The hypervariable HIV-1 capsid protein residues comprise HLA-driven CD8+ T-cell escape mutations and covarying HLA-independent polymorphisms

One proposed HIV vaccine strategy is to induce Gag-specific CD8(+) T-cell responses that can corner the virus, through fitness cost of viral escape and unavailability of compensatory mutations. We show here that the most variable capsid residues principally comprise escape mutants driven by protective alleles HLA-B*57, -5801, and -8101 and covarying HLA-independent polymorphisms that arise in conjunction with these escape mutations. These covarying polymorphisms are potentially compensatory and are concentrated around three tropism-determining loops of p24, suggesting structural interdependencies. Our results demonstrate complex patterns of adaptation of HIV under immune selection pressure, the understanding of which should aid vaccine design.     

Tandem translation generates a chaperone for the Salmonella type III secretion system protein SsaQ

Type III secretion systems (T3SSs) of bacterial pathogens involve the assembly of a surface-localized needle complex, through which translocon proteins are secreted to form a pore in the eukaryotic cell membrane. This enables the transfer of effector proteins from the bacterial cytoplasm to the host cell. A structure known as the C-ring is thought to have a crucial role in secretion by acting as a cytoplasmic sorting platform at the base of the T3SS. Here, we studied SsaQ, an FliN-like putative C-ring protein of the Salmonella pathogenicity island 2 (SPI-2)-encoded T3SS. ssaQ produces two proteins by tandem translation: a long form (SsaQ(L)) composed of 322 amino acids and a shorter protein (SsaQ(S)) comprising the C-terminal 106 residues of SsaQ(L). SsaQ(L) is essential for SPI-2 T3SS function. Loss of SsaQ(S) impairs the function of the T3SS both ex vivo and in vivo. SsaQ(S) binds to its corresponding region within SsaQ(L) and stabilizes the larger protein. Therefore, SsaQ(L) function is optimized by a novel chaperone-like protein, produced by tandem translation from its own mRNA species.     

Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins

E. coli YhbY belongs to a conserved family of hypothetical proteins represented in eubacteria, archaea, and plants (Pfam code UPF0044). Three maize proteins harboring UPF0044-like domains are required for chloroplast group II intron splicing, and bioinformatic data suggest a role for prokaryotic UPF0044 members in translation. The crystal structure of YhbY has been determined. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Modeling studies indicate that the same surface is highly basic in all members of UPF0044, suggesting a conserved RNA binding surface. Taken together, the evidence suggests that members of UPF0044 constitute a previously unrecognized class of RNA binding domain.     

The hydrophobin EAS is largely unstructured in solution and functions by forming amyloid-like structures

BACKGROUND: Fungal hydrophobin proteins have the remarkable ability to self-assemble into polymeric, amphipathic monolayers on the surface of aerial structures such as spores and fruiting bodies. These monolayers are extremely resistant to degradation and as such offer the possibility of a range of biotechnological applications involving the reversal of surface polarity. The molecular details underlying the formation of these monolayers, however, have been elusive. We have studied EAS, the hydrophobin from the ascomycete Neurospora crassa, in an effort to understand the structural aspects of hydrophobin polymerization. RESULTS: We have purified both wild-type and uniformly 15N-labeled EAS from N. crassa conidia, and used a range of physical methods including multidimensional NMR spectroscopy to provide the first high resolution structural information on a member of the hydrophobin family. We have found that EAS is monomeric but mostly unstructured in solution, except for a small region of antiparallel beta sheet that is probably stabilized by four intramolecular disulfide bonds. Polymerised EAS appears to contain substantially higher amounts of beta sheet structure, and shares many properties with amyloid fibers, including a characteristic gold-green birefringence under polarized light in the presence of the dye Congo Red. CONCLUSIONS: EAS joins an increasing number of proteins that undergo a disorder-->order transition in carrying out their normal function. This report is one of the few examples where an amyloid-like state represents the wild-type functional form. Thus the mechanism of amyloid formation, now thought to be a general property of polypeptide chains, has actually been applied in nature to form these remarkable structures.     

