A role for convergent evolution in the secretory life of cells

The role of convergent evolution in biological adaptation is increasingly appreciated. Many clear examples have been described at the level of individual proteins and for organismal morphology, and convergent mechanisms have even been invoked to account for similar community structures that are shared between ecosystems. At the cellular level, an important area that has received scant attention is the potential influence of convergent evolution on complex subcellular features, such as organelles. Here, we show that existing data strongly argue that convergent evolution underlies the similar properties of specialized secretory vesicles, called dense core granules, in the animal and ciliate lineages. We discuss both the criteria for judging convergent evolution and the contribution that such evolutionary analysis can make to improve our understanding of processes in cell biology. The elucidation of these underlying evolutionary relationships is vital because cellular structures that are assumed to be analogous, owing to shared features, might in fact be governed by different molecular mechanisms.     

Mycelium differentiation and antibiotic production in submerged cultures of Streptomyces coelicolor

Despite the fact that most industrial processes for secondary metabolite production are performed with submerged cultures, a reliable developmental model for Streptomyces under these culture conditions is lacking. With the exception of a few species which sporulate under these conditions, it is assumed that no morphological differentiation processes take place. In this work, we describe new developmental features of Streptomyces coelicolor A3(2) grown in liquid cultures and integrate them into a developmental model analogous to the one previously described for surface cultures. Spores germinate as a compartmentalized mycelium (first mycelium). These young compartmentalized hyphae start to form pellets which grow in a radial pattern. Death processes take place in the center of the pellets, followed by growth arrest. A new multinucleated mycelium with sporadic septa (second mycelium) develops inside the pellets and along the periphery, giving rise to a second growth phase. Undecylprodigiosin and actinorhodin antibiotics are produced by this second mycelium but not by the first one. Cell density dictates how the culture will behave in terms of differentiation processes and antibiotic production. When diluted inocula are used, the growth arrest phase, emergence of a second mycelium, and antibiotic production are delayed. Moreover, pellets are less abundant and have larger diameters than in dense cultures. This work is the first to report on the relationship between differentiation processes and secondary metabolite production in submerged Streptomyces cultures.     

Osteogenesis,homology, and function of the intercostal plates in ornithischian dinosaurs (Tetrapoda,Sauropsida)

Intercostal plates are bony structures positioned lateral to the anterior dorsal ribs in some ornithischian dinosaurs. Some propose these plates are homologous, or functionally analogous, with the uncinate processes of extant avian dinosaurs that assist in breathing, while others suggest they served a defensive function. To elucidate their osteogenesis, homology, and function, a histological survey of intercostal plates from three taxa (Hypsilophodon, Talenkauen, and Thescelosaurus) was undertaken. This study reveals that osteogenesis of intercostal plates closely resembles that of secondary centers of ossification in endochondral bone, typically present in the epiphyses of mammalian long bones. In contrast, ossification of avian uncinate processes begins at a primary ossification center via the development of a bony collar around a cartilaginous model. Based on these data, intercostal plates and avian uncinate processes are likely not evolutionary homologs. Dense packets of obliquely oriented Sharpey’s fibers within the parallel-fibered bone of somatically mature intercostal plates indicate these plates were positioned medial to at least a portion of the hypaxial musculature, which does not support their use as bony armor. Rather, we propose that intercostal plates performed some biomechanical function, either assisting in breathing in a way analogous to avian uncinate processes, or working together with the sternal ribs and sternal plates of these ornithischian taxa to provide increased rigidity to the anterior portion of the ribcage.     

Prediction of a conserved, neutralizing epitope in ribosome-inactivating proteins

The secondary structures, side-chain solvent accessibilities, and superpositioned crystal structures of the A-chain of ricin and four other plant rRNA N-glycosidases (ribosome-inactivating proteins, RIPs) were examined. Previously, a 26-residue fragment from the A-chain of ricin was determined to bind to a neutralizing monoclonal antibody. The region in the native ricin A-chain, to which this peptide corresponds, is solvent-exposed and contains a negatively charged residue that has been hypothesized to participate in the toxin's function, namely, rRNA binding and/or enzymatic activity. This region appears to be conserved in all of the structurally defined plant RIPs examined. Moreover, other plant RIPs, whose tertiary structures are, as yet, unknown, were predicted to have an analogous, solvent-exposed region containing a conserved, negatively charged residue. By analogy, these conserved structural and functional features lead to the suggestion that this exposed region represents a logical starting point for experiments designed to locate neutralizing epitopes in these RIPs. In contrast, the tertiary structure of the analogous region in a bacteria-derived RIP (Shiga toxin) is a less solvent-exposed, truncated loop and is a structure that is not as likely to be a neutralizing epitope. Because most of the amino acid residues are not conserved within this exposed region, these RIPs are predicted to be antigenically distinct.     

