Identification of ribosomal proteins specific to higher eukaryotic organisms

This report describes the identification of a novel protein named PS1D (Genbank accession number ), which is composed of an S1-like RNA-binding domain, a (cysteine)x3-(histidine) CCCH-zinc finger, and a very basic carboxyl domain. PS1D is expressed as two isoforms, probably resulting from the alternative splicing of mRNA. The long PS1D isoform differs from the short one by the presence of 48 additional amino acids at its amino-terminal extremity. Analysis of PS1D subcellular distribution by cell fractionation reveals that this protein belongs to the core of the eukaryotic 60S ribosomal subunit. Interestingly, PS1D protein is a highly conserved protein among mammalians as murine, human, and simian PS1D homologues share more than 95% identity. In contrast, no homologous protein is found in lower eukaryotes such as yeast and Caenorhabditis elegans. These observations indicate that PS1D is the first eukaryotic ribosomal protein that is specific to higher eukaryotes.     

Marine Pseudoalteromonas species are associated with higher organisms and produce biologically active extracellular agents

The newly established genus Pseudoalteromonas contains numerous marine species which synthesize biologically active molecules. The production of a range of compounds which are active against a variety of target organisms appears to be a unique characteristic for this genus and may greatly benefit Pseudoalteromonas cells in their competition for nutrients and colonization of surfaces. Species of Pseudoalteromonas are generally found in association with marine eukaryotes and display anti-bacterial, bacteriolytic, agarolytic and algicidal activities. Moreover, several Pseudoalteromonas isolates specifically prevent the settlement of common fouling organisms. While a wide range of inhibitory extracellular agents are produced, compounds promoting the survival of other marine organisms living in the vicinity of Pseudoalteromonas species have also been found.     

Directed evolution: an approach to engineer enzymes

Directed evolution is being used increasingly in industrial and academic laboratories to modify and improve commercially important enzymes. Laboratory evolution is thought to make its biggest contribution in explorations of non-natural functions, by allowing us to distinguish the properties nurtured by evolution. In this review we report the significant advances achieved with respect to the methods of biocatalyst improvement and some critical properties and applications of the modified enzymes. The application of directed evolution has been elaborately demonstrated for protein solubility, stability and catalytic efficiency. Modification of certain enzymes for their application in enantioselective catalysis has also been elucidated. By providing a simple and reliable route to enzyme improvement, directed evolution has emerged as a key technology for enzyme engineering and biocatalysis.     

Microbial fuel cells as an alternative energy source: current status

Microbial fuel cell (MFC) technology is an emerging area for alternative renewable energy generation and it offers additional opportunities for environmental bioremediation. Recent scientific studies have focused on MFC reactor design as well as reactor operations to increase energy output. The advancement in alternative MFC models and their performance in recent years reflect the interests of scientific community to exploit this technology for wider practical applications and environmental benefit. This is reflected in the diversity of the substrates available for use in MFCs at an economically viable level. This review provides an overview of the commonly used MFC designs and materials along with the basic operating parameters that have been developed in recent years. Still, many limitations and challenges exist for MFC development that needs to be further addressed to make them economically feasible for general use. These include continued improvements in fuel cell design and efficiency as well scale-up with economically practical applications tailored to local needs.     

Monoclonal antibodies to the alternative oxidase of higher plant mitochondria

The higher plant mitochondrial electron transport chain contains, in addition to the cytochrome chain which terminates with cytochrome oxidase, an alternative pathway that terminates with an alternative oxidase. The alternative oxidase of Sauromatum guttatum Schott has recently been identified as a cluster of proteins with apparent M_r of 37, 36, and 35 kilodaltons (kD). Monoclonal antibodies have now been prepared to these proteins and designated as AOA (binding all three proteins of the alternative oxidase cluster), AOU (binding the upper or 37 kD protein), and AOL (binding the lower or 36 and 35 kD proteins). All three antibodies bind to their respective alternative oxidase proteins whether the proteins are in their native or denatured states (as on protein blots). AOA and AOU inhibit alternative oxidase activity around 49%, whereas AOL inhibits activity only 14%. When coupled individually to Sepharose 4B, all three monoclonal resins were capable of retaining the entire cluster of alternative oxidase proteins, suggesting that these proteins are physically associated in some manner. The monoclonals were capable of binding similar mitochondrial proteins in a number of thermogenic and nonthermogenic species, indicating that they will be useful in characterizing and purifying the alternative oxidase of different systems. The ability of the monoclonal-Sepharose 4B resins to retain the cluster of previously identified alternative oxidase proteins, along with the inhibition of alternative oxidase activity by these monoclonals, supports the role of these proteins in constituting the alternative oxidase.     

