Phylogenetic Distribution and Evolutionary History of Bacterial DEAD-Box Proteins

DEAD-box proteins are found in all domains of life and participate in almost all cellular processes that involve RNA. The presence of DEAD and Helicase_C conserved domains distinguish these proteins. DEAD-box proteins exhibit RNA-dependent ATPase activity in vitro, and several also show RNA helicase activity. In this study, we analyzed the distribution and architecture of DEAD-box proteins among bacterial genomes to gain insight into the evolutionary pathways that have shaped their history. We identified 1,848 unique DEAD-box proteins from 563 bacterial genomes. Bacterial genomes can possess a single copy DEAD-box gene, or up to 12 copies of the gene, such as in Shewanella. The alignment of 1,208 sequences allowed us to perform a robust analysis of the hallmark motifs of DEAD-box proteins and determine the residues that occur at high frequency, some of which were previously overlooked. Bacterial DEAD-box proteins do not generally contain a conserved C-terminal domain, with the exception of some members that possess a DbpA RNA-binding domain (RBD). Phylogenetic analysis showed a separation of DbpA-RBD-containing and DbpA-RBD-lacking sequences and revealed a group of DEAD-box protein genes that expanded mainly in the Proteobacteria. Analysis of DEAD-box proteins from Firmicutes and γ-Proteobacteria, was used to deduce orthologous relationships of the well-studied DEAD-box proteins from Escherichia coli and Bacillus subtilis. These analyses suggest that DbpA-RBD is an ancestral domain that most likely emerged as a specialized domain of the RNA-dependent ATPases. Moreover, these data revealed numerous events of gene family expansion and reduction following speciation

Vasa-Like DEAD-Box RNA Helicases of Schistosoma mansoni

Genome sequences are available for the human blood flukes, Schistosoma japonicum, S. mansoni and S. haematobium. Functional genomic approaches could aid in identifying the role and importance of these newly described schistosome genes. Transgenesis is established for functional genomics in model species, which can lead to gain- or loss-of-functions, facilitate vector-based RNA interference, and represents an effective forward genetics tool for insertional mutagenesis screens. Progress toward routine transgenesis in schistosomes might be expedited if germ cells could be reliably localized in cultured schistosomes. Vasa, a member of the ATP-dependent DEAD-box RNA helicase family, is a prototypic marker of primordial germ cells and the germ line in the Metazoa. Using bioinformatics, 33 putative DEAD-box RNA helicases exhibiting conserved motifs that characterize helicases of this family were identified in the S. mansoni genome. Moreover, three of the helicases exhibited vasa-like sequences; phylogenetic analysis confirmed the three vasa-like genes—termed Smvlg1, Smvlg2, and Smvlg3—were members of the Vasa/PL10 DEAD-box subfamily. Transcripts encoding Smvlg1, Smvlg2, and Smvlg3 were cloned from cDNAs from mixed sex adult worms, and quantitative real time PCR revealed their presence in developmental stages of S. mansoni with elevated expression in sporocysts, adult females, eggs, and miracidia, with strikingly high expression in the undeveloped egg. Whole mount in situ hybridization (WISH) analysis revealed that Smvlg1, Smvlg2 and Smvlg3 were transcribed in the posterior ovary where the oocytes mature. Germ cell specific expression of schistosome vasa-like genes should provide an informative landmark for germ line transgenesis of schistosomes, etiologic agents of major neglected tropical diseases

Modern Genomic Tools for Pigeonpea Improvement: Status and Prospects

Pigeonpea owing to its ability to sustain harsh environment and limited input/water requirement remains an excellent remunerative crop in the face of increasing climatic adversities. With nearly 70% share in global pigeonpea production, India is the leading pigeonpea producing country. Since the mid-1900s, constant research efforts directed to improve yield and resistance levels of pigeonpea have resulted in the development and deployment of several commercially accepted cultivars in India, accommodating into diverse agro-climatic zones. However, the crop productivity needs incremental improvements in order to meet the growing nutritional demands, especially in developing countries like India where pigeonpea forms a dominant part of vegetarian diet. Empowering crop improvement strategies with genomic tool kit is imperative to attain the project gains in crop yield. In the context, adoption of next-generation sequencing (NGS) technology has helped establish a wide range of genomic resources to support pigeonpea breeding, and the existing molecular tool kit includes genome-wide genetic markers, transcriptome/genome assemblies, and candidate genes/QTLs for target traits. Similarly, availability of whole mitochondrial genome sequence and derived DNA markers is immensely relevant in order to furthering the understanding of cytoplasmic male sterility (CMS) system and hybrid breeding. This chapter covers the progress of developing modern genomic resources in pigeonpea and highlights their vital role in designing future crop breeding schemes

