title: Unique subunit packing in mycobacterial nanoRNase leads to alternate substrate recognitions in DHH phosphodiesterases.
abstract: DHH superfamily includes RecJ, nanoRNases (NrnA), cyclic nucleotide phosphodiesterases and pyrophosphatases. In this study, we have carried out in vitro and in vivo investigations on the bifunctional NrnA-homolog from Mycobacterium smegmatis, MSMEG_2630. The crystal structure of MSMEG_2630 was determined to 2.2-Å resolution and reveals a dimer consisting of two identical subunits with each subunit folding into an N-terminal DHH domain and a C-terminal DHHA1 domain. The overall structure and fold of the individual domains is similar to other members of DHH superfamily. However, MSMEG_2630 exhibits a distinct quaternary structure in contrast to other DHH phosphodiesterases. This novel mode of subunit packing and variations in the linker region that enlarge the domain interface are responsible for alternate recognitions of substrates in the bifunctional nanoRNases. MSMEG_2630 exhibits bifunctional 3'-5' exonuclease [on both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) substrates] as well as CysQ-like phosphatase activity (on pAp) in vitro with a preference for nanoRNA substrates over single-stranded DNA of equivalent lengths. A transposon disruption of MSMEG_2630 in M. smegmatis causes growth impairment in the presence of various DNA-damaging agents. Further phylogenetic analysis and genome organization reveals clustering of bacterial nanoRNases into two distinct subfamilies with possible role in transcriptional and translational events during stress.
authors.affiliation: CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India.
authors.forename: Rajpal
authors.initials: R
authors.lastname: Srivastav
authors.affiliation: CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India.
authors.forename: Dilip
authors.initials: D
authors.lastname: Kumar
authors.affiliation: CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India.
authors.forename: Amit
authors.initials: A
authors.lastname: Grover
authors.affiliation: CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India.
authors.forename: Ajit
authors.initials: A
authors.lastname: Singh
authors.affiliation: European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, Grenoble 38042, France Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, Grenoble 38042, France.
authors.forename: Babu A
authors.initials: BA
authors.lastname: Manjasetty
authors.affiliation: CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India rsharma@igib.res.in.
authors.forename: Rakesh
authors.initials: R
authors.lastname: Sharma
authors.affiliation: CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India btaneja@igib.res.in.
authors.forename: Bhupesh
authors.initials: B
authors.lastname: Taneja
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics / Q000378:metabolism; D020134:Catalytic Domain; D005092:Exonucleases / Q000378:metabolism; D008958:Models, Molecular; D009154:Mutation; D020102:Mycobacterium smegmatis / Q000201:enzymology*; D009876:Operon; D010727:Phosphoric Diester Hydrolases / Q000378:metabolism; D010744:Phosphoric Monoester Hydrolases / Q000378:metabolism; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000737:chemistry / Q000145:classification / Q000235:genetics / Q000378:metabolism; D012260:Ribonucleases / Q000737:chemistry* / Q000145:classification / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D021122:Protein Subunits; D005092:Exonucleases; D012260:Ribonucleases; D010744:Phosphoric Monoester Hydrolases; D010727:Phosphoric Diester Hydrolases