Bacterial cell wall synthesis: new insights from localization studies.

In order to maintain shape and withstand intracellular pressure, most bacteria are surrounded by a cell wall that consists mainly of the cross-linked polymer peptidoglycan (PG). The importance of PG for the maintenance of bacterial cell shape is underscored by the fact that, for various bacteria, several mutations affecting PG synthesis are associated with cell shape defects. In recent years, the application of fluorescence microscopy to the field of PG synthesis has led to an enormous increase in data on the relationship between cell wall synthesis and bacterial cell shape. First, a novel staining method enabled the visualization of PG precursor incorporation in live cells. Second, penicillin-binding proteins (PBPs), which mediate the final stages of PG synthesis, have been localized in various model organisms by means of immunofluorescence microscopy or green fluorescent protein fusions. In this review, we integrate the knowledge on the last stages of PG synthesis obtained in previous studies with the new data available on localization of PG synthesis and PBPs, in both rod-shaped and coccoid cells. We discuss a model in which, at least for a subset of PBPs, the presence of substrate is a major factor in determining PBP localization.     

Dynamics driving function: new insights from electron transferring flavoproteins and partner complexes

Electron transferring flavoproteins (ETFs) are soluble heterodimeric FAD-containing proteins that function primarily as soluble electron carriers between various flavoprotein dehydrogenases. ETF is positioned at a key metabolic branch point, responsible for transferring electrons from up to 10 primary dehydrogenases to the membrane-bound respiratory chain. Clinical mutations of ETF result in the often fatal disease glutaric aciduria type II. Structural and biophysical studies of ETF in complex with partner proteins have shown that ETF partitions the functions of partner binding and electron transfer between (a) a 'recognition loop', which acts as a static anchor at the ETF-partner interface, and (b) a highly mobile redox-active FAD domain. Together, this enables the FAD domain of ETF to sample a range of conformations, some compatible with fast interprotein electron transfer. This 'conformational sampling' enables ETF to recognize structurally distinct partners, whilst also maintaining a degree of specificity. Complex formation triggers mobility of the FAD domain, an 'induced disorder' mechanism contrasting with the more generally accepted models of protein-protein interaction by induced fit mechanisms. We discuss the implications of the highly dynamic nature of ETFs in biological interprotein electron transfer. ETF complexes point to mechanisms of electron transfer in which 'dynamics drive function', a feature that is probably widespread in biology given the modular assembly and flexible nature of biological electron transfer systems.     

Subnuclear organelles: new insights into form and function

The cell nucleus is a complex and highly dynamic environment with many functionally specialized regions of substructure that form and maintain themselves in the absence of membranes. Relatively little is known about the basic physical properties of the nuclear interior or how domains within the nucleus are structurally and functionally organized and interrelated. Here, we summarize recent data that shed light on the structural and functional properties of three prominent subnuclear organelles--nucleoli, Cajal bodies (CBs) and speckles. We discuss how these findings impact our understanding of the guiding principles of nuclear organization and various types of human disease.     

AMID: new insights on its intracellular localization and expression at apoptosis

AMID (apoptosis-inducing factor (AIF)-like mitochondrion-associated inducer of death) is a poorly studied member of the AIF family; despite the given name AMID, predicting its association with mitochondria, its real cellular localization, as well as its role and changes during apoptosis are currently unclear. By means of MALDI-TOF mass spectrometry, we have identified as AMID (accession number AAH38129, sequence coverage 31%) the protein isolated by Pisum sativum lectin-affinity chromatography from the plasma membrane fraction of apoptotic murine leukemia L1210 cells, lacking in the intact cells. The obtained results suggest its possible glycosylation that was further suggested by finding N-glycosylation sequon in the signal peptide of AMID protein (in silica), and by predicting transmembrane localization of its N-terminal part. Using monoclonal antibodies to AMID, we demonstrated an increased expression of AMID in human leukemia Jurkat T-cells after apoptosis induction. Immunocytochemical study suggested its association to the plasma membrane.     