Differential proteomics of dehydration and rehydration in bryophytes: evidence towards a common desiccation tolerance mechanism

All bryophytes evolved desiccation tolerance (DT) mechanisms during the invasion of terrestrial habitats by early land plants. Are these DT mechanisms still present in bryophytes that colonize aquatic habitats? The aquatic bryophyte Fontinalis antipyretica Hedw. was subjected to two drying regimes and alterations in protein profiles and sucrose accumulation during dehydration and rehydration were investigated. Results show that during fast dehydration, there is very little variation in protein profiles, and upon rehydration proteins are leaked. On the other hand, slow dehydration induces changes in both dehydration and rehydration protein profiles, being similar to the protein profiles displayed by the terrestrial bryophytes Physcomitrella patens (Hedw.) Bruch and Schimp. and, to what is comparable with Syntrichia ruralis (Hedw.) F. Weber and D. Mohr. During dehydration there was a reduction in proteins associated with photosynthesis and the cytoskeleton, and an associated accumulation of proteins involved in sugar metabolism and plant defence mechanisms. Upon rehydration, protein accumulation patterns return to control values for both photosynthesis and cytoskeleton whereas proteins associated with sugar metabolism and defence proteins remain high. The current results suggest that bryophytes from different ecological adaptations may share common DT mechanisms.     

Biochemical and physiological mechanisms underlying effects of Cucumber mosaic virus on host‐plant traits that mediate transmission by aphid vectors

The transmission of insect‐vectored diseases entails complex interactions among pathogens, hosts and vectors. Chemistry plays a key role in these interactions; yet, little work has addressed the chemical ecology of insect‐vectored diseases, especially in plant pathosystems. Recently, we documented effects of Cucumber mosaic virus (CMV) on the phenotype of its host (Cucurbita pepo) that influence plant‐aphid interactions and appear conducive to the non‐persistent transmission of this virus. CMV reduces host‐plant quality for aphids, causing rapid vector dispersal. Nevertheless, aphids are attracted to the elevated volatile emissions of CMV‐infected plants. Here, we show that CMV infection (1) disrupts levels of carbohydrates and amino acids in leaf tissue (where aphids initially probe plants and acquire virions) and in the phloem (where long‐term feeding occurs) in ways that reduce plant quality for aphids; (2) causes constitutive up‐regulation of salicylic acid; (3) alters herbivore‐induced jasmonic acid biosynthesis as well as the sensitivity of downstream defences to jasmonic acid; and (4) elevates ethylene emissions and free fatty acid precursors of volatiles. These findings are consistent with previously documented patterns of aphid performance and behaviour and provide a foundation for further exploration of the genetic mechanisms responsible for these effects and the evolutionary processes that shape them.     

Oxygen-induced plasticity in tracheal morphology and discontinuous gas exchange cycles in cockroaches Nauphoeta cinerea

The function and mechanism underlying discontinuous gas exchange in terrestrial arthropods continues to be debated. Three adaptive hypotheses have been proposed to explain the evolutionary origin or maintenance of discontinuous gas exchange cycles (DGCs), which may have evolved to reduce respiratory water loss, facilitate gas exchange in high CO₂ and low O₂ micro-environments, or to ameliorate potential damage as a result of oversupply of O₂. None of these hypotheses have unequivocal support, and several non-adaptive hypotheses have also been proposed. In the present study, we reared cockroaches Nauphoeta cinerea in selected levels of O₂ throughout development, and examined how this affected growth rate, tracheal morphology and patterns of gas exchange. O₂ level in the rearing environment caused significant changes in tracheal morphology and the exhibition of DGCs, but the direction of these effects was inconsistent with all three adaptive hypotheses: water loss was not associated with DGC length, cockroaches grew fastest in hyperoxia, and DGCs exhibited by cockroaches reared in normoxia were shorter than those exhibited by cockroaches reared in hypoxia or hyperoxia.     

