Crystal structure of ubiquitin-like small archaeal modifier protein 1 (SAMP1) from Haloferax volcanii

The ubiquitin-like (Ubl) system has been shown to be ubiquitous in all three kingdoms of life following the very recent characterization of ubiquitin-like small archaeal modifier proteins (SAMP1 and 2) from Haloferax volcanii. The ubiquitin (Ub) and Ubl molecules in eukaryotes have been studied extensively and their cellular functions are well established. Biochemical and structural data pertaining to prokaryotic Ubl protein (Pup) continue to be reported. In contrast to eukaryotes and prokaryotes, no structural information on the archaeal Ubl molecule is available. Here we determined the crystal structure of SAMP1 at 1.55 Å resolution and generated a model of SAMP2. These were then compared with other Ubl molecules from eukaryotes as well as prokaryotes. The structure of SAMP1 shows a β-grasp fold of Ub, suggesting that the archaeal Ubl molecule is more closely related to eukaryotic Ub and Ubls than to its prokaryotic counterpart. The current structure identifies the location of critical elements such a single lysine residue (Lys4), C-terminal di-glycine motif, hydrophobic patches near leucine 60, and uniquely inserted α-helical segments (α1 and α3) in SAMP1. Based on the structure of SAMP1, several Ub-like features of SAMPs such as poly-SAMPylation and non-covalent interactions have been proposed, which should provide the basis for further investigations concerning the molecular function of archaeal Ubls and the large super-family of β-grasp fold proteins in the archaeal kingdom.     

Exploring Protein Space: From Hydrolase to Ligase by Substitution

The understanding of how proteins evolve to perform novel functions has long been sought by biologists. In this regard, two homologous bacterial enzymes, PafA and Dop, pose an insightful case study, as both rely on similar mechanistic properties, yet catalyze different reactions. PafA conjugates a small protein tag to target proteins, whereas Dop removes the tag by hydrolysis. Given that both enzymes present a similar fold and high sequence similarity, we sought to identify the differences in the amino acid sequence and folding responsible for each distinct activity. We tackled this question using analysis of sequence–function relationships, and identified a set of uniquely conserved residues in each enzyme. Reciprocal mutagenesis of the hydrolase, Dop, completely abolished the native activity, at the same time yielding a catalytically active ligase. Based on the available Dop and PafA crystal structures, this change of activity required a conformational change of a critical loop at the vicinity of the active site. We identified the conserved positions essential for stabilization of the alternative loop conformation, and tracked alternative mutational pathways that lead to a change in activity. Remarkably, all these pathways were combined in the evolution of PafA and Dop, despite their redundant effect on activity. Overall, we identified the residues and structural elements in PafA and Dop responsible for their activity differences. This analysis delineated, in molecular terms, the changes required for the emergence of a new catalytic function from a preexisting one.     

Inter-sexual differences in Antarctic fur seal pup growth rates: evidence of environmental regulation?

We investigated the variation of Antarctic fur seal (Arctocephalus gazella) pup growth rates in response to sex, breeding season and duration of both maternal foraging trip and attendance bouts. Data were collected during five consecutive rearing seasons at Cape Shirreff, the most important breeding colony in the South Shetland Islands, Antarctica. Our results showed significant interannual and sexual variations in pup growth rates. Male pups grew significantly faster than female pups during 2000, 2001, 2002 and 2004 seasons, whilst during 2003 no difference was found. The interannual variation in pup growth rates was correlated with the interannual fluctuation in maternal foraging trip and attendance bouts. There was a significant effect of pup sex and maternal foraging trip duration on pup growth rates, which varied between years having foraging trip duration a major effect during 2003, when females spent more time at sea and interestingly on that year there were no sexual differences in pup growth rates. The effect of attendance bout on pup growth rates was not significant. Diet analysis showed that Antarctic krill (Euphausia superba) was the most frequent prey item during the study period. Analysis of krill size distribution showed a significant difference in krill length, during 2003, when A. gazella preyed upon the smallest sizes of krill. In this study, sex was the most important factor on pup growth rates, but when prey availability seemed more limited, there are longer foraging trips and shorter attendance bouts the sex factor became less significant.     

