Collagen gene construction and evolution

Summary Collagen genes appear to have been assembled by the tandem repetition of homologous primary (9 base pair), secondary (54 base pair), and tertiary (702 base pair) modules. In vertebrate interstitial collagen genes many of the secondary modules are separated by introns, but in invertebrate collagen genes the non-coding sequences lie near the ends of supposed tertiary modules and are therefore about 702 (54×13) base pairs apart. The genes for vertebrate interstitial collagens (types I–III) seem to have been constructed by the tandem repetition of five tertiary modules, three of which were subsequently shortened by internal deletions. This shortening of the gene resulted in the non-integral relationship between the period of the fibrils and the length of the molecules of vertebrate collagens, and was therefore responsible for the mechanical properties of the completed product. Comparisons of the amino acid sequences of various collagens indicate that the main types of collagen evolved about 800–900 million years ago, a date that agrees well with the fossil record of primitive Metazoa.     

Stem cells: Insights into the secretome

Stem cells have been considered as possible therapeutic vehicles for different health related problems such as cardiovascular and neurodegenerative diseases and cancer. Secreted molecules are key mediators in cell–cell interactions and influence the cross talk with the surrounding tissues. There is strong evidence supporting that crucial cellular functions such as proliferation, differentiation, communication and migration are strictly regulated from the cell secretome. The investigation of stem cell secretome is accumulating continuously increasing interest given the potential use of these cells in regenerative medicine. The scope of the review is to report the main findings from the investigation of stem cell secretome by the use of contemporary proteomics methods and discuss the current status of research in the field. This article is part of a Special Issue entitled: An Updated Secretome.     

Atypical Cohesin-Dockerin Complex Responsible for Cell Surface Attachment of Cellulosomal Components: BINDING FIDELITY,PROMISCUITY, AND STRUCTURAL BUTTRESSES*

The rumen bacterium Ruminococcus flavefaciens produces a highly organized multienzyme cellulosome complex that plays a key role in the degradation of plant cell wall polysaccharides, notably cellulose. The R. flavefaciens cellulosomal system is anchored to the bacterial cell wall through a relatively small ScaE scaffoldin subunit, which bears a single type IIIe cohesin responsible for the attachment of two major dockerin-containing scaffoldin proteins, ScaB and the cellulose-binding protein CttA. Although ScaB recruits the catalytic machinery onto the complex, CttA mediates attachment of the bacterial substrate via its two putative carbohydrate-binding modules. In an effort to understand the structural basis for assembly and cell surface attachment of the cellulosome in R. flavefaciens, we determined the crystal structure of the high affinity complex (K_d = 20.83 nm) between the cohesin module of ScaE (CohE) and its cognate X-dockerin (XDoc) modular dyad from CttA at 1.97-Å resolution. The structure reveals an atypical calcium-binding loop containing a 13-residue insert. The results further pinpoint two charged specificity-related residues on the surface of the cohesin module that are responsible for specific versus promiscuous cross-strain binding of the dockerin module. In addition, a combined functional role for the three enigmatic dockerin inserts was established whereby these extraneous segments serve as structural buttresses that reinforce the stalklike conformation of the X-module, thus segregating its tethered complement of cellulosomal components from the cell surface. The novel structure of the RfCohE-XDoc complex sheds light on divergent dockerin structure and function and provides insight into the specificity features of the type IIIe cohesin-dockerin interaction.     

Interspecific networks in ground beetle (Coleoptera: Carabidae) assemblages

Although changes to interspecific relationships can significantly alter the composition of insect assemblages, they are often ignored when assessing impacts of environmental change. Long-term ground beetle data were used in this study to analyse ecological networks from three habitats at two sites in Scotland. A Bayesian Network inference algorithm was used to reveal interspecific relationships. The significance and strength of relationships between species (nodes) were estimated along with other network properties. Links were identified as positive relationships if co-occurrences of beetles correlated positively, and as negatives relationships if there was a negative correlation between the occurrences of the species. Most of the species had few links and only 10% of the nodes were connected with several links. Calathus fuscipes, a common carabid in the samples, was the most connected, with nine links to other species. More interspecific relationships were found to be positive than negative, with 48 and 23 links, respectively. The modular structure of the network was assessed and eight separate sub-networks were found. Habitat preferences of the species were clearly represented in the structure of the sets of those five sub-networks containing more than one species and were in line with the findings of the indicator species analysis. In our study, we showed that generated Bayesian networks can model interspecific relationships between carabid species. Due to the relative ease of the collection of field data and the high information content of the results, this method could be incorporated into everyday ecological analysis.     

