Sajjad Asaf

Bio: Sajjad Asaf is an academic researcher from University of Nizwa. The author has contributed to research in topics: Genome & Medicine. The author has an hindex of 27, co-authored 97 publications receiving 1916 citations. Previous affiliations of Sajjad Asaf include Kyungpook National University & University of Houston.

Sphingomonas: from diversity and genomics to functional role in environmental remediation and plant growth

Abstract: The species belonging to the Sphingomonas genus possess multifaceted functions ranging from remediation of environmental contaminations to producing highly beneficial phytohormones, such as sphingan and gellan gum. Recent studies have shown an intriguing role of Sphingomonas species in the degradation of organometallic compounds. However, the actual biotechnological potential of this genus requires further assessment. Some of the species from the genus have also been noted to improve plant-growth during stress conditions such as drought, salinity, and heavy metals in agricultural soil. This role has been attributed to their potential to produce plant growth hormones e.g. gibberellins and indole acetic acid. However, the current literature is scattered, and some of the important areas, such as taxonomy, phylogenetics, genome mapping, and cellular transport systems, are still being overlooked in terms of elucidation of the mechanisms behind stress-tolerance and bioremediation. In this review, we elucidated the prospective role and function of this genus for improved utilization during environmental biotechnology.

Plant Secondary Metabolite Biosynthesis and Transcriptional Regulation in Response to Biotic and Abiotic Stress Conditions

Abstract: Plant secondary metabolites (SMs) play important roles in plant survival and in creating ecological connections between other species. In addition to providing a variety of valuable natural products, secondary metabolites help protect plants against pathogenic attacks and environmental stresses. Given their sessile nature, plants must protect themselves from such situations through accumulation of these bioactive compounds. Indeed, secondary metabolites act as herbivore deterrents, barriers against pathogen invasion, and mitigators of oxidative stress. The accumulation of SMs are highly dependent on environmental factors such as light, temperature, soil water, soil fertility, and salinity. For most plants, a change in an individual environmental factor can alter the content of secondary metabolites even if other factors remain constant. In this review, we focus on how individual environmental factors affect the accumulation of secondary metabolites in plants during both biotic and abiotic stress conditions. Furthermore, we discuss the application of abiotic and biotic elicitors in culture systems as well as their stimulating effects on the accumulation of secondary metabolites. Specifically, we discuss the shikimate pathway and the aromatic amino acids produced in this pathway, which are the precursors of a range of secondary metabolites including terpenoids, alkaloids, and sulfur- and nitrogen-containing compounds. We also detail how the biosynthesis of important metabolites is altered by several genes related to secondary metabolite biosynthesis pathways. Genes responsible for secondary metabolite biosynthesis in various plant species during stress conditions are regulated by transcriptional factors such as WRKY, MYB, AP2/ERF, bZIP, bHLH, and NAC, which are also discussed here.

What Is There in Seeds? Vertically Transmitted Endophytic Resources for Sustainable Improvement in Plant Growth

Abstract: Phytobeneficial microbes, particularly endophytes, such as fungi and bacteria, are concomitant partners of plants throughout its developmental stages, including seed germination, root and stem growth, and fruiting. Endophytic microbes have been identified in plants that grow in a wide array of habitats; however, seed-borne endophytic microbes have not been fully explored yet. Seed-borne endophytes are of great interest because of their vertical transmission; their potential to produce various phytohormones, enzymes, antimicrobial compounds, and other secondary metabolites; and improve plant biomass and yield under biotic and abiotic stresses. This review addresses the current knowledge on endophytes, their ability to produce metabolites, and their influence on plant growth and stress mitigation.

Plant growth promoting endophytic fungi Asprgillus fumigatus TS1 and Fusarium proliferatum BRL1 produce gibberellins and regulates plant endogenous hormones

Abstract: Endophytes can serve as plant growth promoters as they secret a vast array of phytohormones to support host plants. Keeping the growth promoting activity of the endophytes in view, two endophytic fungi, Asprgillus fumigatus TS1 and Fusarium proliferatum BRL1 have been isolated from the roots of Oxalis corniculata. The isolates have been screened initially for growth promoting activities, including siderophores activity, phosphate solubilization, and secreation of indole acetic acid and gibberellins. Further, the isolates have assayed for the ability to promote the growth of mutant rice Waito-C. The plants associated with TS1 and BRL1 have shown higher chlorophyll content, root-shoot length, and biomass production. The growth promoting activity of the endophytes can be attributed to the various types of GAs and IAA that have been observed in the culture filtrates of the endophytes by the Gas chromatography/mass spectrometry (GC/MS). The GC/MS analysis revealed the presence of different gibberellins concentrations (ng/ml) in TS1 and BRL1 culture filtrate, i.e. GA1 (0.091 ± 0.009, 0.392 ± 0.007), GA3 (0.324 ± 0.077, 0.089 ± 0.0007) and GA7 (0.023 ± 0.002, 0.492 ± 0.005), respectively. Besides, a significant up regulation of plant endogenous GA1 (12.443 ± 0.454 and 15.434 ± 0.245) has been obsereved in TS1 and BRL1 associated plants compared to the control. Moreover, semi quantitative RT-PCR has confirmed the presence/invovment of GA pathways genes (P50–1, P450–3, P450–4, ggs2, and des). The results conclude that the endophytes isolated in this study can ably synthesize bioactive compounds, which play an important role in plant growth promotion.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Biochemistry And Molecular Biology Of Plants

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Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria.

Abstract: One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only ‘passengers’ with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as ‘gatekeepers’ to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage ‘priming’ plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production.