Multi-domain, cell-envelope proteinases of lactic acid bacteria

The multi-domain, cell-envelope proteinases encoded by the genes prtB of Lactobacillus delbrueckii subsp. bulgaricus, prtH of Lactobacillus helveticus, prtP of Lactococcus lactis, scpA of Streptococcus pyogenes and csp of Streptococcus agalactiae have been compared using multiple sequence alignment, secondary structure prediction and database homology searching methods. This comparative analysis has led to the prediction of a number of different domains in these cell-envelope proteinases, and their homology, characteristics and putative function are described. These domains include, starting from the N-terminus, a pre-pro-domain for secretion and activation, a serine protease domain (with a smaller inserted domain), two large middle domains A and B of unknown but possibly regulatory function, a helical spacer domain, a hydrophilic cell-wall spacer or attachment domain, and a cell-wall anchor domain. Not all domains are present in each cell-envelope proteinase, suggesting that these multi-domain proteins are the result of gene shuffling and domain swapping during evolution.     

藻类光合作用PSI色素蛋白复合物结构及长波荧光特性

综述了藻类光合作用ＰＳＩ色素蛋白复合物结构及长波荧光特性的研究进展,并同高等植物进行了比较。藻类ＰＳＩ结构和长波荧光的多样性同高等植物ＰＳＩ的同一性形成鲜明对比。认为藻类ＰＳＩ的这种多样性可能具有门类特征。对藻类和高等植物的ＰＳＩ进行比较研究,将有助于了解ＰＳＩ的结构、功能和进化。     

Glycolipid-Enriched Caveolae and Caveolae-Like Domains in the Nervous System

Abstract: Recent years have been characterized by a booming interest in research on caveolae and caveolae-like membrane domains. The interest in this subject grew further, when their involvement in fundamental membrane-associated events, such as signal transmission and lipid/protein sorting, was postulated. Substantial progress has been reached in understanding the biological role of membrane domains in eukaryotic cells. The neuron, however, which perhaps represents one of the greatest challenges to research on membrane traffic and function, has only been partially investigated. The purpose of the present review is to survey this issue in the nervous system. We confine ourselves to the presence of membrane domains in the nervous system and discuss this in the context of three facts: first, glycolipids are peculiarly enriched in both caveolae and caveolae-like domains and are particularly abundant in the nervous system; second, the neuron is characterized by a basic dual polarity, similar in this respect to other polarized cells, where the role of glycolipid-enriched domains for lipid/protein sorting has been better ascertained; and third, neurons evolved from, and are related to, simpler eukaryotic cells, allowing us to find analogies with more investigated nonneuronal cells.     

Critical role for cholesterol in Lyn-mediated tyrosine phosphorylation of FcepsilonRI and their association with detergent-resistant membranes.

Tyrosine phosphorylation of the high affinity immunoglobulin (Ig)E receptor (FcepsilonRI) by the Src family kinase Lyn is the first known biochemical step that occurs during activation of mast cells and basophils after cross-linking of FcepsilonRI by antigen. The hypothesis that specialized regions in the plasma membrane, enriched in sphingolipids and cholesterol, facilitate the coupling of Lyn and FcepsilonRI was tested by investigating functional and structural effects of cholesterol depletion on Lyn/FcepsilonRI interactions. We find that cholesterol depletion with methyl-beta-cyclodextrin substantially reduces stimulated tyrosine phosphorylation of FcepsilonRI and other proteins while enhancing more downstream events that lead to stimulated exocytosis. In parallel to its inhibition of tyrosine phosphorylation, cholesterol depletion disrupts the interactions of aggregated FcepsilonRI and Lyn on intact cells and also disrupts those interactions with detergent-resistant membranes that are isolated by sucrose gradient ultracentrifugation of lysed cells. Importantly, cholesterol repletion restores receptor phosphorylation together with the structural interactions. These results provide strong evidence that membrane structure, maintained by cholesterol, plays a critical role in the initiation of FcepsilonRI signaling.     