New Mechanism for Voltage Induced Charge Movement Revealed in GPCRs - Theory and Experiments

Depolarization induced charge movement associated currents, analogous to gating currents in channels, were recently demonstrated in G-protein coupled receptors (GPCRs), and were found to affect the receptor''s Agonist binding Affinity, hence denoted AA-currents. Here we study, employing a combined theoretical-experimental approach, the properties of the AA-currents using the m2-muscarinic receptor (m2R) as a case study. We found that the AA-currents are characterized by a “bump”, a distinct rise followed by a slow decline, which appears both in the On and the Off responses. The cumulative features implied a directional behavior of the AA-currents. This forced us to abandon the classical chemical reaction type of models and develop instead a model that includes anisotropic processes, thus producing directionality. This model fitted well the experimental data. Our main findings are that the AA-currents include two components. One is extremely fast, , at all voltages. The other is slow, at all voltages. Surprisingly, the slow component includes a process which strongly depends on voltage and can be as fast as at . The reason that it does not affect the overall time constant of the slow component is that it carries very little charge. The two fast processes are suitable candidates to link between charge movement and agonist binding affinity under physiological conditions.     

Yeast adaptor protein, Nbp2p, is conserved regulator of fungal Ptc1p phosphatases and is involved in multiple signaling pathways

Nbp2p is an Src homology 3 (SH3) domain-containing yeast protein that is involved in a variety of cellular processes. This small adaptor protein binds to a number of different proteins through its SH3 domain, and a region N-terminal to the SH3 domain binds to the protein phosphatase, Ptc1p. Despite its involvement in a large number of physical and genetic interactions, the only well characterized function of Nbp2p is to recruit Ptc1p to the high osmolarity glycerol pathway, which results in down-regulation of this pathway. In this study, we have discovered that Nbp2p orthologues exist in all Ascomycete and Basidiomycete fungal genomes and that all possess an SH3 domain and a conserved novel Ptc1p binding motif. The ubiquitous occurrence of these two features, which we have shown are both critical for Nbp2p function in Saccharomyces cerevisiae, implies that a conserved role of Nbp2p in all of these fungal species is the targeting of Ptc1p to proteins recognized by the SH3 domain. We also show that in a manner analogous to its role in the high osmolarity glycerol pathway, Nbp2p functions in the down-regulation of the cell wall integrity pathway through SH3 domain-mediated interaction with Bck1p, a component kinase of this pathway. Based on functional studies on the Schizosaccharomyces pombe and Neurospora crassa Nbp2p orthologues and the high conservation of the Nbp2p binding site in Bck1p orthologues, this function of Nbp2p appears to be conserved across Ascomycetes. Our results also clearly imply a function for the Nbp2p-Ptc1p complex other cellular processes.     

Oxidative metabolism of anandamide

In addition to the well studied hydrolytic metabolism of anandamide, a number of oxidative processes are also possible. Several routes somewhat analogous to the metabolism of free arachidonic acid have been reported. These involve mediation by various lipoxygenases and COX-2 and lead to ethanolamide analogs of the prostaglandins and HETES. The physiological significance of these products is not well understood at this time. There are also preliminary data suggesting a pathway involving oxidation of the hydroxy group of anandamide to a putative metabolite, N-arachidonyl glycine (AA-gly). This molecule displays activities in experimental models that suggest that it may play a role in some of the activities attributed to its precursor, anandamide.     

