Nicking by transesterification: the reaction catalysed by a relaxase

DNA relaxases play an essential role in the initiation and termination of conjugative DNA transfer. Purification and characterization of relaxases from several plasmids has revealed the reaction mechanism: relaxases nick duplex DNA in a site- and strand-specific manner by catalysing a transesterification. The product of the reaction is a nicked double-stranded DNA molecule with a sequestered 3'-OH and the relaxase covalently bound to the 5' end of the cleaved strand via a phosphotyrosyl linkage. The relaxase-catalysed transesterification is isoenergetic and reversible; a second transesterification ligates the nicked DNA. However, the covalent nucleoprotein complex is relatively long-lived, a property that is likely to be essential for its role as an intermediate in the process of conjugative DNA transfer. Subsequent unwinding of the nicked DNA intermediate is required to produce the single strand of DNA transferred to the recipient cell. This reaction is catalysed by a DNA helicase, an activity intrinsic to the relaxase protein in some, but not all, plasmid systems. The first relaxase-catalysed transesterification is essential for initiation of conjugative strand transfer, whereas the second is presumably required for termination of the process. The relaxase, in conjunction with several auxiliary proteins, forms the relaxation complex or relaxosome first described nearly 30 years ago as being associated with conjugative and mobilizable plasmids.     

Identification of C-terminal extensions that protect proteins from intracellular proteolysis

Revertants of defective mutants in the Arc repressor of bacteriophage P22 were isolated. Five of the six reverting mutations were frameshifts near the end of the coding sequence which resulted in proteins with C-terminal extensions. Each of the reverting mutations prolong the half-lives in vivo of the proteins in which they reside, yet they do not alter the thermodynamic stability, structure, oligomeric form, or DNA-binding properties of these proteins. Fusion of one of these tails to the C-terminal end of a mutant form of the N-terminal domain of lambda repressor also prevented proteolysis of this protein. These C-terminal sequences may prevent degradation by blocking the recognition of unstable proteins by the proteolytic machinery in the cell.     

Analysis of the structural specificity of the lactose permease toward sugars

The sugar specificity properties of the lactose permease were investigated. Free galactose was shown to competitively inhibit the lactose permease yielding a Ki value of 7.4 mM. This value was severalfold higher than the observed Km for lactose (1.3 mM). A variety of other monosaccharides also showed significant inhibition of lactose transport. With regard to -OH groups along the galactose ring it appears that the relative importance is OH-3 greater than OH-4 greater than OH-6 greater than OH-2 greater than OH-1. In general, galactosides with alpha-linkages exhibited significantly higher affinities compared with their beta-linked counterparts. An optimal size for the aglycone portion of the galactoside was reached with aglycones containing hexose residues or a benzene ring. The preferred size of the aglycone appears to be hexose, benzene ring greater than methyl group greater than no aglycone much greater than disaccharide greater than trisaccharide. However, neither the specific structure of the aglycone nor its relative hydrophobicity appeared to be important factors in permease recognition. For example, the hydrophobic beta-nitrophenyl-galactosides had lower affinities compared with lactose (a beta-galactoside), whereas the alpha-nitrophenylgalactosides generally had higher affinities compared with melibiose (an alpha-galactoside). In addition, no consistent preference was seen when considering the location of the nitro group on the benzene ring. From this work, a model is presented which depicts the binding of galactosides to the lactose permease.     

An imported thylakoid protein accumulates in the stroma when insertion into thylakoids is inhibited

The light-harvesting chlorophyll a/b protein (LHCP) is synthesized in the cytosol as a precursor (pLHCP) that is imported into chloroplasts and assembled into thylakoid membranes. Under appropriate conditions, either pLHCP or LHCP will integrate into isolated thylakoids. We have identified two situations that inhibit integration in this assay. Ionophores and uncouplers inhibited integration up to 70%. Carboxyl-terminal truncations of pLHCP also interfered with integration. A 22-residue truncation reduced integration to about 25% of control, whereas a 93 residue truncation completely abolished it. When pLHCP was imported into chloroplasts in the presence of uncouplers or when truncated forms of pLHCP were used, significant amounts of the imported proteins failed to insert into thylakoids and instead accumulated in the aqueous stroma. Accumulation of stromal LHCP occurred at uncoupler concentrations required to dissipate the trans-thylakoid proton electrochemical gradient and was enhanced at reduced levels of ATP. The latter effect may be a secondary consequence of a reduction in ATP-dependent degradation within the stroma. These results indicate that the stroma is an intermediate location in the LHCP assembly pathway and provide the first evidence for a soluble intermediate during biogenesis of a chloroplast membrane protein.     