GnRH deficiency: new insights from genetics

The acquisition of a sexually dimorphic phenotype is a critical event in mammalian development. Hypogonadotropic hypogonadism (HH) results from impaired secretion of GnRH. The patients display with delayed puberty, micropenis and cryptorchidism in the male reflecting gonadotropin insufficiency, and amenorrhea in the female. Kallmann's syndrome (KS) is defined by the association of HH and anosmia or hyposmia (absent smelling sense). Segregation analysis in familial cases has demonstrated diverse inheritance patterns, suggesting the existence of several genes regulating GnRH secretion. The X-linked form of the disease was associated with a genetic defect in the KALI gene located on the Xp22.3 region. KAL1 gene encodes an extracellular matrix glycoprotein anosmin-1, which facilitates neuronal growth and migration. Abnormalities in the migratory processes of the GnRH neurons with the olfactory neurons explain the association of HH with anosmia. Recently, mutations in the FGF recepteur 1 (FGFR1) gene were found in KS with autosomal dominant mode of inheritance. The role of FGFR1 in the function of reproduction requires further investigation. Besides HH with anosmia, there are isolated HH (IHH). No human GnRH mutations have been reported although hypogonadal mice due to a GnRH gene deletion exist. In patients with idiopathic HH and without anosmia an increasing number of GnRH receptor (GnRHR) mutations have been described which represent about 50% of familial cases. The clinical features are highly variable and there is a good relationship between genotype and phenotype. A complete loss of function is associated with the most severe phenotype with resistance to pulsatile GnRH treatment, absence of puberty and cryptorchidism in the male. In contrast, milder loss of function mutations causes incomplete failure of pubertal development. The preponderant role of GnRH in the secretion of LH by the gonadotrophs explains the difference of the phenotype between male and female with partial GnRH resistance. Affected females can have spontaneous telarche and normal breast development while affected males exhibit no pubertal development but normal testis volume, a feature described as "fertile-eunuch". High-dose pulsatile GnRH has been used to induce ovulation. Another gene, called GPR54, responsible for idiopathic HH has been recently described by segregation analysis in two different consanguineous families. The GPR54 gene is an orphan receptor, and its putative ligand is the product of the KISS-1 gene, called metastine. Their roles in the function of reproduction are still unknown.     

Microbialite taphonomy and biogenicity: new insights from NanoSIMS

We here show that nano‐scale mapping of elements commonly utilized in biological cycles provides a promising new additional line of evidence when evaluating the extent of the contribution of biology to microbialites. Our case study comes from Lake Clifton in Western Australia, a unique environment where living domical and conical microbialites occur in close proximity to ≤4000‐year‐old fossilized equivalents. The outer margins of a partially lithified, actively growing Lake Clifton microbialite are characterized by abundant filamentous cyanobacteria within a loosely cemented aragonite matrix. Nano‐scale chemical maps have been successfully matched to specific morphological features such as trichomes, sheaths and putative extracellular polymeric substances (EPS). A suite of elements (C, O, Mg, N, Si, S) is concentrated within cyanobacterial sheaths, with carbon, magnesium, nitrogen and sulfur also enriched within trichomes and putative EPS. Calcium distribution highlights the sites of aragonite mineralization. In contrast, the fossilized Lake Clifton microbialite contains only rare, extensively degraded cyanobacterial filaments, the mean diameter of which is <50% of the living equivalents. Nevertheless, nano‐scale chemical maps can again be matched with morphological features. Here, poorly preserved filamentous microfossils are highlighted by enrichments in nitrogen and sulfur. Magnesium is no longer concentrated within the filaments, instead it co‐occurs with calcium and oxygen in the calcite cement. Extension of this study to a ∼2720‐million‐year‐old stromatolitic microbialite from the Tumbiana Formation of Western Australia shows that similar nano‐scale signals, in particular nitrogen and sulfur enrichments, are characteristic of stromatolite laminations, even when morphological microfossils are absent. The close similarities of nano‐scale elemental distributions in organic material from modern and ancient microbialites show that this technique provides a valuable addition to the morphological investigation of such structures, particularly in non‐fossiliferous ancient examples.     

