A peep into the Plant miRNA world

microRNAs constitute a major class of the small regulatory molecules that are involved in regulating the intrinsic normal growth of cells and development of organisms as well as in maintaining the integrity of genomes. The plant miRNA research gained momentum, 2002 onwards with identification of new miRNA molecules and their targets. This was accompanied by the discovery of plant homologs of proteins involved in miRNA biogenesis, including a new member SERRATE. The identification of several diverging and converging functions of miRNAs indicate that they play versatile roles in regulating cell differentiation and tissue development. This article provides an update on the conservation and identification of plant miRNAs. The classical miRNA biogenesis pathway and the associated proteins are discussed along with the emerging concept on the processing of miRNA-encoding introns (mirtrons). It also contains a concise account of plant miRNA targets and functions with focus on the recent successful attempt on engineering synthetic miRNAs to study gene function as well as to impart virus resistance in plants

Begomovirus DNA replication and pathogenicity

Begomoviridae is the largest genus of the family of single stranded DNA plant viruses, Geminiviridae and is responsible for significant agro-economic losses worldwide. Its small single-stranded DNA genome primarily replicates by rolling circle replication (RCR) mode with the help of certain viral and host factors. The role of virus encoded Rep protein in initiation and immediate post-initiation phases of RCR has been the subject of various studies. We have identified many host proteins which interact with Rep protein of a member of Begomovirus, namely, Mungbean yellow mosaic India virus, thereby playing a role in viral DNA replication. Of these, the role of host RAD54 protein is significant as the rad54 mutant of Arabidopsis does not permit mini viral DNA replication. The plant hosts protect themselves from begomoviruses by activating RNA interference (RNAi) pathways targeted against the viruses. However, the virus can also sometime overcome this form of host defence by encoding RNA silencing suppressors, which attenuate host RNAi and are regarded as major pathogenicity determinants. The viral suppressors do not share any signature sequences and are structurally and mechanistically dissimilar. These can be detected effectively, only through specialized functional assays. In this review, we also point out the potential biotechnological applications of the suppressors and discuss about various possible containment strategies for begomoviruses, including an exciting new approach involving artificial micro- RNAs

Isolation and characterisation of the cDNA encoding a glycosylated accessory protein of pea chloroplast DNA polymerase

The cDNA encoding p43, a DNA binding protein from pea chloroplasts (ct) that binds to cognate DNA polymerase and stimulates the polymerase activity, has been cloned and characterised. The characteristic sequence motifs of hydroxyproline-rich glycoproteins (HRGP) are present in the cDNA corresponding to the N-terminal domain of the mature p43. The protein was found to be highly O-arabinosylated. Chemically deglycosylated p43 (i.e. p29) retains its binding to both DNA and pea ct-DNA polymerase but fails to stimulate the DNA polymerase activity. The mature p43 is synthesised as a pre-p43 protein containing a 59 amino acid long transit peptide which undergoes stromal cleavage as evidenced from the post-translational in vitro import of the precursor protein into the isolated intact pea chloroplasts. Surprisingly, p43 is found only in pea chloroplasts. The unique features present in the cloned cDNA indicate that p43 is a novel member of the HRGP family of proteins. Besides p43, no other DNA-polymerase accessory protein with O-glycosylation has been reported yet

Response of Hirayama disease to surgical intervention: case report

Hirayama disease also known as monomelic amyotrophy, primarily involves distal upper limb extremities.It differs from the known types of motor neuron diseases because of its nonprogressive behavior and pathologic findings of focal ischemic changes in the anterior horn of the lower cervical cord. We present a young male with Hirayama disease who had a left upper extremity involvement which was progressive in nature. He didn’t respond with initial treatment of cervical collar. Consequently surgical intervention improves muscle weakness and decrease the neurological deficit. 