Alloparenting in Steller sea lions (<Emphasis Type="Italic">Eumetopias jubatus</Emphasis>): correlations with misdirected care and other observations

Alloparental care is rarely observed in Steller sea lions (Eumetopias jubatus) where maternal care is extended to a single pup for up to 1 year or more. However, we observed 28 allonursing events and one case of adoption at a small breeding rookery in the western Gulf of Alaska between the years 2001 and 2005. Multiparous and primiparous females were observed nursing nonfilial individuals with equal frequency, but primiparous females spent significantly more time nursing nonfilial individuals. Multiparous females allowed allonursing only while sleeping and unaware while most primiparous females were aware that they were allonursing. These results are consistent with the misdirected-care hypothesis suggesting that primiparous (presumably younger) females nurse nonfilial pups due to inexperience, whereas multiparous (presumably older) females are victims of milk stealing during times of inattentiveness. Nonfilial pups were aggressively tossed most often during the pupping season and only by multiparous females, while allonursing events occurred more frequently after the pupping season. Starveling pups were not cared for by any female, but two were attended by a single bull during separate autumn seasons.     

Characterization of maternal motivation in the lactating rat: Contrasts between early and late postpartum responses

We previously assessed the motivational properties of pups relative to those of cocaine in parturient female rats (dams) across the postpartum period and demonstrated that the larger subset of dams in early postpartum (PPD8) preferred the pup-associated chamber, whereas the majority of dams tested in late postpartum (PPD16) preferred the cocaine-associated chamber [Mattson, B.J., Williams, S., Rosenblatt, J.S., Morrell, J.I. 2001. Comparison of two positive reinforcing stimuli: pups and cocaine throughout the postpartum period. Behav. Neurosci., 115, 683-694; Seip, K.M., Morrell, J.I. 2007. Increasing the incentive salience of cocaine challenges preference for pup- over cocaine-associated stimuli during early postpartum: place preference and locomotor analyses in the lactating female rat. Psychopharmacology 194, 309-319]. The present study uses a dual-choice conditioned place preference to ask how the progression of the postpartum period, including natural pup development, influences maternal motivation for pups. Preferences for cued chambers associated with pups that were age-matched to the postpartum stage of the dam in contrast to a stimulus with little incentive salience were higher during the early than the late postpartum, suggesting that the incentive salience of pups diminishes as the postpartum period progresses. Preferences of the early postpartum dams deprived of pups for 15 min, 2, 6, 12 or 22 hrs prior to conditioning and testing did not differ statistically but there was a trend of more pup preference after 22 hr deprivation; pup age was not an important factor in early postpartum. In marked contrast, late postpartum dams only exhibited robust pup-associated place preference when they were conditioned with young (4-7 day-old) pups or after a 22 hr period of deprivation from contemporaneous pups. Together these results suggest that both forces are at work in the mother-pup dyad, changes in the pups as they develop and changes in the physiological and endocrine state of the female as she progresses through the postpartum period.     

Efficient and simple generation of unmarked gene deletions in Mycobacterium smegmatis

Genetic research in molecular laboratories relies heavily on directed mutagenesis and gene deletion techniques. In mycobacteria, however, genetic analysis is often hindered by difficulties in the preparation of deletion mutants. Indeed, in comparison to the allelic exchange systems available for the study of other common model organisms, such as Saccharomyces cerevisiae and Escherichia coli, mycobacterial gene disruption systems suffer from low mutant isolation success rates, mostly due to inefficient homologous recombination and a high degree of non-specific recombination. Here, we present a gene deletion system that combines efficient homologous recombination with advanced screening of mutants. This novel methodology allows for gene disruption in three consecutive steps. The first step relies on the use of phage Che9c recombineering proteins for directed insertion into the chromosome of a linear DNA fragment that encodes GFP and confers hygromycin resistance. In the second step, GFP positive and hygromycin resistant colonies are selected, and in the last step, the gfp-hyg cassette is excised from the chromosome, thus resulting in the formation of an unmarked deletion. We provide a detailed gene deletion methodology and demonstrate the use of this genetic system by deleting the prcSBA operon of Mycobacterium smegmatis.     