Structure and function of lecithin cholesterol acyl transferase: new insights from structural predictions and animal models

The enzyme lecithin cholesterol acyl transferase is responsible for the synthesis of most of the cholesteryl esters in plasma, and therefore plays a key role in lipoprotein metabolism. The relationship between the structure and function of lecithin cholesterol acyl transferase has been extensively studied in the past years, and new data appeared in 1999 documenting the substrate specificity and physiological role of lecithin cholesterol acyl transferase. The discovery of natural mutants, together with the proposal of a three-dimensional model for the enzyme, has provided new tools to unravel the function of specific residues of lecithin cholesterol acyl transferase. The use of transgenic animals and the production of knock-out lecithin cholesterol acyl transferase mice has further contributed to the understanding of the lecithin cholesterol acyl transferase 'in vivo' function. Evidence for a protective role of lecithin cholesterol acyl transferase against the development of atherosclerosis through the hydrolysis of oxidized lipids was recently proposed. Lecithin cholesterol acyl transferase patterns in several pathologies were further clarified. These newer developments are reviewed here.     

Beyond localization: from hodology to function

A century on, Campbell's largely forgotten 1905 monograph on the localization of cerebral function has a distinctly contemporary feel. Although his map of cortical fields has been eclipsed by Brodmann's later contribution, Campbell's project went beyond cytoarchitectonic cartography, attempting to integrate clinical, anatomical and physiological evidence to provide a guide to function. A key component of Campbell's integrative, functional anatomical approach was hodology--the pattern of white matter connections between cortical areas--foreshadowing a recently developed functional anatomical technique: diffusion tensor tractography. Here, we revisit Campbell's model of the human visual system using tractography to illustrate prominent white matter connections within the occipital lobe and from occipital to frontal, parietal and temporal regions. Campbell used his integrative approach to support the view that vision consisted of a "visuo-sensory" and a "visuo-psychic" stage, combining hodological, cytoarchitectonic, physiological and clinicopathological evidence to locate the former within the calcarine cortex and the latter within the cortical field surrounding it. Speaking directly to contemporary debates surrounding the neurobiology of conscious vision and providing a framework with which to shape future developments in tractography, Campbell's integrative functional anatomical approach is as relevant today as it was 100 years ago.     

MECP2 genomic structure and function: insights from ENCODE

MECP2, a relatively small gene located in the human X chromosome, was initially described with three exons transcribing RNA from which the protein MeCP2 was translated. It is now known to have four exons from which two isoforms are translated; however, there is also evidence of additional functional genomic structures within MECP2, including exons potentially transcribing non-coding RNAs. Accompanying the recognition of a higher level of intricacy within MECP2 has been a recent surge of knowledge about the structure and function of human genes more generally, to the extent that the definition of a gene is being revisited. It is timely now to review the published and novel functional elements within MECP2, which is proving to have a complexity far greater than was previously thought.     

Morphogen gradients: new insights from DPP.

The Drosophila TGFbeta family member Decapentaplegic (DPP) has been proposed to function as a morphogen to pattern cell fields in a number of developmental contexts. A series of recent reports add significantly to our knowledge of the mechanisms of DPP-gradient formation and interpretation. These reports identity additional genes and genetic circuitry necessary for this patterning system, and they highlight variations that might reflect developmental constraints within individual target cell fields.     

