Viral adaptation to host: a proteome‐based analysis of codon usage and amino acid preferences

Viruses differ markedly in their specificity toward host organisms. Here, we test the level of general sequence adaptation that viruses display toward their hosts. We compiled a representative data set of viruses that infect hosts ranging from bacteria to humans. We consider their respective amino acid and codon usages and compare them among the viruses and their hosts. We show that bacteria‐infecting viruses are strongly adapted to their specific hosts, but that they differ from other unrelated bacterial hosts. Viruses that infect humans, but not those that infect other mammals or aves, show a strong resemblance to most mammalian and avian hosts, in terms of both amino acid and codon preferences. In groups of viruses that infect humans or other mammals, the highest observed level of adaptation of viral proteins to host codon usages is for those proteins that appear abundantly in the virion. In contrast, proteins that are known to participate in host‐specific recognition do not necessarily adapt to their respective hosts. The implication for the potential of viral infectivity is discussed.     

Model systems for understanding DNA base pairing

The fact that nucleic acid bases recognize each other to form pairs is a canonical part of the dogma of biology. However, they do not recognize each other well enough in water to account for the selectivity and efficiency that is needed in the transmission of biological information through a cell. Thus proteins assist in this recognition in multiple ways, and recent data suggest that these mechanisms of recognition can vary widely with context. To probe how the chemical differences of the four nucleobases are defined in various biological contexts, chemists and biochemists have developed modified versions that differ in their polarity, shape, size, and functional groups. This brief review covers recent advances in this field of research.     

昆虫抗冻蛋白: 规则结构适应功能

抗冻蛋白在环境温度低于体液熔点时能够结合到生物体内的冰核表面,通过限制冰核生长和抑制冰晶重结晶而保护有机体免受结冰引起的伤害。与其他生物抗冻蛋白比较,昆虫抗冻蛋白有很强的活性,结构上具有显著特征,如一级结构规律重复,超二级结构为β-螺旋,可与冰晶发生相互作用,具有TXT基序等。该文综述了近年来关于昆虫抗冻蛋白的结构以及分子生物学等方面研究的新进展,讨论了其结构与功能的关系。     

Chaperone machines in action

How do chaperones operate in cells? For some major chaperones it is clear what they do, though mostly not how they do it. Hsp60, 70 and 100 families carry out folding, unfolding or disaggregation of proteins. Regarding mechanisms of action, we have the clearest picture of the ATP-driven mechanism of the bacterial Hsp60s, and structures of full-length Hsp70 and 90 family members are beginning to give insights into their allosteric mechanisms. Recent advances are giving an improved understanding of the nature of chaperone interactions with their non-native substrate proteins. There have also been significant advances in understanding the engagement of chaperones in preventing the formation of toxic aggregates in degenerative disease and the relationship of protein quality control to complex biological processes such as ageing.     

Plant membrane proteomics

Plant membrane proteins are involved in many different functions according to their location in the cell. For instance, the chloroplast has two membrane systems, thylakoids and envelope, with specialized membrane proteins for photosynthesis and metabolite and ion transporters, respectively. Although recent advances in sample preparation and analytical techniques have been achieved for the study of membrane proteins, the characterization of these proteins, especially the hydrophobic ones, is still challenging. The present review highlights recent advances in methodologies for identification of plant membrane proteins from purified subcellular structures. The interest of combining several complementary extraction procedures to take into account specific features of membrane proteins is discussed in the light of recent proteomics data, notably for chloroplast envelope, mitochondrial membranes and plasma membrane from Arabidopsis. These examples also illustrate how, on one hand, proteomics can feed bioinformatics for a better definition of prediction tools and, on the other hand, although prediction tools are not 100% reliable, they can give valuable information for biological investigations. In particular, membrane proteomics brings new insights over plant membrane systems, on both the membrane compartment where proteins are working and their putative cellular function.     

Proteins secreted by clonal cell lines : Changes in metabolism with culture growth

Clonal cell lines release glycoproteins into their culture medium, some of which appear to be derived from the outer cell surface. These proteins do not originate from lysed cells, nor do they comigrate on SDS acrylamide gels with the proteins of substrate attached material. When the proteins released from exponentially dividing cells are compared with those from stationary phase cells, marked differences are found. In addition, the proteins released from normal stationary cells differ from those precociously growth arrested with db-cAMP or by serum deprivation. The spectrum of proteins released by the serum-deprived cells is more like that of normal stationary phase cells than db-cAMP-inhibited cells.     

