Peptide and protein building blocks for synthetic biology: from programming biomolecules to self-organized biomolecular systems.

There are several approaches to creating synthetic-biological systems. Here, we describe a molecular-design approach. First, we lay out a possible synthetic-biology space, which we define with a plot of complexity of components versus divergence from nature. In this scheme, there are basic units, which range from natural amino acids to totally synthetic small molecules. These are linked together to form programmable tectons, for example, amphipathic alpha-helices. In turn, tectons can interact to give self-assembled units, which can combine and organize further to produce functional assemblies and systems. To illustrate one path through this vast landscape, we focus on protein engineering and design. We describe how, for certain protein-folding motifs, polypeptide chains can be instructed to fold. These folds can be combined to give structured complexes, and function can be incorporated through computational design. Finally, we describe how protein-based systems may be encapsulated to control and investigate their functions.     

Tracks and trackways of Myotragus balearicus Bate (Artiodactyla, Caprinae) in Pleistocene aeolianites from Mallorca (Balearic Islands, Western Mediterranean)

Tracks and trackways of the ruminant goat, Myotragus balearicus Bate, 1909 are abundant in the Late Pleistocene aeolianites of the south coast of Mallorca, Spain. The carbonate aeolianites form impressive dunes and related sand ramps that were initiated as echo dunes in front of a 20–40 m high paleocliff of Miocene reefal limestone. Where the dunes built up to the cliff top, they covered it as an aeolian ramp. The dunes and sand ramps were active during the dry summer months but were passive during the wet winter period. The small, goat-like animals were abundant on the island, and for unknown reasons crossed the aeolian accumulations in large numbers. This study deals with the tracks formed in the dune deposits. All preserved trackways indicate impression into moist sand. Special features of the tracks include the structure produced by the withdrawal of the foot, here called the ‘axis’, and a disturbance zone of plastic deformation around this. On dune crests, the disturbance zone surrounds the axis more or less symmetrically. However, in addition, a ‘pressure pad’ of dislocated, slightly rotated sediment bound by curved microfaults is commonly produced posterior to the axis by propulsive pressure of the foot. On steep stoss and lee slopes, the pressure pad becomes oriented in a down-slope position as a result of gravitational slip of the walking animal. Combination of disturbance of the sediment in this way by manus followed by overprinting of similar disturbance by pes produces highly complicated track structure. This structure may be characteristic of artiodactylous mammals in soft sand, particularly aeolian deposits. The structure is designated as Bifidipes aeolis isp. nov.     

A lipopolysaccharide mutant of Bradyrhizobium japonicum that uncouples plant from bacterial differentiation.

The Tn5-containing fragment from a non-nodulating mutant of Bradyrhizobium japonicum, strain ML142, was introduced into B. japonicum strain 61A101c by marker exchange to construct strain JS314. Strain JS314 failed to nodulate several soybean varieties tested. However, on a few varieties nodulelike structures were induced to a frequency of 54% of the plants inoculated. The ultrastructure of these nodules was studied in detail by light and electron microscopy. The nodules were devoid of internal bacteria, possessed central vascular tissue (unlike the lateral vascular tissue of a normal nodule), and exhibited localized cell death of epidermal cells. Study of the cell surface polysaccharides of strain JS314 revealed that the exopolysaccharide of this strain was identical to that of the wild type. However, the lipopolysaccharide (LPS) of strain JS314 showed gross differences from that isolated from the wild-type strain. Specifically, the LPS of strain JS314 appeared to lack the high molecular weight LPS I form, strongly suggesting that the LPS lacks the O-chain. Glycosyl-composition analysis showed that the LPS of mutant JS314 lacked 2,3-di-O-methylrhamnose, 3-O-methylrhamnose, fucose, and quinovosamine. These results indicate that LPS I in B. japonicum is essential for bacterial infection of soybean, but is not required to initiate plant cortical cell division, an early plant response to infection.     

Increased prolactin binding and morphological changes in the wound epithelium of regenerating limbs of Notophthalmus viridescens

Summary Distribution of prolactin has been examined in regenerating forelimbs from the newt Notophthalmus viridescens. Specific prolactin binding was demonstrated in homogenates of unamputated tissue, and of regenerating limbs at from 3 to 21 days postamputation. Labeled prolactin that was injected intraperitoneally into animals with one regenerating limb accumulated in the most distal portion of the regenerate at 7 and 14 days postamputation. Light microscopic autoradiography demonstrated that labeled prolactin was localized most heavily in the apical, outer layer of the wound epithelium. Scanning electron microscopy demonstrated that, in addition to changes in prolactin affinity following amputation, morphological changes occurred in the apical wound epithelium as well. Cell surfaces of the stump epidermis were characterized by periodic dispersion of papillae among a network of interconnecting structures 1–2 m across. By contrast, the surfaces of cells from the area in which labeled prolactin was found to localize most intensely were characterized by lack of papillae and, depending on the stage of regeneration, a pattern of microvilli and microplicae. These morphological alterations appear to reflect functional and biochemical differences between stump epidermis and wound epithelium.     

Characterization of the genomic RNA from a Rous sarcoma virus mutant temperature sensitive for cell transformation.