A stochastic model for integrating changes in species richness and community similarity across spatial scales

Human activities have elevated the extinction of natural populations as well as the invasion of new areas by non-native species. These dual processes of invasion and extinction may change the richness and similarity of communities, but the form these changes take is likely to depend on the manner in which invasions and extinctions occur and the spatial scale at which the changes are measured. Here, we explore the influence of differing patterns of extinction and invasion on the similarity and richness of a meta-community. In particular, we model simple stochastic processes analogous to realistic modes of human-mediated introduction of non-native species and range expansion by native species. We show that different modes of invasion and extinction can produce very different changes in diversity, and that the relative magnitude of these changes depends both on where in the meta-community diversity is measured and the degree of initial species aggregation. At any spatial scale of measurement, changes in the richness and similarity of communities following invasion and extinction are not necessarily strongly coupled: relatively large increases in richness may or may not also be associated with relatively large increases in similarity among communities. Thus, in real systems, the influence of human-induced invasions and extinctions on diversity will depend on both the precise mode of these processes (especially invasion), and how species populations are distributed across space.     

Complementary molecular models of learning and memory.

The functional capabilities of the brain are formally characterizable interms of a finite system along with a memory space which it can manipulate. Two types of learning are possible: (1) modification-based learning, associated with alternate realizations of the finite system; (2) memory-based learning, associated with the assimilation, manipulation, and retrieval of memories. Constructive models which fulfill these conditions and which at the same time operate on the basis of molecular information processing principles have certain general features. We describe these features in terms of two interfaced submodels, the first for the finite system and the second for the memory space. The finite system may be realized by networks of neurons in which the specificity of enzyme molecules controls the nerve impulse. Such a realization is amenable to modification-based learning mediated by processes analogous to those of natural evolution and selective theories of antibody synthesis. The memory space is realizable by networks of neurons in which the conformation of dendritic receptor molecules controls the nerve impulse. In this case certain neurons firing in response to an external input undergo sensitization at the dendrites and in such a way that they are loadable and later callable by reference neurons, thereby allowing for reconstruction of manipulation of the firing pattern associated with this input. The overall construction makes a large number of biochemical, anatomical, physiological, and psychological predictions which are either testable or in good agreement with fact.     

Are the molecular strategies that control apoptosis conserved in bacteria?

The Staphylococcus aureus cid and lrg operons have been shown to encode putative membrane proteins that are involved in the regulation of murein hydrolase activity and penicillin tolerance. Cid proteins enhance murein hydrolase activity and penicillin sensitivity, whereas Lrg proteins have an inhibitory effect on these processes. It has been proposed that the Cid and Lrg proteins function in a way analogous to bacteriophage-encoded holins and antiholins, respectively, which control the timing of bacteriophage-induced lysis. This article explores the possibility that the Cid-Lrg regulatory system controls bacterial programmed cell death using a molecular strategy that it is functionally analogous to that mediated by the eukaryotic Bcl-2 family of apoptosis regulatory proteins.     

Archaeal DNA replication and repair

Since the first archaeal genome was sequenced, much attention has been focused on the study of these unique microorganisms. We have learnt that although archaeal DNA metabolic processes (replication, recombination and repair) are more similar to the metabolic processes of Eukarya than those of Bacteria, Archaea are not simply 'mini Eukarya'. They are, in fact, a mosaic of the eukaryal and bacterial systems that also possess archaeal-specific features. Recent biochemical and structural studies of the proteins that participate in archaeal DNA replication and repair have increased our understanding of these processes.     

Stabilisation of intertidal cobbles and gravels by Goniastrea aspera: an analogue for substrate colonisation during marine transgressions?

There is a widespread perception that coral larvae require stable (lithified) rock substrates to settle during reef initiation, and that these substrates are typically carbonate. However, reef core data show that reef establishment can also occur directly above a wide range of unlithified, non-carbonate sediment substrates, including relict alluvial sands and gravels. The mechanisms by which these lithic substrates are colonised and stabilised are not, however, well documented. Here, we describe such processes from an intertidal setting on the inner-shelf of the Great Barrier Reef, in a setting directly analogous to that which would have existed around many inner-shelf high islands during the post-glacial marine transgression when mid-Holocene reef initiation was taking place. Communicated by Geology Editor Dr. Bernhard Riegl     

DNA reference alignment benchmarks based on tertiary structure of encoded proteins