Solution NMR of supramolecular complexes: providing new insights into function

Solution NMR spectroscopy is an extremely powerful technology for the study of biomolecular dynamics and site-specific molecular interactions. An important limitation in the past has been molecule size, with molecular weights of targets seldom exceeding 50 kDa. New labeling technology and NMR experiments are changing this paradigm so that applications for investigating supramolecular complexes are starting to become feasible. Here we describe a strategy developed in our laboratory that involves the use of labeled methyl groups of isoleucine, leucine and valine residues in proteins as probes, along with experiments that significantly enhance the lifetimes of the resulting signals. We describe the application of these methods to a number of systems with molecular weights in the hundreds of kilodaltons.     

Lessons from a tarantula: new insights into muscle thick filament and myosin interacting-heads motif structure and function

The tarantula skeletal muscle X-ray diffraction pattern suggested that the myosin heads were helically arranged on the thick filaments. Electron microscopy (EM) of negatively stained relaxed tarantula thick filaments revealed four helices of heads allowing a helical 3D reconstruction. Due to its low resolution (5.0 nm), the unambiguous interpretation of densities of both heads was not possible. A resolution increase up to 2.5 nm, achieved by cryo-EM of frozen-hydrated relaxed thick filaments and an iterative helical real space reconstruction, allowed the resolving of both heads. The two heads, “free” and “blocked”, formed an asymmetric structure named the “interacting-heads motif” (IHM) which explained relaxation by self-inhibition of both heads ATPases. This finding made tarantula an exemplar system for thick filament structure and function studies. Heads were shown to be released and disordered by Ca²⁺-activation through myosin regulatory light chain phosphorylation, leading to EM, small angle X-ray diffraction and scattering, and spectroscopic and biochemical studies of the IHM structure and function. The results from these studies have consequent implications for understanding and explaining myosin super-relaxed state and thick filament activation and regulation. A cooperative phosphorylation mechanism for activation in tarantula skeletal muscle, involving swaying constitutively Ser35 mono-phosphorylated free heads, explains super-relaxation, force potentiation and post-tetanic potentiation through Ser45 mono-phosphorylated blocked heads. Based on this mechanism, we propose a swaying-swinging, tilting crossbridge-sliding filament for tarantula muscle contraction.     

Protist tubulins: new arrivals, evolutionary relationships and insights to cytoskeletal function

The protists exhibit probably the most extravagant expression of microtubule-containing structures found in any organism. These structures--flagella, cilia, axostyles, spindles and a veritable constellation of microtubule bundles and cortical arrays--provide shape, form, motility, anchorage and apparatuses for feeding. The cytoskeletal structures have a precise order (i.e. size, position and number) that must be replicated and segregated with fidelity at each division, some components being inherited conservatively and others semi-conservatively. Intriguingly, it is now apparent that much of the high-order organisation, which was recognised and described by light and electron microscopy during the last century, is a reflection of molecular polarities set by assembly of constituent proteins. Tubulins and microtubules lie at the heart of this morphogenetic pattern.     

Convergence in pigmentation at multiple levels: mutations,genes and function

Convergence—the independent evolution of the same trait by two or more taxa—has long been of interest to evolutionary biologists, but only recently has the molecular basis of phenotypic convergence been identified. Here, we highlight studies of rapid evolution of cryptic coloration in vertebrates to demonstrate that phenotypic convergence can occur at multiple levels: mutations, genes and gene function. We first show that different genes can be responsible for convergent phenotypes even among closely related populations, for example, in the pale beach mice inhabiting Florida''s Gulf and Atlantic coasts. By contrast, the exact same mutation can create similar phenotypes in distantly related species such as mice and mammoths. Next, we show that different mutations in the same gene need not be functionally equivalent to produce similar phenotypes. For example, separate mutations produce divergent protein function but convergent pale coloration in two lizard species. Similarly, mutations that alter the expression of a gene in different ways can, nevertheless, result in similar phenotypes, as demonstrated by sister species of deer mice. Together these studies underscore the importance of identifying not only the genes, but also the precise mutations and their effects on protein function, that contribute to adaptation and highlight how convergence can occur at different genetic levels.