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Author Arati Ramesh

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Discovery of iron-sensing bacterial riboswitches.

Siladitya Bandyopadhyay, Susmitnarayan Chaudhury, Dolly Mehta, Arati Ramesh,

Despite the central role of iron in biology, our understanding of how cells sense iron is limited to protein-dependent mechanisms. Here, we report the discovery of iron-sensing riboswitches (named Sensei). Present across bacterial phyla, these RNAs reside in the 5' untranslated regions or within coding regions of messenger RNAs (mRNAs) ... Read more >>

Nat Chem Biol (Nature chemical biology)
[2020, :]

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Diversity and prevalence of ANTAR RNAs across actinobacteria

Dolly Mehta, Arati Ramesh,

ABSTRACT Computational approaches are often used to predict regulatory RNAs in bacteria, but their success is limited to RNAs that are highly conserved across phyla, in sequence and structure. The ANTAR regulatory system consists of a family of RNAs (the ANTAR-target RNAs) that selectively recruit ANTAR proteins. This protein-RNA complex ... Read more >>

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Nitric oxide-inducible Fe-S cluster biogenesis enables Mycobacterium tuberculosis to persist in mice

Kushi Anand, Ashutosh Tripathi, Kaustubh Shukla, Nitish Malhotra, Anilkumar Jamithireddy, Rajiv Kumar Jha, Susmit Narayan Chaudhury, Raju Rajmani, Arati Ramesh, Valakunja Nagaraja, Balasubramanian Gopal, Ganesh Nagaraju, Aswin Sai Narain Seshayee, Amit Singh,

Abstract Host-inducible nitric oxide (NO) suppresses Mycobacterium tuberculosis ( Mtb ) without eradicating it. Mechanisms underlying the persistence of residual bacteria in a hostile host environment are not known. Since NO damages Fe-S clusters of essential enzymes, the mechanism used to repair Fe-S clusters could help Mtb persist in host ... Read more >>

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Discovery of ANTAR-RNAs and their Mechanism of Action in Mycobacteria.

Dolly Mehta, Anjali Koottathazhath, Arati Ramesh,

Non-coding RNAs play pivotal roles in bacterial signaling. However, RNAs from certain phyla (specially high-GC actinobacteria) still remain elusive. Here, by re-engineering the existing genome-wide search approach, we discover a family of structurally conserved RNAs that are present ubiquitously across actinobacteria, including mycobacteria. In vitro analysis shows that RNAs belonging ... Read more >>

J. Mol. Biol. (Journal of molecular biology)
[2020, 432(14):4032-4048]

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Non-coding RNAs control metabolic state in mycobacteria

Dolly Mehta, Anjali, Achuthan, Ritu Gupta, Arati Ramesh,

ABSTRACT Non-coding RNAs play pivotal roles in bacterial signaling. However, RNAs from certain phyla (specially high-GC actinobacteria) remain elusive. Here, by revamping existing approaches we discover a family of structurally conserved RNAs in actinobacteria. These RNAs function by the recruiting ANTAR proteins to select transcripts; regulating them via translational repression. ... Read more >>

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Loss of function from widely distributed, synonymous mutations at single codons

Kritika Gupta, Jyothi Prabha, Soumyanetra Chandra, Shruti Khare, Sonali Vishwa Mohan, Pehu Kohli, Aparna Asok, Harsha Gowda, Arati Ramesh, Raghavan Varadarajan,

Abstract Mutational tolerance inferred from laboratory-based mutational studies is typically much higher than observed natural sequence variation. Using saturation mutagenesis, we show that the ccdA antitoxin component of the ccdAB toxin-antitoxin system is unusually sensitive to mutation with over 60% of mutations leading to loss of function. Multi-base synonymous mutations ... Read more >>

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FMRP Interacts with C/D Box snoRNA in the Nucleus and Regulates Ribosomal RNA Methylation.