Characterization of the cellulolytic complex (cellulosome) of Clostridium acetobutylicum

A large cellulosomal gene cluster was identified in the recently sequenced genome of Clostridium acetobutylicum ATCC 824. Sequence analysis revealed that this cluster contains the genes for the scaffolding protein CipA, the processive endocellulase Cel48A, several endoglucanases of families 5 and 9, the mannanase Man5G, and a hydrophobic protein, OrfXp. Surprisingly, genetic organization of this large cluster is very similar to that of Clostridium cellulolyticum, the model of mesophilic clostridial cellulosomes. As C. acetobutylicum is unable to grow on cellulosic substrates, the existence of a cellulosomal gene cluster in the genome raises questions about its expression, function and evolution. Biochemical evidence for the expression of a cellulosomal protein complex was investigated. The results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis, N-terminal sequencing and Western blotting with antibodies against specific components of the C. cellulolyticum cellulosome suggest that at least four major cellulosomal proteins are present. In addition, despite the fact that no cellulolytic activities were detected, we report here the evidence for the production of a high molecular mass cellulosomal complex in C. acetobutylicum.     

C6-Like and C3-Like Molecules from the Cephalochordate, Amphioxus, Suggest a Cytolytic Complement System in Invertebrates

The mammalian immune system has cytotoxic mechanisms, both cellular and humoral, that destroy the membrane integrity of target cells. The main effector molecules of these cytolytic mechanisms—perforin, used by killer lymphocytes, and the membrane attack complex (MAC) components of the complement system—share a unique module called the MAC/perforin module. Until now, both immunological cytotoxicity and the MAC/perforin module have been reported only in jawed vertebrates. Here, we report the identification of a protein containing the MAC/perforin module from the invertebrate cephalochordate, amphioxus (Branchiostoma belcheri), using expressed sequence tag (EST) analysis of the notochord. The deduced amino acid sequence of this molecule is most similar to the primary structure of human complement component C6 and is designated AmphiC6. AmphiC6 shares a unique modular structure, including the MAC/perforin module, with human C6 and other MAC components. Another EST clone predicts the presence of a thioester-containing protein with the closest structural similarity to vertebrate C3 (therefore designated AmphiC3). AmphiC3 retains most of the functionally important residues of vertebrate C3 and is shown by phylogenetic analysis to be derived directly from the common ancestor of vertebrate C3, C4, and C5. Only opsonic activity has been assigned to the invertebrate complement system until now. Therefore, this is the first molecular evidence for complement-mediated immunological cytotoxicity in invertebrates. Received: 24 August 2001 / Accepted: 12 November 2001     

A Modular Flat Panel Photobioreactor (MFPP) for indoor mass cultivation of Nannochloropsis sp. under artificial illumination

Nannochloropsis sp. was grown in a Modular FlatPanel Photobioreactor (MFPP) consisting of sixalveolar panels each with 20.5 L culture volume and3.4 m² illuminated surface area. The panelsformed a closely-packed unit with illuminationprovided by banks of fluorescent tubes placed betweenthe panels. The whole unit was contained in athermoregulated cabinet. Continuous illumination ofone side of the panels with 115 molphoton m^-2 s^-1 attained a mean volumetricproductivity of 0.61 g (d. wt) L^-1 24 h^-1,increasing to 0.97 g (d. wt) L^-1 24 h^-1 whenthe same irradiance was provided on both sides of thepanels. With 230 mol photon m^-2 s^-1 onone side of the panel, a mean productivity of 0.85 g(d. wt) L^-1 24 h^-1 was achieved, whichreached 1.45 g (d. wt) L^-1 24 h^-1 when bothsides were illuminated. Increasing the amount of lightprovided to the culture (either by increasingirradiance or the illuminated surface area) decreasedpigment and enhanced the total fatty acid content, butdid not change significantly the content ofeicosapentaenoic acid. A MFPP of the presentdimensions could produce sufficient microalgae tosupport a hatchery producing 6 million sea breamfingerlings annually.     

Facile conversion of RNA aptamers to modular fluorescent sensors with tunable detection wavelengths

A GTP aptamer was converted to a modular fluorescent GTP sensor by conjugation of RRE (Rev responsive element) RNA and successive complex formation with a fluorophore-modified Rev peptide. Structural changes associated with substrate binding in the RNA aptamer were successfully transduced into changes in fluorescence intensity because of the modular structure of ribonucleopeptides. A simple modular strategy involving conjugation of a fluorophore-modified ribonucleopeptide to the stem region of an RNA aptamer deduced from secondary structural information helps produce fluorescent sensors, which allow tuning of excitation and detection wavelengths through the replacement of the fluorophore at the N-terminal of the Rev peptide.     

泉州市不同利用方式下土壤磷的吸附与解吸特性

分析了不同利用方式下泉州市土壤磷素吸附-解吸特征.结果表明:Langmuir等温方程式可以很好地表征土壤磷素的吸附特性;旱地和轮作地土壤对磷的吸附能力较强,而草地和林地土壤对磷的吸附能力较弱;磷的流失风险顺序为轮作地＞草地＞林地＞旱地;指导施磷量与吸附常数、最大缓冲量的大小顺序一致,为旱地＞轮作地＞林地＞草地;轮作地和草地的解吸率高于旱地和林地,土壤的缓冲能力顺序为旱地＞林地＞轮作地＞草地.主成分分析表明,平均解吸率、易解吸磷、磷吸附指数和磷零吸持平衡浓度4个指标最能反映土壤磷素流失潜力,可作为评价流失潜力的主要指标.