Catchment Scale Simulations of Soil Moisture Dynamics Using an Equivalent Cross-Section based Hydrological Modelling Approach

Physically based distributed hydrological models are useful for simulating the spatial distribution of hydrologic fluxes across the catchment under various climate and land cover change scenarios. However, complexities associated with their implementation at large scales make their applications limited. Previously, an equivalent cross-section (ECS) based distributed hydrological modelling approach was developed for first order sub-basins to reduce the computational time/effort. Here, the ECS approach is modified for semi-distributed hydrological modelling at the catchment scale. The modelling approach is implemented for a 314 km2 McLaughlin catchment located in south-eastern New South Wales (NSW), Australia that consists of 822 first order sub-basins. A 26 year long streamflow record simulated using an ECS based modelling approach are compared against daily observed streamflow and four calibrated lumped conceptual hydrologic models, and found to be consistent. Further, the simulated actual evapotranspiration and soil moisture from the ECS approach are compared against the Australian Water Availability Project (AWAP) model simulations and results found to be consistent. In addition, the temporal dynamics of simulated soil moisture from the ECS approach is consistent with the satellite derived European Space Agency Climate Change Initiative (ESA CCI) surface soil moisture data. In the ECS based semi-distributed modelling, all parameters are derived from the actual topographic and physiographic information of the catchment and none of the parameters is calibrated. Therefore, this approach has the advantage of simulating streamflow in ungauged catchments compared to lumped conceptual models. The impact of spatially distributed climatic forcing and land cover on soil moisture is investigated across four landforms (upslope, midslope, footslope and alluvial-flats) and at various soil depths. Our results show increase of mean soil moisture in shallow layers of upslope toward alluvial-flats. However, mean soil moisture in deeper horizons remained almost constant across all landforms. The variability of daily soil moisture at surface soil layers is higher than the deeper soil layers for all landforms. Our results illustrated that disaggregation of a catchment to a series of ECS at the scale of first order sub-basins, captures dynamics of soil moisture and actual evapotranspiration across the landscape and results are consistent with the climatology, land cover type, topography and soil hydraulic properties. Further, the use of ECS approach in the McLaughlin catchment reduced the number of computational units by 40 times in comparison to 3-d grid based distributed modelling setup

The 1994 plague epidemic of India: Molecular diagnosis and characterization of Yersinia pestis isolates from Surat and Beed

PCR analysis of formalin-fixed human autopsy tissues, rodent tissues, fleas and bacterial isolates from pneumonic patients from the 1991 plague epidemic confirmed the presence of the f1 and pla genes of Yersinia pestis in these samples, Several Y. pestis isolates from the epidemic areas were studied in respect of their plasmid profile, expression of FI antigen and ribotype pattern, All the three plasmids known to be associated with virulence were present in the Surat isolates of Y. pestis. Presence of the F1 antigen, clasically used for diagnosis of Y. pestis infection, was demonstrated by immunoblotting. All the Indian isolates from the 1994 epidemic showed an identical ribotype profile, This profile, however, was different from those of Y. pestis isolates tested from other regions of the world. Upon digestion with EcoRI and EcoRV, and probing with E. coli 16S and 23S rRNA genes, DNA from these Y. pestis isolates gave two distinct profiles which, taken together, suggest that the present Indian isolates represent a new ribotype. The presence of Y. pestis signature genes in 5 out of 7 fleas collected from rodents in the affected areas, and the occurrence of the same ribotype in the Y. pestis isolates from domestic rodents, sylvatic rodents and the patients are strongly indicative of a clonal origin of this Indian strain and an epidemiological linkage among wild rodents, domestic rats and humans in the epidemic are