Interaction between coat protein and replication initiation protein of Mung bean yellow mosaic India virus might lead to control of viral DNA replication

In addition to their encapsidation function, viral coat proteins (CP) contribute to viral life cycle in many different ways. The CPs of the geminiviruses are responsible for intra- as well as inter-plant virus transmission and might determine the yield of viral DNA inside the infected tissues by either packaging the viral DNA or interfering with the viral replicative machinery. Since the cognate Rep largely controls the rolling circle replication of geminiviral DNA, the interaction between Rep and CP might be worthwhile to examine for elucidation of CP-mediated control of the viral DNA copy number. Here a reasonably strong interaction between Rep and CP of the geminivirus Mung bean yellow mosaic India virus is reported. The domain of interaction has been mapped to a central region of Rep. The replication initiation activity of Rep, i.e., its nicking and closing function, is down regulated by CP. This report highlights how CP could be important in controlling geminiviral DNA replication

Propagation of elastic waves in DNA

The mathematical analyses of longitudinal and torsional elastic waves transmitted along DNA molecule undergoing Brownian motion in solution are presented. Longitudinal vibrations in DNA are shown to be responsible for drug intercalation and breathing. The near neighbor exclusion mode of drug intercalation is explained. Torsional oscillations in DNA are shown to be responsible for conformation transitions from a right handed to a left handed form, depending on sequence specificity in high salt concentration

The oligomeric Rep protein of Mungbean yellow mosaic India virus (MYMIV) is a likely replicative helicase

Geminiviruses replicate by rolling circle mode of replication (RCR) and the viral Rep protein initiates RCR by the site-specific nicking at a conserved nonamer (TAATATT↓ AC) sequence. The mechanism of subsequent steps of the replication process, e.g. helicase activity to drive fork-elongation, etc. has largely remained obscure. Here we show that Rep of a geminivirus, namely, Mungbean yellow mosaic India virus (MYMIV), acts as a replicative helicase. The Rep-helicase, requiring ≥6 nt space for its efficient activity, translocates in the 3'→5' direction, and the presence of forked junction in the substrate does not influence the activity to any great extent. Rep forms a large oligomeric complex and the helicase activity is dependent on the oligomeric conformation (∼24mer). The role of Rep as a replicative helicase has been demonstrated through ex vivo studies in Saccharomyces cerevisiae and in planta analyses in Nicotiana tabacum. We also establish that such helicase activity is not confined to the MYMIV system alone, but is also true with at least two other begomoviruses, viz., Mungbean yellow mosaic virus (MYMV) and Indian cassava mosaic virus (ICMV)

Characterisation and mode of in vitro replication of pea chloroplast OriA sequences

A partially purified replicative system of pea chloroplast that replicates recombinant DNAs containing pea chloroplast origin sequences has been characterised. Polymerisation by this system is very fast and insensitive to chain terminators like dideoxynucleotides, arabinosylcytosine 5'-triphosphate, etc. Both strands of template DNA are synthesized and single-stranded DNA templates undergo more than one round of replication. When sequences of either of the two chloroplast origins of replication (OriA or OriB) are used as templates, the replicative intermediates are found to have sigma structures. Electron microscopic analysis of the sigma structures restricted with various enzymes reveals that the initiation site of in vitro replication maps near the displacement-loop regions where replication initiates also in vivo. Although the observed replication initiation in the OriA recombinant template is chloroplast-DNA-specific, the mode of replication is different from that observed in vivo with intact ctDNA. However, when the template DNA contains both the OriA and OriB sequences, the in vitro replication proceeds in the theta mode, the mode of replication usually observed in vivo

Identification of mirtrons in rice using MirtronPred: a tool for predicting plant mirtrons.

article i nfo Studies from flies and insects have reported the existence of a special class of miRNA, called mirtrons that are produced from spliced-out introns in a DROSHA-independent manner. The spliced-out lariat is debranched and refolded into a stem-loop structure resembling the pre-miRNA, which can then be processed by DICER into mature ~21 nt species. The mirtrons have not been reported from plants. In this study, we present Mir- tronPred, a web based server to predict mirtrons from intronic sequences. We have used the server to predict 70 mirtrons in rice introns that were put through a stringent selection filter to shortlist 16 best sequences. The prediction accuracy was subsequently validated by northern analysis and RT-PCR of a predicted Os- mirtron-109. The target sequences for this mirtron were also found in the rice degradome database. The pos- sible role of the mirtron in rice regulon is discussed. The MirtronPred web server is available at http://bioinfo. icgeb.res.in/mirtronPred