selected publicatons
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Morris A, Hoopman J, Nandana V, Lian CG, Pochet E, Ruiz M, Su B, Efimov A, Myers C, Tao Y, Saieva L, Lu G, Golemis E, Pellizzoni L, Chen L. Intranucleolar Invasion of Cajal Body Remnants Suppresses Ribosomal Biogenesis in cis and Telomerase Functions in trans. bioRxiv 2026.
Depletion of a key snRNP chaperone protein, SMN leads to disruption of Cajal body and mis-localization of its key scaffold protein Coilin and its interactors to nucleolus suppressing rRNA production and telomeric synthesis. This was demonstrated by employing advance technologies such as 3D-holotomography and CUT&RUN assays.
de Amorim AM, Xue G, Dittmers T, He W, Lewandowski S, Borrajero CP, Bethmann J, Mateva N, Krage C, Nandana V, Hennig J, Urlaub H, Marzluff WF, Chakrabarti. Molecular mechanisms of recruitment, function and regulation of the RNA helicase UPF1 in replication-dependent histone mRNA decay. Nature Communications 2026.
Replication dependent histone mRNAs have an interesting feature at their 3' end, a stem loop structure decorated by RNA binding proteins. While this RNP is crucial for histone mRNA biogenesis, it also poses a hindrance for histone mRNA decay. In this structural biochemistry paper, we found that while RNA dependent helicase UPF1 at the 5' end of histone mRNA stem loop enhances histone mRNA decay by 3'-5' exonuclease 3'hExo, UPF1's helicase activity is strictly not required for enhancement of histone mRNA decay.
Ortiz-Rodríguez, L.A., Yassine H., Hatami A., Nandana V., Azaldegui C.A., Cheng J., Zhu Y., Schrader J.M., Biteen J.S. Stress Changes the Material State of a Bacterial Biomolecular Condensate and Shifts its Function from mRNA Decay to Storage. Nature Communications 2025.
Bacterial Ribonucleoprotein body (BR-body) organizes mRNA decay in actively growing bacterial cells but how does BR-body behave in stressed bacterial cells? Employing single molecule microscopy, cell biology and in-vitro reconstitutions, we show in stressed bacterial cells BR-body changes its material property and becomes solid-like which inhibits mRNA decay and acts as a RNA storage compartment. This paper has been highlighted as the 'Editors pick'.
Mallikaarachchi KS, Huang JL, Madras S, Cuellar RA, Huang Z, Gega A, Rathnayaka-Mudiyanselage IW, Nandana V, Al-Husini N, Saldaña Rivera N, Ma LH, Ng E, Christensen K, Pendar N, Li S, Deleon NR, Chen JC, Schrader JM. 2025. Sinorhizobium meliloti BR-bodies promote fitness during host colonization. mBio 2025.
This paper examine the functions of BR-bodies in the nitrogen-fixing endosymbiont Sinorhizobium meliloti, which colonizes the roots of compatible legume plants. Employing a combination of in-vitro, in-vivo and RNA-seq methods, we show that the absence of BR-bodies results in slower mRNA decay, sensitivity to environmental stresses, and ineffective symbiosis, suggesting that BR-bodies play critical roles in regulating biochemical pathways and promoting fitness during host colonization.
Nandana, V., Al-Husini, N., Vaishnav, A., Dilrangi, K.H., and Schrader, J.M. Caulobacter crescentus RNase E condensation contributes to autoregulation and fitness. Molecular Biology of the Cell 2024.
Endonucleases such as RNase E have an autoregulation mechanism to keep their enzymatic activity in check to prevent uncontrolled RNA cleavage. In this paper we found that RNase E from fresh water bacteria Caulobacter crescentus is no exception. What is more interesting is the condensation property of RNase E that enhances this autoregulation mechanism.
IW Rathnayaka-Mudiyanselage, V Nandana, JM Schrader. Proteomic composition of eukaryotic and bacterial RNA decay condensates suggests convergent evolution. Current Opinion in Microbiology 2024.
This review article is follow-up of our BR-body proteomics paper. Here we make interesting parallels between bacterial and eukaryotic RNA decay condensates. Despite using fundamentally different molecular machinery, bacterial BR-bodies and eukaryotic RNA decay condensates have evolved strikingly similar protein compositions and functions, indicating that biomolecular condensates represent a universal and evolutionarily convergent strategy for organizing RNA metabolism.
Nandana, V., Rathnayaka-Mudiyanselage, I.W., Muthunayake, N.S., Hatami, A. Mousseau, C.B., Ortiz-Rodríguez, L.A., Vaishnav, J., Collins, M., Gega, A., Mallikaarachchi, K.S., Yassine, H., Ghosh,A., Biteen, J.S., Zhu, Y., Champion, M.M., Childers, W.S., Schrader, J.M. The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions. Cell Reports 2023.
Mass-spectrometry analysis combined with in-vitro reconstitutions, cell biology and microscopy revealed that bacterial biomolecular condensate organizing mRNA decay (BR-body) is enriched with about 100 proteins of various molecular pathways including transcription termination, translation regulation, CH and CHO metabolism reflecting the existence of heterogenous BR-bodies. What is intriguing is the utilization of an endonuclease RNase E as the central scaffolding protein of heterogenous BR-bodies that are specialized in organizing various molecular pathways. This study is the first proteomic study of a bacterial biomolecular condensate.
Collins, M.J., Tomares, D.T., Nandana, V, Schrader J.M, Childers, W.S. RNase E biomolecular condensates stimulate PNPase activity. Scientific Reports 2023.
RNase E phase separation creates specialized biomolecular condensates that recruit PNPase and enhance its catalytic efficiency and substrate selectivity. This enhancement arises primarily from scaffolding and concentration effects within the condensate rather than direct allosteric activation. Furthermore, phosphate, a critical PNPase reactant, negatively regulates RNase E phase separation, establishing a feedback loop that couples environmental phosphate availability to BR-body formation and RNA degradation. These findings reveal how bacterial biomolecular condensates actively regulate enzyme function and RNA metabolism rather than merely serving as passive sites of localization.
Nandana V, Schrader J.M. Roles of liquid-liquid phase separation in bacterial RNA metabolism. Current Opinion in Microbiology 2021.
Review article highlighting the widespread observation of biomolecular condensates in bacterial RNA metabolism. This article also draws interesting parallels nucleolus in eukaryotes and nucleolus like structure in bacteria.