Shifting abundances of communities associated with nitrogen cycling in soils promoted by sugarcane harvest systems

Sugarcane cultivation supports Brazil as one of the largest world sugar and ethanol producer. In order to understand the impact of changing sugarcane harvest from manual to mechanized harvest, we studied the effect of machinery traffic on soil and consequently soil compaction upon soil microbial communities involved in nitrogen cycling. The impact of sugarcane harvest was dependent on soil depth and texture. At deeper soil layers, mechanized harvesting increases the abundance of nitrogen fixers and denitrifying communities (specifically nosZ clade I and II) while manual harvesting increases the abundance of ammonia oxidizers (specifically AOA) and increases denitrifying communities (nosZ clade I and II) on top and at intermediate depth. The effect of change on the harvest system is more evident on sandy soil than on clay soil, where soil indicators of compaction (bulk density and penetration resistance) were negatively correlated with soil microorganisms associated with the nitrogen cycle. Our results point to connections between soil compaction and N transformations in sugarcane fields, besides naming biological variables to be used as proxies for alterations in soil structure.     

Ecological and social determinants of association and proximity patterns in the fission–fusion society of spider monkeys (Ateles geoffroyi)

Some social species exhibit high levels of fission–fusion dynamics (FFD) that improve foraging efficiency. In this study, we shed light on the way that FFD allows animal groups to cope with fluctuations in fruit availability. We explore the relative contribution of fruit availability and social factors like sex in determining association and proximity patterns in spider monkeys. We tested the influence of fruit availability and social factors on the association and proximity patterns using three-year data from a group of spider monkeys in the Yucatan Peninsula of Mexico. We identified subgroup members and estimated their Interindividual distances through instantaneous scan sampling. We evaluated fruit availability by monitoring the phenology of the 10 most important food tree species for spider monkeys in the study site. Social network analyses allowed us to evaluate association and proximity patterns in subgroups. We showed that association patterns vary between seasons, respond to changes in fruit availability, and are influenced by the sex of individuals, likely reflecting biological and behavioral differences between sexes and the interplay between ecological and social factors. In contrast, proximity patterns were minimally affected by changes in fruit availability, suggesting that social factors are more important than food availability in determining cohesion within subgroups.     

Profiles of Alexandrium catenella cysts in Puget Sound sediments and the relationship to paralytic shellfish poisoning events

The magnitude of paralytic shellfish poisoning (PSP) toxins in shellfish and the geographical scope of shellfish closures in Puget Sound have increased in recent decades. PSP, monitored by the Washington Department of Health, has spread from Sequim Bay in the 1950s into central Puget Sound in the 1970s and throughout Puget Sound by the 1990s. Alexandrium catenella, the species responsible for PSP toxins, produces a benthic resting cyst that, upon germinating, can seed blooms. This study examined whether there is a relationship between profiles of cysts in the sediment and temporal variation in PSP in shellfish and if the history of the toxin's southward expansion through Puget Sound can be seen in the cyst record. To address this question, sediment cores were collected from three Puget Sound basins, Sequim Bay, Penn Cove, and Carr Inlet, and cyst profiles were determined. Activities of ²¹⁰Pb were fitted to a depth-dependent diagenetic model to date the sediment cores and determine mixing and sediment-accumulation rates. In order to compare historical variation in PSP with cyst profiles that have been altered by bioturbation, a depth and time-dependent diagenetic model was then used to predict vertical profiles of cysts that would occur under the assumption that cyst deposition rates are proportional to PSP concentration in shellfish measured over several decades at each site. The cyst profiles predicted by the model were compared to measured cyst profiles. These comparisons suggested that Alexandrium blooms and resulting PSP concentration in shellfish are more closely linked to cyst germination and deposition at some stations than at others. Sequim Bay had relatively large numbers of cysts and it is likely that the persistent toxicity here is the result of recurrent seeding from the cyst bed. Penn Cove and Carr Inlet had few cysts despite occasional blooms, suggesting that blooms are transported into those areas, perhaps from other sites of cyst germination. Sequim Bay and Penn Cove had cysts from top to bottom of the cores so it was not possible to determine the date when cysts were first introduced into these bays, but it is likely that A. catenella has been in Penn Cove since at least 1955 or for about two decades before the WDOH PSP toxicity data would indicate. The cyst profile in Carr Inlet suggested a first appearance date of 1985 that is consistent with the first appearance of PSP in shellfish in 1988.