Bacterial Evolution: Rewiring Modules to Get in Shape

SummaryBacterial species take on a wide variety of shapes, but the mechanisms by which specific shapes evolve have remained poorly understood. A recent study demonstrates that two Asticcacaulis species repurposed an ancestral regulatory protein to rewire the modules of stalk regulation, localization, and synthesis, thereby generating new shapes

The curved shape of Caulobacter crescentus enhances surface colonization in flow

Each bacterial species has a characteristic shape, but the benefits of specific morphologies remain largely unknown. To understand potential functions for cell shape, we focused on the curved bacterium Caulobacter crescentus. Paradoxically, C. crescentus curvature is robustly maintained in the wild but straight mutants have no known disadvantage in standard laboratory conditions. Here we demonstrate that cell curvature enhances C. crescentus surface colonization in flow. Imaging the formation of microcolonies at high spatial and temporal resolution indicates that flow causes curved cells to orient such that they arc over the surface, thereby decreasing the distance between the surface and polar adhesive pili, and orienting pili to face the surface. C. crescentus thus repurposes pilus retraction, typically used for surface motility, for surface attachment. The benefit provided by curvature is eliminated at high flow intensity, raising the possibility that diversity in curvature adapts related species for life in different flow environments

KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences.

BACKGROUND: Transposable element-embedded regulatory sequences (TEeRS) and their KRAB-containing zinc finger protein (KZFP) controllers are increasingly recognized as modulators of gene expression. We aim to characterize the contribution of this system to gene regulation in early human development and germ cells. RESULTS: Here, after studying genes driven by the long terminal repeat (LTR) of endogenous retroviruses, we identify the ape-restricted ZNF676 as the sequence-specific repressor of a subset of contemporary LTR12 integrants responsible for a large fraction of transpochimeric gene transcripts (TcGTs) generated during human early embryogenesis. We go on to reveal that the binding of this KZFP correlates with the epigenetic marking of these TEeRS in the germline, and is crucial to the control of genes involved in ciliogenesis/flagellogenesis, a biological process that dates back to the last common ancestor of eukaryotes. CONCLUSION: These results illustrate how KZFPs and their TE targets contribute to the evolutionary turnover of transcription networks and participate in the transgenerational inheritance of epigenetic traits

Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation

Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behavior. Bacterial biofilms are more than the sum of their parts: single-cell behavior has a complex relation to collective community behavior, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: we highlight the work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labor

Bacterial evolution: rewiring modules to get in shape

Bacterial species take on a wide variety of shapes, but the mechanisms by which specific shapes evolve have remained poorly understood. A recent study demonstrates that two Asticcacaulis species repurposed an ancestral regulatory protein to rewire the modules of stalk regulation, localization, and synthesis, thereby generating new shapes

MicroRNA profiling by simultaneous selective isotachophoresis and hybridization with molecular beacons

We present and demonstrate a novel assay for the detection and quantification of microRNA (miRNA) that leverages isotachophoresis (ITP) and molecular beacon (MB) hybridization. We use ITP to selectively preconcentrate miRNA from total RNA. We simultaneously focus MBs and use the ITP zone as a 10 pL reactor with active mixing where MBs fluoresce upon hybridization to target miRNA. To increase both sensitivity and selectivity, we leverage a multistage ITP strategy composed of three discrete regions of different concentrations of denaturant, sieving matrix, and magnesium chloride. We show that ITP hybridization is specific and selective to the miRNA target. We demonstrate ITP hybridization of miRNA in a biologically relevant case by detecting and quantifying miR-122 in human kidney and liver. ITP hybridization is a cheap, simple, high-speed, and amplification-free miRNA profiling method which requires small amounts (order 100 ng) of sample. The technique therefore represents an attractive alternative to PCR or Northern blot for miRNAs

MicroRNA profiling by simultaneous selective isotachophoresis and hybridization with molecular beacons

We present and demonstrate a novel assay for the detection and quantification of microRNA (miRNA) that leverages isotachophoresis (ITP) and molecular beacon (MB) hybridization. We use ITP to selectively preconcentrate miRNA from total RNA. We simultaneously focus MBs and use the ITP zone as a 10 pL reactor with active mixing where MBs fluoresce upon hybridization to target miRNA. To increase both sensitivity and selectivity, we leverage a multistage ITP strategy composed of three discrete regions of different concentrations of denaturant, sieving matrix, and magnesium chloride. We show that ITP hybridization is specific and selective to the miRNA target. We demonstrate ITP hybridization of miRNA in a biologically relevant case by detecting and quantifying miR-122 in human kidney and liver. ITP hybridization is a cheap, simple, high-speed, and amplification-free miRNA profiling method which requires small amounts (order 100 ng) of sample. The technique therefore represents an attractive alternative to PCR or Northern blot for miRNAs