Late glacial and Holocene environmental changes inferred from sediments in Lake Myklevatnet,Nordfjord, western Norway

Late Glacial and Holocene environmental changes were reconstructed using physical, chemical and biological proxies in Lake Myklevatnet, Allmenningen, (5º13′17″E, 61º55′13″N) located at the northern side of Nordfjorden at the coast of western Norway. Myklevatnet (123 m a.s.l.) lies above the Late Glacial marine limit and contains sediments back to approximately 14,300 years before a.d. 2000 (b2k). Because the lake is located ~48 km beyond the margin of the Younger Dryas (YD) fjord and valley glaciers further inland, and did not receive glacier meltwater from local glaciers during the YD, the lake record provides supplementary information to Lake Kråkenes that received glacial meltwater from a local YD glacier. Lake Myklevatnet has a small catchment and is sensitive to Late Glacial and Holocene climate and environmental changes in the coastal region of western Norway. The age-depth relationship was inferred from a radiocarbon- and tephra-based smoothing-spline model with correlated ages from oxygen isotope maxima and minima in the Late Glacial sequence of the NGRIP ice core (in years b2k) to refine the basal chronology in the Myklevatnet record. The results indicate a two-step YD warming, colder early YD temperatures than in the later part of the YD, and considerably more climate and environmental variability during the late Holocene in western Norway than recorded previously in the oxygen isotopes from Greenland ice cores. The Myklevatnet record is also compared with other Late Glacial and Holocene terrestrial and marine proxy reconstructions in the North Atlantic realm.     

Redox‐dependent lipoylation of mitochondrial proteins in Plasmodium falciparum

Lipoate scavenging from the human host is essential for malaria parasite survival. Scavenged lipoate is covalently attached to three parasite proteins: the H‐protein and the E2 subunits of branched chain amino acid dehydrogenase (BCDH) and α‐ketoglutarate dehydrogenase (KDH). We show mitochondrial localization for the E2 subunits of BCDH and KDH, similar to previously localized H‐protein, demonstrating that all three lipoylated proteins reside in the parasite mitochondrion. The lipoate ligase 1, LipL1, has been shown to reside in the mitochondrion and it catalyses the lipoylation of the H‐protein; however, we show that LipL1 alone cannot lipoylate BCDH or KDH. A second mitochondrial protein with homology to lipoate ligases, LipL2, does not show ligase activity and is not capable of lipoylating any of the mitochondrial substrates. Instead, BCDH and KDH are lipoylated through a novel mechanism requiring both LipL1 and LipL2. This mechanism is sensitive to redox conditions where BCDH and KDH are exclusively lipoylated under strong reducing conditions in contrast to the H‐protein which is preferentially lipoylated under less reducing conditions. Thus, malaria parasites contain two different routes of mitochondrial lipoylation, an arrangement that has not been described for any other organism.     

Impact of the functional status of saeRS on in vivo phenotypes of Staphylococcus aureus sarA mutants

We investigated the in vivo relevance of the impact of sarA and saeRS on protease production using derivatives of the USA300 strain LAC. The results confirmed that mutation of saeRS or sarA reduces virulence in a bacteremia model to a comparable degree. However, while eliminating protease production restored virulence in the sarA mutant, it had little impact in the saeRS mutant. Additionally, constitutive activation of saeRS (saeRS^C) enhanced the virulence of LAC and largely restored virulence in the isogenic sarA mutant. Based on these results, together with our analysis of the representative virulence factors alpha toxin, protein A (Spa), and extracellular nucleases, we propose a model in which the attenuation of saeRS mutants is defined primarily by decreased production of such factors, while constitutive activation of saeRS increases virulence, and reverses the attenuation of sarA mutants, because it results in both increased production and decreased protease‐mediated degradation of these same factors. This regulatory balance was also apparent in a murine model of catheter‐associated infection, with the results suggesting that the impact of saeRS on nuclease production plays an important role during the early stages of these infections that is partially offset by increased protease production in sarA mutants.