Structural Basis for Non-Covalent Interaction Between Ubiquitin and the Ubiquitin Conjugating Enzyme Variant Human MMS2

Modification of proteins by post-translational covalent attachment of a single, or chain, of ubiquitin molecules serves as a signaling mechanism for a number of regulatory functions in eukaryotic cells. For example, proteins tagged with lysine-63 linked polyubiquitin chains are involved in error-free DNA repair. The catalysis of lysine-63 linked polyubiquitin chains involves the sequential activity of three enzymes (E1, E2, and E3) that ultimately transfer a ubiquitin thiolester intermediate to a protein target. The E2 responsible for catalysis of lysine-63 linked polyubiquitination is a protein heterodimer consisting of a canonical E2 known as Ubc13, and an E2-like protein, or ubiquitin conjugating enzyme variant (UEV), known as Mms2. We have determined the solution structure of the complex formed by human Mms2 and ubiquitin using high resolution, solution state nuclear magnetic resonance (NMR) spectroscopy. The structure of the Mms2–Ub complex provides important insights into the molecular basis underlying the catalysis of lysine-63 linked polyubiquitin chains.     

Genetic differentiation and relationships of populations in the Cycas balansae complex (Cycadaceae) and its conservation implications

BACKGROUND AND AIMS: The Cycas balansae complex is arguably a controversial group with regard to species delineation. Some taxonomists recognize a single polymorphic species while others distinguish five narrowly defined ones. The unresolved taxonomy has the potential to bring about significant problems for species conservation. Thus, an investigation to examine the genetic diversity and differentiation in the C. balansae complex was performed to determine the relationship of populations and to test whether the morphologically defined segregations represent genetically distinct units. METHODS: Inter-simple sequence repeat (ISSR) markers were employed to assess the genetic diversity in the C. balansae complex with a sample of 158 individuals from all extant populations in China. KEY RESULTS: ISSR markers revealed low genetic diversity in all populations studied (H(E) and H(O) averaged 0.0639 and 0.0798 at the population level, respectively). Phenetic analysis showed that the C. balansae complex grouped into five clusters closely corresponding to the narrowly defined C. balansae, C. parvula, C. shiwandashanica, C. tanqingii and C. simplicipinna. CONCLUSIONS: ISSR data suggest that the C. balansae complex has evolved into five genetically distinct units. These might be derived from a relatively widespread common ancestor through multiple vicariant events including geographical isolation resulting from the collision of the Indian plate with the Eurasian plate and from Pleistocene glaciations. In conservation, attention should be paid to each genetic unit.     

The SV40 TC-II(kappa B) enhanson binds ubiquitous and cell type specifically inducible nuclear proteins from lymphoid and non-lymphoid cell lines.

We have characterized the complexes resulting from the specific binding in vitro of proteins present in nuclear extracts of several lymphoid and non-lymphoid cell lines to the TC-I and TC-II sequences of the simian virus 40 (SV40) enhancer. No proteins could be detected, binding selectively to the TC-I sequence, but two proteins TC-IIA and TC-IIB were identified interacting specifically with both the TC-II/kappa B enhanson, 5'-GGAAAGTCCCC-3' (important for the activity of the SV40 enhancer in vivo), and with the related H-2Kb enhanson, 5'-TGGGGATTCCCCA-3'. The binding of these two proteins to mutated TC-II enhansons correlates with the effect of these mutations in vivo, suggesting that both proteins may be important for SV40 enhancer activity. The TC-IIA binding activity was present in nuclear extracts of mature lymphoid B cells and was increased in pre-B cell nuclear extracts by lipopolysaccharide (LPS) and cycloheximide treatment. Furthermore, complex formation between the TC-IIA protein and the TC-II enhanson was efficiently competed by the kappa B motif from the kappa chain enhancer, indicating that TC-IIA is the NF-kappa B factor or a closely related protein. However, in contrast to previous reports, a TC-IIA/NF-kappa B-like protein whose properties could not be distinguished from those of the TC-IIA protein present in lymphoid B cells, was found in nuclear extracts of several untreated non-lymphoid cell lines, notably of HeLa cells, but not of undifferentiated F9 embryonal carcinoma (EC) cells [F9(ND)]. The TC-IIA binding activity which was moderately increased in HeLa cell nuclear extracts by 12-O-tetradecanoylphorbol-13-acetate (TPA) and/or cycloheximide treatment could be induced in nuclear extracts of F9(ND) cells by cycloheximide, but not by TPA. Moreover, the TC-IIA binding activity could be induced in cytosolic fractions from F9(ND) cells by treatment with deoxycholate, indicating that these cells contain an inhibitor protein similar to the previously described NF-kappa B inhibitor, I kappa B. The second TC-II enhanson binding protein, TC-IIB, which could be clearly distinguished from the TC-IIA/NF-kappa B-like protein, by a number of differential properties, resembles the previously described KBF1/H2TF1 protein as it binds with a higher affinity to the H-2Kb enhanson than to the TC-II/kappa B enhanson, and its pattern of methylation interference on the H-2Kb and TC-II/kappa B enhansons is identical to that reported for the KBF1/H2TF1 protein.(ABSTRACT TRUNCATED AT 400 WORDS)     

