Single-Molecule/Cell Analyses Reveal Principles of Genome-Folding Mechanisms in the Three Domains of Life

Comparative structural/molecular biology by single-molecule analyses combined with single-cell dissection, mass spectroscopy, and biochemical reconstitution have been powerful tools for elucidating the mechanisms underlying genome DNA folding. All genomes in the three domains of life undergo stepwise folding from DNA to 30–40 nm fibers. Major protein players are histone (Eukarya and Archaea), Alba (Archaea), and HU (Bacteria) for fundamental structural units of the genome. In Euryarchaeota, a major archaeal phylum, either histone or HTa (the bacterial HU homolog) were found to wrap DNA. This finding divides archaea into two groups: those that use DNA-wrapping as the fundamental step in genome folding and those that do not. Archaeal transcription factor-like protein TrmBL2 has been suggested to be involved in genome folding and repression of horizontally acquired genes, similar to bacterial H-NS protein. Evolutionarily divergent SMC proteins contribute to the establishment of higher-order structures. Recent results are presented, including the use of Hi-C technology to reveal that archaeal SMC proteins are involved in higher-order genome folding, and the use of single-molecule tracking to reveal the detailed functions of bacterial and eukaryotic SMC proteins. Here, we highlight the similarities and differences in the DNA-folding mechanisms in the three domains of life.

Septin-microtubule association via a motif unique to the isoform 1 of septin 9 tunes stress fibers

Septins, a family of GTP-binding proteins assembling into higher order structures, interface with the membrane, actin filaments and microtubules, which positions them as important regulators of cytoarchitecture. Septin 9 (SEPT9), which is frequently overexpressed in tumors and mutated in hereditary neuralgic amyotrophy (HNA), mediates the binding of septins to microtubules, but the molecular determinants of this interaction remained uncertain. We demonstrate that a short MAP-like motif unique to SEPT9 isoform 1 (SEPT9_i1) drives septin octamer-microtubule interaction in cells and in vitro reconstitutions. Septin-microtubule association requires polymerizable septin octamers harboring SEPT9_i1. Although outside of the MAP-like motif, HNA mutations abrogates this association, identifying a putative regulatory domain. Removal of this domain from SEPT9_i1 sequesters septins on microtubules, promotes microtubule stability and alters actomyosin fiber distribution and tension. Thus, we identify key molecular determinants and potential regulatory roles of septin-microtubule interaction, paving the way to deciphering the mechanisms underlying septin-associated pathologies.

Bayesian Covariance Representation with Global Informative Prior for 3D Action Recognition

For the merits of high-order statistics and Riemannian geometry, covariance matrix has become a generic feature representation for action recognition. An independent action can be represented by an empirical statistics over all of its pose samples. Two major problems of covariance include the following: (1) it is prone to be singular so that actions fail to be represented properly, and (2) it is short of global action/pose-aware information so that expressive and discriminative power is limited. In this article, we propose a novel Bayesian covariance representation by a prior regularization method to solve the preceding problems. Specifically, covariance is viewed as a parametric maximum likelihood estimate of Gaussian distribution over local poses from an independent action. Then, a Global Informative Prior (GIP) is generated over global poses with sufficient statistics to regularize covariance. In this way, (1) singularity is greatly relieved due to sufficient statistics, (2) global pose information of GIP makes Bayesian covariance theoretically equivalent to a saliency weighting covariance over global action poses so that discriminative characteristics of actions can be represented more clearly. Experimental results show that our Bayesian covariance with GIP efficiently improves the performance of action recognition. In some databases, it outperforms the state-of-the-art variant methods that are based on kernels, temporal-order structures, and saliency weighting attentions, among others.

Septin Assembly and Remodeling at the Cell Division Site During the Cell Cycle

The septin family of proteins can assemble into filaments that further organize into different higher order structures to perform a variety of different functions in different cell types and organisms. In the budding yeast Saccharomyces cerevisiae, the septins localize to the presumptive bud site as a cortical ring prior to bud emergence, expand into an hourglass at the bud neck (cell division site) during bud growth, and finally “split” into a double ring sandwiching the cell division machinery during cytokinesis. While much work has been done to understand the functions and molecular makeups of these structures, the mechanisms underlying the transitions from one structure to another have largely remained elusive. Recent studies involving advanced imaging and in vitro reconstitution have begun to reveal the vast complexity involved in the regulation of these structural transitions, which defines the focus of discussion in this mini-review.

