Chemiosmotic concept of the membrane bioenergetics: What is already clear and what is still waiting for elucidation?

The present state of the chemiosmotic concept is reviewed. Special attention is paid to (i) further progress in studies on the Na⁺-coupled energetics and (ii) paradoxical bioenergetic effects when protonic or sodium potentials are utilized outside the coupling membrane (TonB-mediated uphill transports across the outer bacterial membrane). A hypothesis is put forward assuming that the same principle is employed in the bacterial flagellar motor.     

Do Protoplasmic Connections Function in the Phototactic Coordination of the Volvox Colony During Light Stimulation?*

SYNOPSIS. The flagellar behavior of the colonial flagellates Volvox carteri Stein and Volvox perglobator Powers was examined by placing 1.01 μm polystyrene particles in solution with swimming colonies, and photographing these particle movements. When directional light stimulation was administered to individual colonies, a cessation of flagellar activity occurred in the anterior cells of the stimulated side in both species. Since Volvox perglobator possesses prominent intercellular connections and Volvox carteri does not, the results of these experiments suggest that the connections linking colony members in some species do not function in the coordination of flagellar activity associated with light orientation behavior.     

Compositional variation of leaf pocket sesquiterpenes in Trachylobium verrucosum

Greenhouse-grown plants originating from Kenyan and Madagascan populations of Trachylobium verrucosum are qualitatively identical in leaf pocket resin sesquiterpene composition, but differ quantitatively.     

The Differentiation of Herpetomonas megaseliae: Ultrastructural Observations*

Ultrastructure of both undifferentiated (promastigote and paramastigote) and differentiated (opisthomastigote) forms of Herpetomonas megaseliae is described. There is a posterior migration of the kinetoplast at the end of the exponential growth phase. The posterior extension of the flagellar pocket precedes migration of the kinetoplast. Opisthomastigotes have an electron-translucent mitochondrial matrix in comparison with undifferentiated forms. The Golgi body changes from a stack of flattened sacs to an aggregation of vesicles. Several structures previously reported from Trypanosomatidae, e.g. subpellicular organelles, pellicular microtubules, membrane whorls, stored metabolic products, surface blebs, and an intraflagellar body are also present in H. megaseliae.     

An amino acid code to define a protein's tertiary packing surface

One difficult aspect of the protein‐folding problem is characterizing the nonspecific interactions that define packing in protein tertiary structure. To better understand tertiary structure, this work extends the knob‐socket model by classifying the interactions of a single knob residue packed into a set of contiguous sockets, or a pocket made up of 4 or more residues. The knob‐socket construct allows for a symbolic two‐dimensional mapping of pockets. The two‐dimensional mapping of pockets provides a simple method to investigate the variety of pocket shapes to understand the geometry of protein tertiary surfaces. The diversity of pocket geometries can be organized into groups of pockets that share a common core, which suggests that some interactions in pockets are ancillary to packing. Further analysis of pocket geometries displays a preferred configuration that is right‐handed in α‐helices and left‐handed in β‐sheets. The amino acid composition of pockets illustrates the importance of nonpolar amino acids in packing as well as position specificity. As expected, all pocket shapes prefer to pack with hydrophobic knobs; however, knobs are not selective for the pockets they pack. Investigating side‐chain rotamer preferences for certain pocket shapes uncovers no strong correlations. These findings allow a simple vocabulary based on knobs and sockets to describe protein tertiary packing that supports improved analysis, design, and prediction of protein structure. Proteins 2016; 84:201–216. © 2015 Wiley Periodicals, Inc.     

Probing the Monophyly of the Sphaeropleales (Chlorophyceae) Using Data From Five Genes

Molecular phylogenetic analyses have had a major impact on the classification of the green algal class Chlorophyceae, corroborating some previous evolutionary hypotheses, but primarily promoting new interpretations of morphological evolution. One set of morphological traits that feature prominently in green algal systematics is the absolute orientation of the flagellar apparatus in motile cells, which correlates strongly with taxonomic classes and orders. The order Sphaeropleales includes diverse green algae sharing the directly opposite (DO) flagellar apparatus orientation of their biflagellate motile cells. However, algae across sphaeroplealean families differ in specific components of the DO flagellar apparatus, and molecular phylogenetic studies often have failed to provide strong support for the monophyly of the order. To test the monophyly of Sphaeropleales and of taxa with the DO flagellar apparatus, we conducted a molecular phylogenetic study of 16 accessions representing all known families and diverse affiliated lineages within the order, with data from four plastid genes (psaA, psaB, psbC, rbcL) and one nuclear ribosomal gene (18S). Although single‐gene analyses varied in topology and support values, analysis of combined data strongly supported a monophyletic Sphaeropleales. Our results also corroborated previous phylogenetic hypotheses that were based on chloroplast genome data from relatively few taxa. Specifically, our data resolved Volvocales, algae possessing predominantly biflagellate motile cells with clockwise (CW) flagellar orientation, as the monophyletic sister lineage to Sphaeropleales, and an alliance of Chaetopeltidales, Chaetophorales, and Oedogoniales, orders having multiflagellate motile cells with distinct flagellar orientations involving the DO and CW forms.     

Surface Domains in the Pathogenic Protozoan Tritrichomonas foetus

ABSTRACT The quick-freezing and freeze-etching techniques were used to analyze surface domains of Tritrichomonas foetus . The surface of the protozoan body was not smooth, presenting surface projections, except on the flagellar surface. Images of the actual surface of the anterior flagella revealed the presence of intramembranous particles that form rosettes, as observed on the protoplasmic fracture face. They may represent integral transmembrane proteins exposed at the cell surface. Surface specializations were also observed at the flagella base and where the recurrent flagellum attaches to the cell body.     

The Fine Structure of the Colonial Colorless Flagellates Rhipidodendron splendidum Stein and Spongomonas uvella Stein with Special Reference to the Flagellar Apparatus

SYNOPSIS. The cell structure of the colorless colonial flagellates Rhipidodendron splendidum Stein and Spongomonas uvella Stein has been examined by electron microscopy to assertain their phylogenetic affinities. The cylindrical cells of R. splendidum have 2 smooth flagella of equal length, an asymmetrical flagellar pocket supported by microtubules, and a curved pit between the latter and an anterior prolongation of the cell. The matrix of the branched tubes comprising the fanshaped colony is composed largely of dense spherules which are produced in special cytoplasmic vesicles some of which contain symbiotic bacteria. The anterior nucleus has a flattened sac pressed closely against its posterior end. The sac has a long tail extending deep into the cytoplasm, a single bounding membrane and homogeneous contents. Several types of vesicle are described but food vacuoles and contractile vacuoles could not be positively identified. A kinetoplast mitochondrion is not present. The various cross-banded, microtubular and amorphous components of the complex and highly asymmetrical flagellar root system are described in detail and a 3-dimensional reconstruction is provided.
The ovoid cells of S. uvella are basically similar to those of R. splendidum ; though a nuclear sac is missing, there are some detailed differences in the structure of the flagellar root system, and bacteria are never present in the vesicles producing the matrix granules. Notwithstanding much similarity, Rhipidodendron is not combined with Spongomonas because of the basic difference in colony structure.
The possible relationships of R. splendidum and S. uvella with other groups are examined and it is concluded that they cannot be considered as colorless chrysomonads as previously thought or considered to be related to any of the other orders comprising the class Phytomastigophorea. They do not, however, appear to be related to any of the orders at present comprising the Zoomastigophorea.