上海崇明东滩堤内次生人工湿地鸟类冬春季生境选择的因子分析

2004年12月—2005年5月,对上海崇明东滩98海堤内200hm2次生人工湿地进行鸟类调查,在冬季统计到鸟类8目15科56种,以游、涉禽为主;在春季统计到鸟类10目19科55种,以涉禽为主。运用多元回归对鸟类种类数、数量、物种多样性、均匀性指数和科属多样性等群落特征以及调查样点内水位、水面积、植被盖度、底栖动物密度、鱼类捕捞和人类干扰等环境因子进行鸟类生境选择分析。回归模型显示冬季鸟类种类数与植被盖度呈显著正相关,鸟类数量、物种多样性、科属多样性等群落特征与水位高低、水面积比例以及鱼类捕捞强度等有关,底栖动物密度影响鸟类均匀度和数量;春季鸟类数量与鱼塘的水面积呈正相关,而种类和数量与水位呈显著负相关,物种多样性和均匀性明显受水位、水面积和植被盖度影响,鸟类科属多样性与底栖动物密度呈显著相关,捕捞状况对春季鸟类群落影响不大。     

崇明东滩春季鸟类群落特征

2003年春季对崇明东滩潮间带不同生境的鸟类群落进行了调查,共记录到鸟类64种,隶属7目15科。崇明东滩潮间带春季鸟类平均密度为14.60只/hm2,鸟类多样性指数2.08、均匀度指数0.49、优势度指数0.22。芦苇带、海三棱草带和盐渍藻类带是东滩潮间带典型的生境,各生境的鸟类种类、密度和多样性差异较大。其中芦苇带25种,平均密度2.56只/hm2;海三棱草带有48种,平均密度15.38只/hm2;盐渍藻类带36种,平均密度21.04只/hm2。3种生境中盐渍藻类带鸟类的生物多样性最高,海三棱草带最低。研究表明,滩涂围垦、人类活动干扰、互花米草的入侵是影响鸟类在东滩栖息的主要因素。     