Evidence for a primary endocytic vesicle involved in synaptic vesicle biogenesis

The regulated release of neurotransmitters at synapses is mediated by the fusion of neurotransmitter-filled synaptic vesicles with the plasma membrane. Continuous synaptic activity relies on the constant recycling of synaptic vesicle proteins into newly formed synaptic vesicles. At least two different mechanisms are presumed to mediate synaptic vesicle biogenesis at the synapse as follows: direct retrieval of synaptic vesicle proteins and lipids from the plasma membrane, and indirect passage of synaptic vesicle proteins through an endosomal intermediate. We have identified a vesicle population with the characteristics of a primary endocytic vesicle responsible for the recycling of synaptic vesicle proteins through the indirect pathway. We find that synaptic vesicle proteins colocalize in this vesicle with a variety of proteins known to recycle from the plasma membrane through the endocytic pathway, including three different glucose transporters, GLUT1, GLUT3, and GLUT4, and the transferrin receptor. These vesicles differ from "classical" synaptic vesicles in their size and their generic protein content, indicating that they do not discriminate between synaptic vesicle-specific proteins and other recycling proteins. We propose that these vesicles deliver synaptic vesicle proteins that have escaped internalization by the direct pathway to endosomes, where they are sorted from other recycling proteins and packaged into synaptic vesicles.     

Developmental modulation of embryonic cardiac myocyte adhesion to cardiac collagens in vitro.

The goal of this investigation is to identify molecules that mediate embryonic cardiac myocyte adhesion during chick cardiac morphogenesis. The assay used employs culturing embryonic myocytes on substrata containing embryonic heart proteins separated by molecular weight. This assay shows that embryonic myocytes from 10- to 14-day-old embryos will bind to 140,000 and 128,000 Da proteins present in embryonic hearts and do not require Mg2+ or Ca2+ for adhesion. Myocytes from embryos younger than 10 days or older than 14 days display little or no binding. Embryonic heart fibroblasts collected at these same ages do not bind to these proteins. The 140- and 128-kDa proteins were found to copurify in extraction procedures for procollagens. Amino acid analysis shows that both proteins contain high glycine and hydroxyproline, indicating that they are collagens. However, glycine and imino acid levels are low relative to other known collagens, indicating a nonhelical domain present in each molecule and most closely resembled levels present in procollagens. Immunoblots show that antisera to chick collagen type I recognizes the 128-kDa protein while anti-collagen type III recognizes the 140-kDa protein. Monoclonal antibodies to the amino terminal propeptide of collagen type I recognize the 128-kDa protein in immunoblotting procedures. Embryonic chick myocytes bind to 140/128 kDa proteins present in extracts of sympathetic trunk, although they do not bind to 140/128 kDa proteins in embryonic tendon. The findings thereby indicate that forms of type III and type I collagens in embryonic heart support direct adhesion of embryonic myocytes for a restricted period of cardiac myogenesis and that these proteins differ from collagen types I and III present in other tissues and from fully processed collagen types I and III.     

Tyrosine kinases in control of cell growth and transformation

The growth of normal cells in tissues is strictly controlled, partly through intercellular communication by polypeptide growth factors. Malignantly transformed cells are independent from external growth factors to a certain extent, but their mechanisms for achieving growth autonomy differ from case to case. Several of the oncogene-encoded proteins are known to participate in the hormonal regulation of cell growth (for a recent review on tyrosine kinase oncogenes see ref. 21). Recent advances in molecular biology have shown important mechanisms for cell emancipation from growth regulatory hormonal signaling systems. A few such examples are discussed below.     

Natively unfolded proteins: a point where biology waits for physics

The experimental material accumulated in the literature on the conformational behavior of intrinsically unstructured (natively unfolded) proteins was analyzed. Results of this analysis showed that these proteins do not possess uniform structural properties, as expected for members of a single thermodynamic entity. Rather, these proteins may be divided into two structurally different groups: intrinsic coils, and premolten globules. Proteins from the first group have hydrodynamic dimensions typical of random coils in poor solvent and do not possess any (or almost any) ordered secondary structure. Proteins from the second group are essentially more compact, exhibiting some amount of residual secondary structure, although they are still less dense than native or molten globule proteins. An important feature of the intrinsically unstructured proteins is that they undergo disorder-order transition during or prior to their biological function. In this respect, the Protein Quartet model, with function arising from four specific conformations (ordered forms, molten globules, premolten globules, and random coils) and transitions between any two of the states, is discussed.