Search bioRxiv⌕ Search

Biology subjects

Ray, M. K.

Publications and source records attributed to Ray, M. K..

6 recordsLinked to original sources

A targeted bispecific TGFBR2 antagonist antibody demonstrates cell selectivity and enhanced potency on human fibroblasts

Beyond its critical roles in development and tissue homeostasis, TGF{beta} signaling promotes key aspects of cancer progression and is a primary driver of fibrosis. Although blocking TGF{beta} signaling has great therapeutic potential for cancer and fibrotic diseases such as idiopathic pulmonary fibrosis (IPF), preclinical and clinical studies revealed that non-specific alteration of the pathway can have severe adverse consequences; therefore, inhibiting TGF{beta} signaling in a cell-type specific manner may avoid systemic toxic effects while preserving potential therapeutic effects. The parasitic helminth Heligmosomoides polygyrus has evolved cell-type-targeted modulators of TGF{beta} signaling. With insights from the development of other targeted signaling modulators and using the worm proteins as a guide, we sought to develop a human-fibroblast-targeted TGFBR2 antagonist. Here, we report mechanistic insights into the targeted worm TGFBR2 antagonist TGM6 and fusion proteins containing the TGM6 targeting domains. We created a bispecific antibody TGFBR2 antagonist that binds PDGFRA as a targeting receptor and demonstrates cell selectivity and enhanced potency in fibroblasts. Our findings suggest a viable path for developing targeted TGF{beta} signaling antagonists as therapeutics for cancer and tissue fibrosis.

cell biology↗

Generation of a Nr2f2-driven inducible Cre mouse to target interstitial cells in the reproductive system

The orphan nuclear receptor Nr2f2, also known as COUP-TFII, play important roles in development and function of multiple organs, including the reproductive system. NR2F2 is expressed in the interstitial cells of both embryonic and adult testes, ovaries, and reproductive tracts. Taking advantage of such unique expression pattern, we have developed a tamoxifen inducible Cre model, Nr2f2-iCreERT2, which specifically and efficiently targets interstitial cells in both male and female reproductive organs across embryonic and adult stages. This model offers a powerful tool for gene knockout studies specifically in the interstitial compartment, without affecting the supporting or germ cells. Additionally, it enables interstitial cell lineage tracing, facilitating the assessment of the interstitials contribution to non-interstitial cell types during development and differentiation.

developmental biology↗

Re-examination of the taxonomic status of the Antarctic Pseudomonas syringae Lz4W isolate and proposal to rename it as a novel species Pseudomonas cryophila sp. nov.

A taxonomic re-evaluation of the Antarctic psychrotrophic bacterium Pseudomonas syringae Lz4W was performed in the light of its available genome sequence and due to a revision in the key phenotypic characteristics that are in conflict with the "syringae" group of Pseudomonads. A 16S rRNA gene sequence based phylogenetic analysis suggested that Lz4WT strain belongs to "fragi" cluster of Pseudomonas species, with closest similarity (99.72%) to the type strain P. deceptionensis M1T. However, in silico analysis of the Lz4W genome sequence using SpecI (species identification tools), ANI (average nucleotide identity), and GBDP (Genome Blast Distance phylogeny) methods suggest that Lz4WT strain cannot be delineated with any of the type strains of "fragi" cluster of species. Based on predictive low DNA-DNA hybridization value (<29.9%) and differences in phenotypic features with the related species we suggest that Lz4WT is a novel species under the Pseudomonas genus, and we propose that the strain be named as Pseudomonas cryophila sp. nov. The type strain is Lz4WT (=CFBP 8403T =KCTC 42933T =LMG 29591T =MTCC 673T).

microbiology↗

Exoribonuclease RNase R protects Antarctic Pseudomonas syringae Lz4W from DNA damage and oxidative stress