Vitamin D content in Alaskan Arctic zooplankton,fishes, and marine mammals

We postulated that dietary ingestion of vitamin D may be used by some Alaskan Arctic marine mammal species in addition to, or instead of, cutaneous production to meet nutritional requirements. Zooplankton (n=5) sampled near Kaktovik, Alaska, contained no measurable vitamin D₂ or D₃, but did contain provitamin D (7‐dehydrocholesterol), the cutaneous precursor for previtamin D₃ in mammals. Fillets and livers from five fish species were sampled near Barrow, Alaska, and evaluated for vitamin D₃ content (no vitamin D₂ was detected). Differences in vitamin D₃ content appeared significant (P≤0.10) among fish livers (Kruskal‐Wallis [H test]=8.25, df=4, P=0.08) and among fish fillets (H=7.80, df=4, P=0.01). We also found significant differences in several pairwise comparisons (Mann‐Whitney U‐test) of vitamin D₃ levels in fillets and livers. Blubber from six species of marine mammals had no detectable vitamin D₂. The H test results for blubber vitamin D₃ concentration were highly significant: 28.12, df=5, P<0.001. There were also significant differences in vitamin D₃ content from blubber in pairwise comparisons of primarily invertebrate feeders (bowhead whale (Balaena mysticetus) [mean=4.20 SD±1.10 ng/g], and Pacific walrus (Odobenus rosmarus divergens) [5.43±2.82 ng/g]) vs. primarily piscivorous feeders (ringed seal (Phoca hispida) [746.57±493.00 ng/g] and beluga whale (Delphinapterus leucas) [426.00±174.92 ng/g]) and a semiaquatic terrestrial carnivore (polar bear (Ursus maritimus) [406.17±311.70 ng/g]). The bearded seal (Erignathus barbatus) had intermediate blubber vitamin D₃ concentration (156.83±139.25 ng/g), which may reflect an intermediate‐type feeding strategy or an artifact of the small sample size. Zoo Biol 23:33–43, 2004. © 2004 Wiley‐Liss, Inc.     

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML Database – Xindice

Background  

Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of these data of different formats and structure imposes a great challenge to us. The XML technology presents a promise in handling this task due to its simplicity and flexibility. Nasopharyngeal carcinoma (NPC) is one of the most common cancers in southern China and Southeast Asia, which has marked geographic and racial differences in incidence. Although there are some cancer proteome databases now, there is still no NPC proteome database.     

The mechanism of action of ramoplanin and enduracidin

The lipoglycodepsipeptide antibiotic ramoplanin is proposed to inhibit bacterial cell wall biosynthesis by binding to intermediates along the pathway to mature peptidoglycan, which interferes with further enzymatic processing. Two sequential enzymatic steps can be blocked by ramoplanin, but there is no definitive information about whether one step is inhibited preferentially. Here we use inhibition kinetics and binding assays to assess whether ramoplanin and the related compound enduracidin have an intrinsic preference for one step over the other. Both ramoplanin and enduracidin preferentially inhibit the transglycosylation step of peptidoglycan biosynthesis compared with the MurG step. The basis for stronger inhibition is a greater affinity for the transglycosylase substrate Lipid II over the MurG substrate Lipid I. These results provide compelling evidence that ramoplanin's and enduracidin's primary cellular target is the transglycosylation step of peptidoglycan biosynthesis.     

Polygenic Analysis of Late-Onset Alzheimer’s Disease from Mainland China

Recently, a number of single nucleotide polymorphisms (SNPs) were identified to be associated with late-onset Alzheimer disease (LOAD) through genome-wide association study data. Identification of SNP-SNP interaction played an important role in better understanding genetic basis of LOAD. In this study, fifty-eight SNPs were screened in a cohort of 229 LOAD cases and 318 controls from mainland China, and their interaction was evaluated by a series of analysis methods. Seven risk SNPs and six protective SNPs were identified to be associated with LOAD. Risk SNPs included rs9331888 (CLU), rs6691117 (CR1), rs4938933 (MS4A), rs9349407 (CD2AP), rs1160985 (TOMM40), rs4945261 (GAB2) and rs5984894 (PCDH11X); Protective SNPs consisted of rs744373 (BIN1), rs1562990 (MS4A), rs597668 (EXOC3L2), rs9271192 (HLA-DRB5/DRB1), rs157581 and rs11556505 (TOMM40). Among positive SNPs presented above, we found the interaction between rs4938933 (risk) and rs1562990 (protective) in MS4A weakened their each effect for LOAD; for three significant SNPs in TOMM40, their cumulative interaction induced the two protective SNPs effects lost and made the risk SNP effect aggravate for LOAD. Finally, we found rs6656401-rs3865444 (CR1-CD33) pairs were significantly associated with decreasing LOAD risk, while rs28834970-rs6656401 (PTK2B-CR1), and rs28834970-rs6656401 (PTK2B-CD33) were associated with increasing LOAD risk. In a word, our study indicates that SNP-SNP interaction existed in the same gene or cross different genes, which could weaken or aggravate their initial single effects for LOAD.