At the end of the multistep transcription process, the elongating RNA polymerase (RNAP) is dislodged from the DNA template either at specific DNA sequences, called the terminators, or by a nascent ...RNA-dependent helicase, Rho. In
Escherichia coli
, about half of the transcription events are terminated by the Rho protein. Rho utilizes its RNA-dependent ATPase activities to translocate along the mRNA and eventually dislodges the RNAP via an unknown mechanism. The transcription elongation factor NusG facilitates this termination process by directly interacting with Rho. In this review, we discuss current models describing the mechanism of action of this hexameric transcription terminator, its regulation by different
cis
and
trans
factors, and the effects of the termination process on physiological processes in bacterial cells, particularly
E. coli
and
Salmonella enterica
Typhimurium.
One of the major ways of acquiring multidrug resistance in bacteria is via drug influx and efflux pathways. Here, we show that
with compromised Rho-dependent transcription termination function has ...enhanced broad-spectrum antibiotic susceptibility, which arises from the inefficient TolC-efflux process and increased permeability of the membrane. The Rho mutants have altered morphology, distinct cell surface, and increased levels of lipopolysaccharide in their outer membrane, which might have rendered the TolC efflux pumps inefficient. These alterations are due to the upregulations of poly-N-acetyl-glucosamine and lipopolysaccharide synthesis operons because of inefficient Rho functions. The Rho mutants are capable of growing on various dipeptides and carbohydrate sources, unlike their WT counterpart. Dipeptides uptake arises from the upregulations of the di-peptide permease operon in these mutants. The metabolomics of the Rho mutants revealed the presence of a high level of novel metabolites. Accumulation of these metabolites in these Rho mutants might titrate out the TolC-efflux pumps, which could further reduce their efficiency. We conclude that the transcription termination factor, Rho, regulates the broad-spectrum antibiotic susceptibility of
through multipartite pathways in a TolC-dependent manner. The involvement of Rho-dependent termination in multiple pathways and its association with antibiotic susceptibility should make Rho-inhibitors useful in the anti-bacterial treatment regimen.
In bacteria, transcription-coupled repair of DNA lesions initiates after the Mfd protein removes RNA polymerases (RNAPs) stalled at the lesions. The bacterial RNA helicase, Rho, is a transcription ...termination protein that dislodges the elongation complexes. Here, we show that Rho dislodges the stalled RNAPs at DNA lesions. Strains defective in both Rho and Mfd are susceptible to DNA-damaging agents and are inefficient in repairing or propagating UV-damaged DNA. In vitro transcription assays show that Rho dissociates the stalled elongation complexes at the DNA lesions. We conclude that Rho-dependent termination recycles stalled RNAPs, which might facilitate DNA repair and other DNA-dependent processes essential for bacterial cell survival. We surmise that Rho might compete with, or augment, the Mfd function.
The nickel–ceria nanocomposite coatings have been pulse electrodeposited from a Watts-type electrolyte containing nano-sized ceria particles have been synthesized by high energy ball milling ...technique. The influence of the stirring rate of the plating bath on the microstructure and hardness of nickel–ceria nanocomposite coating has been investigated and the corrosion property of the nanocomposite coatings has also been studied. Experimental results show that both the co-deposition of ceria particles in the Ni matrix and microhardness of the composite coating increase up to the stirring rate of 450rpm. Beyond this stirring rate the co-deposition of ceria particles decreases in the Ni matrix resulting in a decrease in the hardness of the composite coating. Another reason of decreasing hardness of the composite coating is the agglomerations of ceria particles that take place after the stirring rate of 450rpm. Higher corrosion resistance has been found for the nickel–ceria nanocomposite coating electrodeposited from electrolyte with the stirring rate of 450rpm.
► The nano-sized ceria, produced by high energy ball milling technique, co-electrodeposited successfully in the nanocrystalline nickel matrix for producing Ni-CeO2 nanocomposite. ► SEM micrographs reveal that the approximately uniform distribution of the ceria in the nickel matrix upto the stirring rate of 450 rpm, beyond that agglomeration of ceria take place in the coating with pits. ► The hardness of the nanocomposite coating increases with the increase of the stirring rate upto 450 rpm. Beyond this amount, the hardness decreases due to agglomeration of the ceria particles in the nickel matrix. ► For Ni–CeO2 nanocomposite coatings the polarization resistance increases and corrosion rate decreases upto the stirring rate of 450 rpm.
A decline of skeletal muscle strength with aging is a primary cause of mobility loss and frailty in older persons, but the molecular mechanisms of such decline are not understood. Here, we performed ...quantitative proteomic analysis from skeletal muscle collected from 58 healthy persons aged 20 to 87 years. In muscle from older persons, ribosomal proteins and proteins related to energetic metabolism, including those related to the TCA cycle, mitochondria respiration, and glycolysis, were underrepresented, while proteins implicated in innate and adaptive immunity, proteostasis, and alternative splicing were overrepresented. Consistent with reports in animal models, older human muscle was characterized by deranged energetic metabolism, a pro-inflammatory environment and increased proteolysis. Changes in alternative splicing with aging were confirmed by RNA-seq analysis. We propose that changes in the splicing machinery enables muscle cells to respond to a rise in damage with aging.