Michelle Ninochka D'Souza, Naveen Kumar Chandappa Gowda, Vishal Tiwari, Rosana Ottakandathil Babu, Praveen Anand, Sudhriti Ghosh Dastidar, Randhir Singh, Owen G James, Bhuvaneish Selvaraj, Rakhi Pal, Arati Ramesh, Sumantra Chattarji, Siddharthan Chandran, Akash Gulyani, Dasaradhi Palakodeti, Ravi S Muddashetty,

iScience (iScience)
[2019, 12:368]

Cited: 1 time

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FMRP Interacts with C/D Box snoRNA in the Nucleus and Regulates Ribosomal RNA Methylation.

Michelle Ninochka D'Souza, Naveen Kumar Chandappa Gowda, Vishal Tiwari, Rosana Ottakandathil Babu, Praveen Anand, Sudhriti Ghosh Dastidar, Randhir Singh, Owen G James, Bhuvaneish Selvaraj, Rakhi Pal, Arati Ramesh, Sumantra Chattarji, Siddharthan Chandran, Akash Gulyani, Dasaradhi Palakodeti, Ravi S Muddashetty,

FMRP is an RNA-binding protein that is known to localize in the cytoplasm and in the nucleus. Here, we have identified an interaction of FMRP with a specific set of C/D box snoRNAs in the nucleus. C/D box snoRNAs guide 2'O methylations of ribosomal RNA (rRNA) on defined sites, and ... Read more >>

iScience (iScience)
[2018, 9:399-411]

Cited: 2 times

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Second messenger - Sensing riboswitches in bacteria.

Arati Ramesh,

Signal sensing in bacteria has traditionally been attributed to protein-based factors. It is however becoming increasingly clear that bacteria also exploit RNAs to serve this role. This review discusses how key developmental processes in bacteria, such as community formation, choice of a sessile versus motile lifestyle, or vegetative growth versus ... Read more >>

Semin. Cell Dev. Biol. (Seminars in cell & developmental biology)
[2015, 47-48:3-8]

Cited: 6 times

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Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters.

Kazuhiro Furukawa, Arati Ramesh, Zhiyuan Zhou, Zasha Weinberg, Tenaya Vallery, Wade C Winkler, Ronald R Breaker,

Bacteria regularly encounter widely varying metal concentrations in their surrounding environment. As metals become depleted or, conversely, accrue to toxicity, microbes will activate cellular responses that act to maintain metal homeostasis. A suite of metal-sensing regulatory ("metalloregulatory") proteins orchestrate these responses by allosterically coupling the selective binding of target metals ... Read more >>

Mol Cell (Molecular cell)
[2015, 57(6):1088-1098]

Cited: 38 times

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Riboswitches. A riboswitch-containing sRNA controls gene expression by sequestration of a response regulator.

Sruti DebRoy, Margo Gebbie, Arati Ramesh, Jonathan R Goodson, Melissa R Cruz, Ambro van Hoof, Wade C Winkler, Danielle A Garsin,

The ethanolamine utilization (eut) locus of Enterococcus faecalis, containing at least 19 genes distributed over four polycistronic messenger RNAs, appears to be regulated by a single adenosyl cobalamine (AdoCbl)-responsive riboswitch. We report that the AdoCbl-binding riboswitch is part of a small, trans-acting RNA, EutX, which additionally contains a dual-hairpin substrate ... Read more >>

Science (Science (New York, N.Y.))
[2014, 345(6199):937-940]

Cited: 50 times

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Metabolite-binding ribozymes.

Arati Ramesh, Wade C Winkler,

Catalysis in the biological context was largely thought to be a protein-based phenomenon until the discovery of RNA catalysts called ribozymes. These discoveries demonstrated that many RNA molecules exhibit remarkable structural and functional versatility. By virtue of these features, naturally occurring ribozymes have been found to be involved in catalyzing ... Read more >>

Biochim. Biophys. Acta (Biochimica et biophysica acta)
[2014, 1839(10):989-994]

Cited: 4 times

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The mechanism for RNA recognition by ANTAR regulators of gene expression.