MOTIVATION: Multiple sequence alignments (MSAs) are at the heart of bioinformatics analysis. Recently, a number of multiple protein sequence alignment benchmarks (i.e. BAliBASE, OXBench, PREFAB and SMART) have been released to evaluate new and existing MSA applications. These databases have been well received by researchers and help to quantitatively evaluate MSA programs on protein sequences. Unfortunately, analogous DNA benchmarks are not available, making evaluation of MSA programs difficult for DNA sequences. RESULTS: This work presents the first known multiple DNA sequence alignment benchmarks that are (1) comprised of protein-coding portions of DNA (2) based on biological features such as the tertiary structure of encoded proteins. These reference DNA databases contain a total of 3545 alignments, comprising of 68 581 sequences. Two versions of the database are available: mdsa_100s and mdsa_all. The mdsa_100s version contains the alignments of the data sets that TBLASTN found 100% sequence identity for each sequence. The mdsa_all version includes all hits with an E-value score above the threshold of 0.001. A primary use of these databases is to benchmark the performance of MSA applications on DNA data sets. The first such case study is included in the Supplementary Material.     

Physiological roles of microglia during development

In all the species examined thus far, the behavior of microglia during development appears to be highly stereotyped. This reproducibility supports the notion that these cells have a physiological role in development. Microglia are macrophages that migrate from the yolk sac and colonize the central nervous system early during development. The first invading yolk-sac macrophages are highly proliferative and their role has not yet been addressed. At later developmental stages, microglia can be found throughout the brain and tend to preferentially reside at specific locations that are often associated with known developmental processes. Thus, it appears that microglia concentrate in areas of cell death, in proximity of developing blood vessels, in the marginal layer, which contains developing axon fascicles, and in close association with radial glial cells. This review describes the main features of brain colonization by microglia and discusses the possible physiological roles of these cells during development.     

Global patterns of diversity and community structure in marine bacterioplankton

Because of their small size, great abundance and easy dispersal, it is often assumed that marine planktonic microorganisms have a ubiquitous distribution that prevents any structured assembly into local communities. To challenge this view, marine bacterioplankton communities from coastal waters at nine locations distributed world-wide were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes, used as operational taxonomic units (OTU). Our survey and analyses show that there were marked differences in the composition and richness of OTUs between locations. Remarkably, the global marine bacterioplankton community showed a high degree of endemism, and conversely included few cosmopolitan OTUs. Our data were consistent with a latitudinal gradient of OTU richness. We observed a positive relationship between the relative OTU abundances and their range of occupation, i.e. cosmopolitans had the largest population sizes. Although OTU richness differed among locations, the distributions of the major taxonomic groups represented in the communities were analogous, and all local communities were similarly structured and dominated by a few OTUs showing variable taxonomic affiliations. The observed patterns of OTU richness indicate that similar evolutionary and ecological processes structured the communities. We conclude that marine bacterioplankton share many of the biogeographical and macroecological features of macroscopic organisms. The general processes behind those patterns are likely to be comparable across taxa and major global biomes.     

Kinetics of thermal denaturation of met-hemoglobin in perturbed solvent: Relevance of bulk-electrostatic and hydrophobic interactions

We studied the kinetics of the heat denaturation (at 50°C) of met-hemoglobin in the presence of various monohydric alcohols. The denaturation rate was slowed by the presence of small concentrations of methanol and ethanol; in all the other cases, i.e., at high concentrations of methanol and ethanol, and in the whole concentration range studied for iso- and n-propanol, an increase in the denaturation rate was observed. Following a procedure already applied to the study of the effects of the same alcohols on the reaction of hemoglobin with oxygen, we separated the overall observed effects into contributions related to the variation of the bulk dielectric constant of the medium (bulk-electrostatic contributions) and contributions not related to variations in this parameter (nonbulk-electrostatic contributions). For all the alcohols, we found a unique correlation law connecting the above nonbulk-electrostatic contributions with the analogous ones previously reported for the T → R transition of hemoglobin. This fact strongly supports the validity of the procedure used and suggests that nonbulk-electrostatic contributions, relative to these two different processes, have a common background and are univocally determined by the extent of the “solvent perturbation” imposed by the presence of the perturbing cosolvents.