Understanding the topological configurations of chromatin may reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here, we generate ...high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor cells. We observe a hierarchy of 3D interactions that undergo marked reorganization at the submegabase scale during differentiation. Distinct combinations of CCCTC-binding factor (CTCF), Mediator, and cohesin show widespread enrichment in chromatin interactions at different length scales. CTCF/cohesin anchor long-range constitutive interactions that might form the topological basis for invariant subdomains. Conversely, Mediator/cohesin bridge short-range enhancer-promoter interactions within and between larger subdomains. Knockdown of Smc1 or Med12 in embryonic stem cells results in disruption of spatial architecture and downregulation of genes found in cohesin-mediated interactions. We conclude that cell-type-specific chromatin organization occurs at the submegabase scale and that architectural proteins shape the genome in hierarchical length scales.
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•Genome architecture is reorganized at the sub-Mb scale during differentiation•CTCF, Mediator, and cohesin have widespread and unique roles in genome organization•CTCF and cohesin anchor long-range, constitutive interactions•Mediator and cohesin bridge short-range, cell-type-specific interactions
The differentiation of embryonic stem cells to neural progenitors is accompanied by submegabase changes in chromatin architecture. Distinct combinations of CTCF, Mediator and cohesin play specific roles in this chromatin reorganization, maintaining long-range interactions, while facilitating changes in short-range, promoter-enhancer contacts.
α-Synuclein (α-syn) is a pre-synaptic protein which progressively accumulates in neuronal and non-neuronal cells in neurodegenerative diseases such as Parkinson's disease (PD), dementia with Lewy ...bodies (DLB), and multiple system atrophy. Recent evidence suggests that aberrant immune activation may be involved in neurodegeneration in PD/DLB. While previous studies have often focused on the microglial responses, less is known about the role of the peripheral immune system in these disorders.
To understand the involvement of the peripheral immune system in PD/DLB, we evaluated T cell populations in the brains of α-syn transgenic (tg) mice (e.g., Thy1 promoter line 61) and DLB patients.
Immunohistochemical analysis showed perivascular and parenchymal infiltration by CD3+/CD4+ helper T cells, but not cytotoxic T cells (CD3+/CD8+) or B cells (CD20+), in the neocortex, hippocampus, and striatum of α-syn tg mice. CD3+ cells were found in close proximity to the processes of activated astroglia, particularly in areas of the brain with significant astrogliosis, microgliosis, and expression of pro-inflammatory cytokines. In addition, a subset of CD3+ cells co-expressed interferon γ. Flow cytometric analysis of immune cells in the brains of α-syn tg mice revealed that CD1d-tet+ T cells were also increased in the brains of α-syn tg mice suggestive of natural killer T cells. In post-mortem DLB brains, we similarly detected increased numbers of infiltrating CD3+/CD4+ T cells in close proximity with blood vessels.
These results suggest that infiltrating adaptive immune cells play an important role in neuroinflammation and neurodegeneration in synucleinopathies and that modulating peripheral T cells may be a viable therapeutic strategy for PD/DLB.
Age-associated changes in gene expression in skeletal muscle of healthy individuals reflect accumulation of damage and compensatory adaptations to preserve tissue integrity. To characterize these ...changes, RNA was extracted and sequenced from muscle biopsies collected from 53 healthy individuals (22-83 years old) of the GESTALT study of the National Institute on Aging-NIH. Expression levels of 57,205 protein-coding and non-coding RNAs were studied as a function of aging by linear and negative binomial regression models. From both models, 1134 RNAs changed significantly with age. The most differentially abundant mRNAs encoded proteins implicated in several age-related processes, including cellular senescence, insulin signaling, and myogenesis. Specific mRNA isoforms that changed significantly with age in skeletal muscle were enriched for proteins involved in oxidative phosphorylation and adipogenesis. Our study establishes a detailed framework of the global transcriptome and mRNA isoforms that govern muscle damage and homeostasis with age.
The life cycle of phonological processes (e.g. Bermúdez-Otero 2015) provides an account of how a sound change might develop over the history of a language, from its beginnings in the pressures of ...speaking and hearing, through its progress to a cognitively-controlled process and maturation into a categorical phenomenon, to its final resting-place as a lexical or morphological pattern. It has been the subject of increased research in recent times, but has faced strikingly few challenges to its diachronic aspects, notably its predictions of unidirectionality and cycle-based dialectal splits. Furthermore, the cognitive mechanisms rooted in morpheme-based learning which are required to predict domain narrowing (phrase > word > stem) rather than broadening need to be tested through child (and adult) acquisition studies. This paper examines how a historical phonologist might go about interrogating the life-cycle model using extensive historical data spanning several centuries, and methodically ascertaining what the model predicts in order to know what to look for. The paper concludes by briefly addressing some of the many other questions raised by the model which have faced comparatively little investigation given the purported pervasiveness of the life cycle.
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