Arati Ramesh, Sruti DebRoy, Jonathan R Goodson, Kristina A Fox, Herbey Faz, Danielle A Garsin, Wade C Winkler,

ANTAR proteins are widespread bacterial regulatory proteins that have RNA-binding output domains and utilize antitermination to control gene expression at the post-initiation level. An ANTAR protein, EutV, regulates the ethanolamine-utilization genes (eut) in Enterococcus faecalis. Using this system, we present genetic and biochemical evidence of a general mechanism of antitermination ... Read more >>

PLoS Genet. (PLoS genetics)
[2012, 8(6):e1002666]

Cited: 25 times

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Insights into metalloregulation by M-box riboswitch RNAs via structural analysis of manganese-bound complexes.

Arati Ramesh, Catherine A Wakeman, Wade C Winkler,

The M-box riboswitch couples intracellular magnesium levels to expression of bacterial metal transport genes. Structural analyses on other riboswitch RNA classes, which typically respond to a small organic metabolite, have revealed that ligand recognition occurs through a combination of base-stacking, electrostatic, and hydrogen-bonding interactions. In contrast, the M-box RNA triggers ... Read more >>

J Mol Biol (Journal of molecular biology)
[2011, 407(4):556-570]

Cited: 20 times

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Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis.

Kristina A Fox, Arati Ramesh, Jennifer E Stearns, Agathe Bourgogne, Angelica Reyes-Jara, Wade C Winkler, Danielle A Garsin,

Ethanolamine, a product of the breakdown of phosphatidylethanolamine from cell membranes, is abundant in the human intestinal tract and in processed foods. Effective utilization of ethanolamine as a carbon and nitrogen source may provide a survival advantage to bacteria that inhabit the gastrointestinal tract and may influence the virulence of ... Read more >>

Proc. Natl. Acad. Sci. U.S.A. (Proceedings of the National Academy of Sciences of the United States of America)
[2009, 106(11):4435-4440]

Cited: 54 times

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Magnesium-sensing riboswitches in bacteria.

Arati Ramesh, Wade C Winkler,

All living organisms require mechanisms for coordination of intracellular metal concentrations. Many types of metal-sensing regulatory proteins have been described previously. Data in recent years have revealed that posttranscriptional mechanisms are also utilized for control of metal ion homeostasis in bacteria. In particular, two classes of RNA structural elements have ... Read more >>

RNA Biol (RNA biology)
[2010, 7(1):77-83]

Cited: 29 times

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Multiple metal-binding cores are required for metalloregulation by M-box riboswitch RNAs.

Catherine A Wakeman, Arati Ramesh, Wade C Winkler,

Riboswitches are regulatory RNAs that control downstream gene expression in response to direct association with intracellular metabolites or metals. Typically, riboswitch aptamer domains bind to a single small-molecule metabolite. In contrast, an X-ray crystallographic structural model for the M-box riboswitch aptamer revealed the absence of an organic metabolite ligand but ... Read more >>

J Mol Biol (Journal of molecular biology)
[2009, 392(3):723-735]

Cited: 17 times

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Crystal structure of Rsr, an ortholog of the antigenic Ro protein, links conformational flexibility to RNA binding activity.

Arati Ramesh, Christos G Savva, Andreas Holzenburg, James C Sacchettini,

Ro ribonucleoproteins are a class of antigenic ribonucleoproteins associated with rheumatic autoimmune diseases like systemic lupus erythematosus and Sjögrens syndrome in humans. Ro ribonucleoproteins are mostly composed of the 60-kDa Ro protein and small cytoplasmic RNAs, called Y RNAs, of unknown function. In eukaryotes, where Ro has been found to ... Read more >>

J. Biol. Chem. (The Journal of biological chemistry)
[2007, 282(20):14960-14967]

Cited: 8 times

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CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator.

Tong Liu, Arati Ramesh, Zhen Ma, Sarah K Ward, Limei Zhang, Graham N George, Adel M Talaat, James C Sacchettini, David P Giedroc,

Copper is an essential element that becomes highly cytotoxic when concentrations exceed the capacity of cells to sequester the ion. Here, we identify a new copper-specific repressor (CsoR) of a copper-sensitive operon (cso) in Mycobacterium tuberculosis (Mtb) that is representative of a large, previously uncharacterized family of proteins (DUF156). Electronic ... Read more >>

Nat. Chem. Biol. (Nature chemical biology)
[2007, 3(1):60-68]

Cited: 177 times

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