RNase R is a highly processive, 3 -5 exoribonuclease involved in RNA degradation, maturation, and processing in bacteria. In Pseudomonas syringae Lz4W, RNase R interacts with RNase E to form the RNA degradosome complex and is essential for growth at low temperature. RNase R is also implicated in general stress response in many bacteria. We show here that the deletion mutant of rnr gene (encoding RNase R) of P. syringae is highly sensitive to various DNA damaging agents and oxidative stress. RNase R is a multidomain protein comprised of CSD, RNB and S1 domains. We investigated the role of each domain of RNase R and its exoribonuclease activity in nucleic acid damage and oxidative stress response. Our results revealed that the RNB domain alone without its exoribonuclease activity is sufficient to protect against DNA damage and oxidative stress. We also show that the association of RNase R with the degradosome complex is not required for this function. Our study has discovered for the first time a hitherto unknown role of RNase R in protecting P. syringae Lz4W against DNA damage and oxidative stress. ImportanceBacterial exoribonucleases play a crucial role in RNA maturation, degradation, quality control and turnover. In this study, we have uncovered a previously unknown role of 3-5 exoribonuclease RNase R of P. syringae Lz4W in DNA damage and oxidative stress response. Here, we show that neither the exoribonuclease function of RNase R, nor its association with the RNA degradosome complex is essential for this function. Interestingly, in P. syringae Lz4W, hydrolytic RNase R exhibits physiological roles similar to phosphorolytic 3-5 exoribonuclease PNPase of E. coli. Our data suggest that during the course of evolution, mesophilic E. coli and psychrotrophic P. syringae have apparently swapped these exoribonucleases to adapt to their respective environmental growth conditions.

microbiology↗

Role of DEAD Box RNA helicases in low temperature adapted growth of Antarctic Pseudomonas syringae Lz4W

Nucleic acid metabolism plays an important role in adaptation of organisms to environment. For adaptation to cold environment, organisms need to overcome the impediments in complex RNA secondary structures that are highly stabilized at low temperature affecting metabolism and growth of the organisms. Employing gene disruption through homologous recombination, we investigated the role of all major DEAD box RNA helicases (rhlE, srmB, csdA, dbpA and rhlB) in cold adapted growth of Pseudomonas syringae. Our findings concluded that srmB and dbpA genes are important for cold adapted growth, whereas csdA is indispensable for growth at low temperature. Helicase genes rhlB and rhlE have no appreciable role in cold adapted growth of Pseudomonas syringae. Functional complementation studies revealed that RNA helicases dont have any redundant functions, as the roles performed by different helicases are individual and specific.

microbiology↗

Biochemical Characterization of RecBCD Enzyme from An Antarctic Pseudomonas Species and Identification of Its Cognate Chi (χ) Sequence

Pseudomonas syringae Lz4W RecBCD enzyme, RecBCDPs, is a trimeric protein complex comprised of RecC, RecB, and RecD subunits. RecBCD enzyme is essential for P. syringae growth at low temperature, and it protects cells from low temperature induced replication arrest. In this study, we show that the RecBCDPs enzyme displays distinct biochemical behaviors. Unlike E. coli RecBCD enzyme, the RecD subunit is indispensable for RecBCDPs function. The RecD motor activity is essential for the Chi-like fragments production in P. syringae, highlighting a distinct role for P. syringae RecD subunit in DNA repair and recombination process. Further, the ssDNA-dependent endonuclease activity is notably absent in RecBCDPs enzyme. Here, we demonstrate that the RecBCDPs enzyme recognizes a unique octameric DNA sequence, 5'-GCTGGCGC-3' (ChiPs) that attenuates nuclease activity of the enzyme when it enters dsDNA from the 3'-end. We propose that the reduced translocation activities manifested by motor-defective mutants cause cold sensitivity in P. syrinage; emphasizing the importance of DNA processing and recombination functions in rescuing low temperature induced replication fork arrest.\n\nAbbreviations

biochemistry↗