis revealed the existence of five distinct gene pools across the study area; three were located in Greece, one on the northwestern coast of the Iberian peninsula and a large gene pool covering the rest of the Mediterranean basin. The implications of the results are discussed in relation to developing conservation strategies for chestnut genetic resources in Europe.     

Cell Surface Sialylation and Fucosylation Are Regulated by L1 via Phospholipase Cγ and Cooperate to Modulate Neurite Outgrowth,Cell Survival and Migration

Background

Cell surface glycosylation patterns are markers of cell type and status. However, the mechanisms regulating surface glycosylation patterns remain unknown.

Methodology/Principal Findings

Using a panel of carbohydrate surface markers, we have shown that cell surface sialylation and fucosylation were downregulated in L1^−/y neurons versus L1^+/y neurons. Consistently, mRNA levels of sialyltransferase ST6Gal1, and fucosyltransferase FUT9 were significantly reduced in L1^−/y neurons. Moreover, treatment of L1^+/y neurons with L1 antibodies, triggering signal transduction downstream of L1, led to an increase in cell surface sialylation and fucosylation compared to rat IgG-treated cells. ShRNAs for both ST6Gal1 and FUT9 blocked L1 antibody-mediated enhancement of neurite outgrowth, cell survival and migration. A phospholipase Cγ (PLCγ) inhibitor and shRNA, as well as an Erk inhibitor, reduced ST6Gal1 and FUT9 mRNA levels and inhibited effects of L1 on neurite outgrowth and cell survival.

Conclusions

Neuronal surface sialylation and fucosylation are regulated via PLCγ by L1, modulating neurite outgrowth, cell survival and migration.     

Ebola virus matrix protein VP40 uses the COPII transport system for its intracellular transport

The Ebola virus matrix protein VP40 plays an important role in virion formation and viral egress from cells. However, the host cell proteins and mechanisms responsible for intracellular transport of VP40 prior to its contribution to virion formation remain to be elucidated. Therefore we used coimmunoprecipitation and mass spectrometric analyses to identify host proteins interacting with VP40. We found that Sec24C, a component of the host COPII vesicular transport system, interacts specifically with VP40 via VP40 amino acids 303 to 307. Coimmunoprecipitation and dominant-negative mutant studies indicated that the COPII transport system plays a critical role in VP40 intracellular transport to the plasma membrane. Marburg virus VP40 was also shown to use the COPII transport system for intracellular transport. These findings identify a conserved intersection between a host pathway and filovirus replication, an intersection that can be targeted in the development of new antiviral drugs.     

CCR5Δ32 Genotypes in a German HIV-1 Seroconverter Cohort and Report of HIV-1 Infection in a CCR5Δ32 Homozygous Individual

Background

Homozygosity (Δ32/Δ32) for the 32 bp deletion in the chemokine receptor 5 (CCR5) gene is associated with strong resistance against HIV infection. Heterozygosity is associated with protection of HIV-1 disease progression.

Methodology/Principal Findings

We genotyped a population of 737 HIV-positive adults and 463 healthy controls for the CCR5Δ32 deletion and found heterozygous frequencies of 16.2% (HIV-negative) and 17.5% (HIV-positive) among Caucasian individuals. Analysis of CCR5Δ32 influence on disease progression showed notably lower viral setpoints and a longer time to a CD4 count of <200 µl⁻¹ in seroconverters heterozygous for the deletion. Furthermore, we identified one HIV-positive man homozygous for the Δ32 deletion.

Conclusions/Significance

The protective effect of CCR5 Δ32 heterozygosity is confimed in a large cohort of German seroconverters. The HIV-infected CCR5 Δ32 homozygous individual, however, displays extremely rapid disease progression. This is the 12th case of HIV-infection in this genotype described worldwide.     

Hepatic overexpression of hormone-sensitive lipase and adipose triglyceride lipase promotes fatty acid oxidation, stimulates direct release of free fatty acids, and ameliorates steatosis

Hepatic steatosis is often associated with insulin resistance and obesity and can lead to steatohepatitis and cirrhosis. In this study, we have demonstrated that hormone-sensitive lipase (HSL) and adipose triglyceride lipase (ATGL), two enzymes critical for lipolysis in adipose tissues, also contribute to lipolysis in the liver and can mobilize hepatic triglycerides in vivo and in vitro. Adenoviral overexpression of HSL and/or ATGL reduced liver triglycerides by 40-60% in both ob/ob mice and mice with high fat diet-induced obesity. However, these enzymes did not affect fasting plasma triglyceride and free fatty acid levels or triglyceride and apolipoprotein B secretion rates. Plasma 3-beta-hydroxybutyrate levels were increased 3-5 days after infection in both HSL- and ATGL-overexpressing male mice, suggesting an increase in beta-oxidation. Expression of genes involved in fatty acid transport and synthesis, lipid storage, and mitochondrial bioenergetics was unchanged. Mechanistic studies in oleate-supplemented McA-RH7777 cells with adenoviral overexpression of HSL or ATGL showed that reduced cellular triglycerides could be attributed to increases in beta-oxidation as well as direct release of free fatty acids into the medium. In summary, hepatic overexpression of HSL or ATGL can promote fatty acid oxidation, stimulate direct release of free fatty acid, and ameliorate hepatic steatosis. This study suggests a direct functional role for both HSL and ATGL in hepatic lipid homeostasis and identifies these enzymes as potential therapeutic targets for ameliorating hepatic steatosis associated with insulin resistance and obesity.