In vivo and in vitro phosphorylation of Candida albicans 20S proteasome

In this paper we demonstrate that the Candida albicans 20S proteasome is in vivo phosphorylated and is a good in vitro substrate (S(0.5) 14nM) of homologous protein kinase CK2 (CK2). We identify alpha6/C2, alpha3/C9, and alpha5/Pup2 proteasome subunits as the main in vivo phosphorylated and in vitro CK2-phosphorylatable proteasome components. In vitro phosphorylation by homologous CK2 holoenzyme occurs only in the presence of polylysine, a characteristic that distinguishes the yeast proteasomes from mammalian proteasomes which are phosphorylated by CK2 in the absence of polycations. The major in vivo phosphate acceptor is the alpha3/C9 subunit, being phosphorylated in serine, both in vivo and in vitro. The phosphopeptides generated by endoproteinase Glu-C digestion from in vivo labeled alpha3/C9 subunit, from in vitro phosphorylation by homologous CK2 holoenzyme, and from the recombinant alpha3/C9 subunit phosphorylated by recombinant human CK2-alpha subunit are identical, suggesting that CK2 is likely responsible for in vivo phosphorylation of this subunit. Direct mutational analysis shows that serine 248 is the residue of the alpha3/C9 subunit phosphorylated by CK2. The in vitro stoichiometry of phosphorylation of the alpha6/C2 and alpha3/C9 proteasome subunits by CK2 can be estimated as 0.7-0.8 and 0.4-0.5 mol of phosphate per mole of subunit, respectively. These results are consistent with the relative abundance of the unphosphorylated and phosphorylated isoforms of these subunits present in the purified 20S proteasome preparation. Our demonstration of phosphorylation of C. albicans proteasome suggests that phosphorylation might be a general mechanism of regulation of proteasome activity.     

Pup-蛋白酶体系统的作用机制和生物学功能

Pup-蛋白酶体系统（Pup-proteasome system,PPS）是原核生物的一种翻译后蛋白质修饰降解体系,在去酰胺酶（deamidase of Pup,Dop）和蛋白酶体辅助因子A (proteasome accessory factorA,PafA)两种酶的作用下,原核生物类泛素蛋白（prokaryotic ubiquitin-like protein,Pup）可以标记靶蛋白,并介导靶蛋白经蛋白酶体降解。在分枝杆菌中PPS参与氧化应激、营养缺乏、热激、DNA损伤等多种应激反应,并在金属离子稳态调控、毒素-抗毒素系统（toxin-antitoxin system,TA system）的调节以及抵抗宿主免疫等过程中发挥作用。PPS与结核分枝杆菌（Mycobacterium tuberculosis,Mtb）的持留性和致病性直接相关,因此PPS中的PafA、Dop和蛋白酶体均是抗结核药物开发的新靶点,筛选针对PPS的小分子抑制剂将成为新型抗结核药物研发的一个新途径。此外,Paf A催化的蛋白质Pup化被应用于生物技术的研发,形成了一种新的邻近标记技术——基于Pup化的邻近标记技术...     

广西发现局部白化中蹄蝠幼仔一例

2008年6月,在广西桂林市郊冷水塘村发现一例白化雌性中蹄蝠(Hipposideros larvatus)幼仔,属局部白化现象,白化区域包括背部中线靠右侧的小区域以及尾膜边缘和右足.该中蹄蝠幼仔前臂长49.1mm,体重10.8 g.