Prevalence and species distribution of the low-complexity,amyloid-like,reversible, kinked segment structural motif in amyloid-like fibrils

Membraneless organelles (MLOs) are vital and dynamic reaction centers in cells that compartmentalize the cytoplasm in the absence of a membrane. Multivalent interactions between protein low-complexity domains contribute to MLO organization. Previously, we used computational methods to identify structural motifs termed low-complexity amyloid-like reversible kinked segments (LARKS) that promote phase transition to form hydrogels and that are common in human proteins that participate in MLOs. Here, we searched for LARKS in the proteomes of six model organisms: Homo sapiens, Drosophila melanogaster, Plasmodium falciparum, Saccharomyces cerevisiae, Mycobacterium tuberculosis, and Escherichia coli to gain an understanding of the distribution of LARKS in the proteomes of various species. We found that LARKS are abundant in M. tuberculosis, D. melanogaster, and H. sapiens but not in S. cerevisiae or P. falciparum. LARKS have high glycine content, which enables kinks to form as exemplified by the known LARKS-rich amyloidogenic structures of TDP43, FUS, and hnRNPA2, three proteins that are known to participate in MLOs. These results support the idea of LARKS as an evolved structural motif. Based on these results, we also established the LARKSdb Web server, which permits users to search for LARKS in their protein sequences of interest.     

Association between DNA cleavage during apoptosis and regions of chromatin replication

We have addressed the association between the site of DNA cleavage during apoptosis and DNA replication. DNA double strand breaks were introduced into chromatin containing pulse labeled nascent DNA by the induction of apoptosis or autocleavage of isolated nuclei. The location of these breaks in relation to nascent DNA were revealed by Bal 31 exonuclease digestion at the cut sites. Our data show that Bal31 accessible cut sites are directly linked to regions enriched in nascent DNA. We suggest that these regions coincide with the termini of replication domains, possibly linked by strong DNA-matrix interactions with biophysically defined topological structures of 0.5 - 1.3 Mbp in size. The 50 kbp fragments that are commonly observed as products of apoptosis are also enriched in nascent DNA within internal regions but not at their termini. It is proposed that these fragments contain a subset of replicon DNA that is excised during apoptosis through recognition of their weak attachment to the nuclear matrix within the replication domain.J. Cell. Biochem. 70:604-615, 1998. © 1998 Wiley-Liss, Inc. © 1998 Wiley-Liss, Inc.     

Temporal-spatial distribution,environmental significance and release risks of phosphorus in the sediments of a tropical mountain’s deep drinking water reservoir in southeastern China

In this study, the fractionation and distribution of phosphorus (P) in the core sediments of the Shanmei reservoir were investigated by using the chemical extraction method in directions for the first time in order to understand its bio-availability, adsorption characteristics, potential release and environmental significance. The results of the study showed that P in the sediments mainly consisted of inorganic phosphorus (IP) and that IP mainly consisted of non-apatite phosphorus (NAIP). The horizontal and temporal distributions of the P fractions were different from each other, but the vertical distribution was similar, which indicated a trend of stabilization after falling. The content of total phosphorus (TP), IP, organic phosphorus (OP), NAIP, apatite phosphorus (AP), and bio-available phosphorus (BAP) in the sediments during the three seasons ranged from 193.85 to 1664.05 mg·kg^?1, 126.90 to 1127.70 mg·kg^?1, 43.74 to 669.29 mg·kg^?1, 57.62 to 937.07 mg·kg^?1, 32.58 to 250.71 mg·kg^?1, and 41.06 to 871.82 mg·kg^?1, respectively. NAIP contents in the sediments accounted for more than 50% of TP. Using an analysis from three aspects, the eutrophication risk index (ERI) could be used to assess the potential release of P in the sediments, and there was a high release risk of P in the sediments in the Shanmei reservoir.     

Loss of CpSRP54 function leads to a truncated light-harvesting antenna size in Chlamydomonas reinhardtii

The Chlamydomonas reinhardtii truncated light-harvesting antenna 4 (tla4) DNA transposon mutant has a pale green phenotype, a lower chlorophyll (Chl) per cell and a higher Chl a/b ratio in comparison with the wild type. It required a higher light intensity for the saturation of photosynthesis and displayed a greater per chlorophyll light-saturated rate of oxygen evolution than the wild type. The Chl antenna size of the photosystems in the tla4 mutant was only about 65% of that measured in the wild type. Molecular genetic analysis revealed that a single plasmid DNA insertion disrupted two genes on chromosome 11 of the mutant. A complementation study identified the “chloroplast signal recognition particle 54” gene (CpSRP54), as the lesion causing the tla4 phenotype. Disruption of this gene resulted in partial failure to assemble and, therefore, lower levels of light-harvesting Chl-binding proteins in the C. reinhardtii thylakoids. A comparative in silico 3-D structure-modeling analysis revealed that the M-domain of the CpSRP54 of C. reinhardtii possesses a more extended finger loop structure, due to different amino acid composition, as compared to that of the Arabidopsis CpSRP54. The work demonstrated that CpSRP54 deletion in microalgae can serve to generate tla mutants with a markedly smaller photosystem Chl antenna size, improved solar energy conversion efficiency, and photosynthetic productivity in high-density cultures under bright sunlight conditions.