We have found that the LA23 t/s mutant of Rous sarcoma virus (phenotype Prague B), even when passaged repeatedly at high multiplicity of infection, does not give rise to transformation defective deletion mutants comparable to those derived from RSV. In view of this fact and of the high rate of production of this mutant at 41 degrees C, we have undertaken a detailed analysis of the genome of this virus by ordering all large T1 oligonucleotides and by determining their nucleotide sequences. The results indicate a high degree of mutation in the onc gene as compared to that of Pr-A or Pr-B.     

Ultrastructure of the antennal sensilla of aphids

Summary An electron microscopical study of aphid antennal sensilla has revealed two types of trichoid sensilla. Type I, innervated by a single neuron is mechanoreceptive; type II, innervated by three to five neurons is both mechanoreceptive and chemoreceptive with possibly a third function. Johnston's organ in the pedicel comprises a peripheral ring of scolopidia inserted into the joint with the flagellum; two non-peripheral groups of scolopidia lie in the lumen with attachment points in the wall of the third segment. The fine structure of a campaniform sensillum on the pedicel is described together with two homologous and previously unknown sense organs at the joint between the fifth and sixth antennal segments. An unusually placed scolopidium in the lumen of the sixth segment has also been found. The function of this scolopidium is unknown but Johnston's organ, the campaniform sensillum and joint receptors are suggested to act as antennal proprioceptors.The authors thank the Long Ashton Research Station, Bristol for use of the SEM facilities. A.K. Bromley gratefully acknowledges the tenure of a S.R.C. CASE Studentship and thanks Professor L.H. Finlayson for research facilities     

Catabolism of protocatechuate by Bacillus macerans.

An aerobic endospore-forming bacterium, tentatively identified as a strain (JJ-lb) of Bacillus macerans, was isolated by enrichment on 4-hydroxybenzoate (4HBA), using as an inoculum soil taken from a 50 degrees C Iadho hot spring. Enzymatic analyses of cells grown on succinate and 4HBA indicated that strain JJ-1b degrades 4HBA by way of the novel protocatechuate (PCA) 2,3-dioxygenase pathway. Purification of the PCA 2,3-dioxygenase by affinity chromatography allowed the first observation of the immediate ring fission product of PCA, namely, 5-carboxy-2-hydroxymuconic semialdehyde (CHMS; labmda max at pH 7.0 = 348 nm). An affinity column fraction was obtained that decarboxylated CHMS to 2-hydroxymuconic semialdehyde (HMS; lambdamax at pH 7.0 = 375 nm). Thus, conversion of PCA to HMS is accomplished in two steps, 2,3-fission of the PCA ring followed by enzymatic decarboxylation of the ring fission product, forming HMS.     

New procedure for isolation of Rous sarcoma virus-specific RNA from infected cells.

The use of mercurated "strong stop" complementary DNA (complementary to the 5'-terminal 101 nucleotides of Rous sarcoma virus RNA) in the isolation of virus-specific RNA from infected chicken embryo fibroblasts is described. Strong stop Rous sarcoma virus complementary DNA was mercurated chemically, and, as a result of the low complexity of this DNA, short hybridization times (up to 15 min) and heating in the absence of formamide were found to be adequate conditions for the isolation of virus-specific RNA. The purity of the isolated RNA was demonstrated by analysis of labeled RNase T1-resistant oligonucleotides by two-dimensional polyacrylamide gel electrophoresis. The isolated RNA could be translated in the in vitro protein synthesis system derived from rabbit reticulocytes, and an analysis of polypeptides programmed by isolated RNA before and after immunoprecipitation further demonstrated both the purity of the isolated mRNA and the quantitative nature of the isolation procedure.     

Metabolism of cationized lipoproteins by human fibroblasts: biochemical and morphologic correlations

Human plasma low density lipoprotein (LDL) that had been rendered polycationic by coupling with N, N-dimethyl-1, 3-propanediamine (DMPA) was shown by electron microscopy to bind in clusters to the surface of human fibroblasts. The clusters resembled those formed by polycationic ferritin (DMPA-feritin), a visual probe that binds to anionic site on the plasma membrane. Biochemical studies with (125)I-labeled DMPA-LDL showed that the membrane-bound lipoprotein was internalized and hydrolyzed in lysosomes. The turnover time for cell bound (125)I-DMPA-LDL, i.e., the time in which the amount of (125)I-DMPA-LDL degraded was equal to the steady-state cellular content of the lipoprotein, was about 50 h. Because the DMPA-LDL gained access to fibroblasts by binding nonspecifically to anionic sites on the cell surface rather than by binding to the physiologic LDL receptor, its uptake failed to be regulated under conditions in which the uptake of native LDL was reduced by feedback suppression of the LDL receptor. As a result, unlike the case with native LDL, the DMPA-LDL accumulated progressively within the cell, and this led to a massive increase in the cellular content of both free and esterified cholesterol. Studies with (14)C-oleate showed that at least 20 percent of the accumulated cholesteryl esters represented cholesterol that had been esterified within the cell. After 4 days of incubation with 10 μg/ml of DMPA-LDL, fibroblasts had accumulated so much cholesteryl ester that neutral lipid droplets were visible at the light microscope level with Oil Red O staining. By electron microscopy, these intracellular lipid droplets were observed to lack a tripartite limiting membrane. The ability to cause the overaccumulation of cholesteryl esters within cells by using DMPA-LDL provides a model system for study of the pathologic consequences at the cellular level of massive deposition of cholesteryl ester.