The Structural Biology of Septins and Their Filaments: An Update

In order to fully understand any complex biochemical system from a mechanistic point of view, it is necessary to have access to the three-dimensional structures of the molecular components involved. Septins and their oligomers, filaments and higher-order complexes are no exception. Indeed, the spontaneous recruitment of different septin monomers to specific positions along a filament represents a fascinating example of subtle molecular recognition. Over the last few years, the amount of structural information available about these important cytoskeletal proteins has increased dramatically. This has allowed for a more detailed description of their individual domains and the different interfaces formed between them, which are the basis for stabilizing higher-order structures such as hexamers, octamers and fully formed filaments. The flexibility of these structures and the plasticity of the individual interfaces have also begun to be understood. Furthermore, recently, light has been shed on how filaments may bundle into higher-order structures by the formation of antiparallel coiled coils involving the C-terminal domains. Nevertheless, even with these advances, there is still some way to go before we fully understand how the structure and dynamics of septin assemblies are related to their physiological roles, including their interactions with biological membranes and other cytoskeletal components. In this review, we aim to bring together the various strands of structural evidence currently available into a more coherent picture. Although it would be an exaggeration to say that this is complete, recent progress seems to suggest that headway is being made in that direction.

A Trypanosoma brucei orphan kinesin employs a convergent microtubule organization strategy to complete cytokinesis

Many single-celled eukaryotes have complex cell morphologies defined by cytoskeletal elements comprising microtubules arranged into higher-order structures. Trypanosoma brucei (T. brucei) cell polarity is mediated by a parallel array of microtubules that underlie the plasma membrane and define the auger-like shape of the parasite. The subpellicular array must be partitioned and segregated using a microtubule-based mechanism during cell division. We previously identified an orphan kinesin, KLIF, that localizes to the division plane and is essential for the completion of cytokinesis. To gain mechanistic insight into how this novel kinesin functions to complete cleavage furrow ingression, we characterized the biophysical properties of the KLIF motor domain in vitro. We found that KLIF is a non-processive dimeric kinesin that dynamically crosslinks microtubules. Microtubules crosslinked in an antiparallel orientation are translocated relative to one another by KLIF, while microtubules crosslinked parallel to one another remain static, resulting in the formation of organized parallel bundles. In addition, we found that KLIF stabilizes the alignment of microtubule plus ends. These features provide a mechanistic understanding for how KLIF functions to form a new pole of aligned microtubule plus ends that defines the shape of the new posterior, which is a unique requirement for the completion of cytokinesis in T. brucei.

Stable Fluorescence of Eu3+ Complex Nanostructures Beneath a Protein Skin for Potential Biometric Recognition

We designed and realized highly fluorescent nanostructures composed of Eu3+ complexes under a protein coating. The nanostructured material, confirmed by photo-induced force microscopy (PiFM), includes a bottom fluorescent layer and an upper protein layer. The bottom fluorescent layer includes Eu3+ that is coordinated by 1,10-phenanthroline (Phen) and oleic acid (O). The complete complexes (OEu3+Phen) formed higher-order structures with diameter 40–150 nm. Distinctive nanoscale striations reminiscent of fingerprints were observed with a high-resolution transmission electron microscope (HRTEM). Stable fluorescence was increased by the addition of Eu3+ coordinated by Phen and 2-thenoyltrifluoroacetone (TTA), and confirmed by fluorescence spectroscopy. A satisfactory result was the observation of red Eu3+ complex emission through a protein coating layer with a fluorescence microscope. Lanthanide nanostructures of these types might ultimately prove useful for biometric applications in the context of human and non-human tissues. The significant innovations of this work include: (1) the structural set-up of the fluorescence image embedded under protein “skin”; and (2) dual confirmations of nanotopography and unique nanofingerprints under PiFM and under TEM, respectively.