Elucidating the mechanism of DNA-dependent ATP hydrolysis mediated by DNA-dependent ATPase A, a member of the SWI2/SNF2 protein family

The active DNA-dependent ATPase A domain (ADAAD), a member of the SWI2/SNF2 family, has been shown to bind DNA in a structure-specific manner, recognizing DNA molecules possessing double-stranded to single-stranded transition regions leading to ATP hydrolysis. Extending these studies we have delineated the structural requirements of the DNA effector for ADAAD and have shown that the single-stranded and double-stranded regions both contribute to binding affinity while the double-stranded region additionally plays a role in determining the rate of ATP hydrolysis. We have also investigated the mechanism of interaction of DNA and ATP with ADAAD and shown that each can interact independently with ADAAD in the absence of the other. Furthermore, the protein can bind to dsDNA as well as ssDNA molecules. However, the conformation change induced by the ssDNA is different from the conformational change induced by stem-loop DNA (slDNA), thereby providing an explanation for the observed ATP hydrolysis only in the presence of the double-stranded:single-stranded transition (i.e. slDNA)

Molecular insight into the expression of metal transporter genes in Chryseobacterium sp. PMSZPI isolated from uranium deposit.

Metal tolerant bacterium Chryseobacterium sp. PMSZPI previously isolated and characterized from uranium ore deposit was studied for elucidating the role of metal transporter genes belonging to the Cation Diffusion Facilitator (CDF), Root-Nodulation-Division (RND) and PIB-type ATPase family in cadmium and uranium tolerance. The bacterium showed tolerance towards cadmium (MIC~6mM) and uranium (MIC~2mM) and was found to harbor metal transporter genes belonging to CDF, RND and PIB-type ATPase family of proteins. Expression studies by real-time PCR showed an upregulation of czcA(RND), czcD(CDF) and cadA(PIB-type ATPase) genes in presence of cadmium or uranium. Higher expression of czcA and czcD was found when the bacterium was treated with cadmium and uranium respectively. This study provides significant insight into the molecular mechanism that plays a role in cadmium and uranium tolerance in bacteria

Growth media composition and heavy metal tolerance behaviour of bacteria characterized from the sub-surface soil of uranium rich ore bearing site of Domiasiat in Meghalaya

115-119Enrichment based cultivation method was utilised to isolate uranium (U)-tolerant bacteria from the sub-surface soil of U-rich ore bearing site of Domiasiat in Meghalaya, India. Two isolates with distinct colony morphology and pigmentation were closely matched as Serratia marcescens PKRS1 and Pseudomonas ficuserectae PKRS11 based on 16S rRNA gene sequence similarity analysis and phylogenetic clustering approach. Mueller-Hinton (MH) and Low phosphate (LP) medium were used for comparative determination of the minimum inhibitory concentration (MIC) of U and other metals against the identified bacteria. The wild isolates tolerated higher amount of U and other metals when compared to the type strain S. <i style="mso-bidi-font-style: normal">marcescens ATCC13880. Higher MIC was observed in MH than LP medium. The present study reveals that the metal-microbe interaction, such as, uptake and precipitation, are highly influenced by growth media composition. LP medium as the basal medium offers more authentic results due to low carbon source and negligible phosphates, which provides lower precipitation affinity to metals making it uniformly available to the isolates during growth as compared to complex MH medium

Occurrence of horizontal gene transfer of P(IB)-type ATPase genes among bacteria isolated from the uranium rich deposit of Domiasiat in North East India.

Uranium (U) tolerant aerobic heterotrophs were isolated from the subsurface soils of one of the pre-mined U-rich deposits at Domiasiat located in the north-eastern part of India. On screening of genomic DNA from 62 isolates exhibiting superior U and heavy metal tolerance, 32 isolates were found to be positive for P(IB)-type ATPase genes. Phylogenetic incongruence and anomalous DNA base compositions revealed the acquisition of P(IB)-type ATPase genes by six isolates through horizontal gene transfer (HGT). Three of these instances of HGT appeared to have occurred at inter-phylum level and the other three instances indicated to have taken place at intra-phylum level. This study provides an insight into one of the possible survival strategies that bacteria might employ to adapt to environments rich in uranium and heavy metals

Bioprospecting of Plant Growth Promoting Bacilli and Related Genera Prevalent in Soils of Pristine Sacred Groves: Biochemical and Molecular Approach.

Bacillus spp. and related genera native to soils of the pristine sacred groves from Meghalaya, India were characterized using biochemical and 16S rRNA gene analysis which revealed dominance of Bacillus, Paenibacillus, Lysinibacillus and Viridibacillus in the groves. Biochemical estimation was carried out for in vitro testing of plant growth promoting traits present in these isolates. PCR screening were performed for plant growth-promoting related genes involved in the biosynthesis of acid phosphatase (AcPho), indolepyruvate decarboxylase (ipdC), 1-aminocyclopropane-1-carboxylate deaminase (accd) and siderophore biosynthesis protein (asbA). 76% of the sacred grove isolates gave an amplified fragment for AcPho. Three of the isolates gave an amplified fragment for IpdC gene. Apart from 2 isolates, all the other isolates including the reference strains were positive for the amplification of the accd gene indicating their potential to produce ACC deaminase enzyme. 42% of the isolates gave an amplified fragment for asbA gene indicating the potential ability of these isolates to produce the catechol type siderophore, petrobactin. Overall findings indicated multiple PGP genetic traits present in these isolates which suggested that these isolates are capable of expressing multiple PGP traits. Phylogenetic and sequence analysis of accd and asbA genes from the isolates revealed that asbA genes from Paenibacillus taichungiensis SG3 and Paenibacillus tylopili SG24 indicated the occurrence of intergeneric horizontal transfer between Paenibacillus and Bacillus

Comparative matches for the closest phylogenetic neighbours obtained for the isolates based on profile of 16S rRNA gene and P_IB-type ATPases gene.

<p>Comparative matches for the closest phylogenetic neighbours obtained for the isolates based on profile of 16S rRNA gene and P_IB-type ATPases gene.</p

Molecular evidence for horizontal gene transfer among Domiasiat isolates.

<p>The genes encoding (A) 16S rRNA and (B) <i>zntA/cadA/pbrA</i>-like transporters.of uranium and heavy metal tolerant isolates obtained from subsurface soils of U-rich deposits of the Domiasiat site were subjected to neighbor-joining analysis. Respective accession numbers of gene nucleotide sequences are indicated in brackets. P_IB-type ATPase positive isolates predicted to have undergone HGT are connected by dotted lines. The scale bars indicate 0.05 change per nucleotide position for the 16S rRNA gene and 0.1 change per amino acid position for P_IB-type ATPase phylogeny.</p