Microbial biomass: an economical alternative for removal of heavy metals from waste water

Today indiscriminate and uncontrolled discharge of metal contaminated industrial effluents into the environment has become an issue of major concern. Heavy metals, being non-biodegradable and persistent, beyond a permissible concentration form unspecific compounds inside the cells thereby causing cellular toxicity. The only alternative to remove them from the wastewater is by immobilizing them. The conventional methods adopted earlier for this purpose included chemical precipitation, oxidation, reduction, filtration, electrochemical treatment, evaporation, adsorption and ion-exchange resins. These methods require high energy inputs especially when it refers to dilute solutions. Here microbial biomass offers an economical option for removing heavy metals by the phenomenon of biosorption. Non-living or dead biomass sequester metal(s) on their cell surface due to certain reactive groups available like carboxyl, amine, imidazole, phosphate, sulphydryl, sulfate and hydroxyl. The process can be made economical by procuring spent biomass from industry or naturally available bulk biomass. A batch or a continuous process of removal of heavy metals directly from effluents can be developed in a fixed bed reactor using the immobilized biomass. Further biosorption potential of the biomass can be improved by various physical and chemical treatments. The availability of variety of microbial biomass and their metal binding potential makes it a economical and sustainable option for developing effluent treatment process for removal and recovery of heavy metals.     

Microbial transformation of 3-hydroxy-5,6-cyclopropanocholestanes--an alternative route to 6-methylsteroids

Incubation of 3beta-hydroxy-5,6alpha-cyclopropano-5alpha-cholestane (4), 3beta-hydroxy-5,6beta-cyclopropano-5beta-cholestane (5), and 3beta-hydroxy-5,6alpha-cyclopropano-5alpha-cholest-7-e ne (6) with Mycobacterium sp. (NRRL B-3805) gave a mixture of side chain cleaved 17-keto steroids as the major products in 52, 57, and 69% yields, respectively. Among these 17-keto steroids, the cyclopropyl ring eliminated product, androst-4-ene-3,17-dione (9), was isolated in 6, 4, and 8% yields, respectively. A cyclopropyl ring migration product, 6alpha,7alpha-cyclopropanoandrost-4-ene-3,17-dione (16), was isolated from the incubation mixture of 6 in 4% yield, also 10% yield of 16 was obtained when 5, 6alpha-cyclopropano-5alpha-androst-7-ene-3,17-dione (12) was incubated. The cyclopropyl ring opening and subsequent reduction followed by oxidation of the two major biotransformation products, 5, 6beta-cyclopropano-5beta-androsta-3,17-dione (10) and 5, 6alpha-cyclopropano-5alpha-androsta-3,17-dione (7), gave 6beta- and 6alpha-methylandrost-4-ene-3,17-dione in 60, and 45% yields, respectively.     

Microbial inoculants with higher capacity to colonize soils improved wheat drought tolerance

Microbial inoculants have gained increasing attention worldwide as an eco-friendly solution for improving agriculture productivity. Several studies have demonstrated their potential benefits, such as enhanced resistance to drought, salinity, and pathogens. However, the beneficial impacts of inoculants remain inconsistent. This variability is attributed to limited knowledge of the mechanisms by which microbial inoculants affect crop growth and a lack of ecological characteristics of these inoculants that limit our ability to predict their beneficial effects. The first important step is believed to be the evaluation of the inoculant's ability to colonize new habitats (soils and plant roots), which could provide crops with beneficial functions and improve the consistency and efficiency of the inoculants. In this study, we aimed to investigate the impact of three microbial inoculants (two bacterial: P1 and P2, and one fungal: P3) on the growth and stress responses of three wheat varieties in two different soil types under drought conditions. Furthermore, we investigated the impact of microbial inoculants on soil microbial communities. Plant biomass and traits were measured, and high-throughput sequencing was used to characterize bulk and rhizosphere soil microbiomes after exposure to drought stress. Under drought conditions, plant shoot weight significantly increased (11.37%) under P1 treatments compared to uninoculated controls. In addition, total nitrogen enzyme activity increased significantly under P1 in sandy soil but not in clay soil. Importantly, network analyses revealed that P1, consisting of Bacillus paralicheniformis and Bacillus subtilis, emerged as the keystone taxa in sandy soil. Conversely, P2 and P3 failed to establish as keystone taxa, which may explain their insignificant impact on wheat performance under drought conditions. In conclusion, our study emphasizes the importance of effective colonization by microbial inoculants in promoting crop growth under drought conditions. Our findings support the development of microbial inoculants that robustly colonize plant roots for improved agricultural productivity.     

Getting from an RNA world to modern cells just got a little easier

Our understanding of the early steps in the evolution of life is hampered by a Catch-22: Darwinian selection leading to longer genomes requires as prerequisite increased replicative fidelity. Yet a genome at capacity cannot increase in size; it will be catastrophically mutated out of existence if fidelity has not already increased. Traditionally the problem has been considered for genotypes but can be down-sized if multiple genotypes specify the same phenotype. Kun and colleagues put empirical meat on theoretical bone by analysing ribozyme mutagenesis data, concluding that modest replication fidelities could permit a primordial genome with up to 100 genes.     

When are alternative stable states more likely to occur?

T. Fukami and W. G. Lee argue that the logical expectation from ecological theory is that competitively-structured assemblages will be more likely to exhibit alternative stable states than abiotically-structured assemblages. We suggest that there are several important misinterpretations in their arguments, and that the substance of their hypothesis has both a weak basis in ecological theory and is not supported by empirical evidence which shows that alternative stable states occur more frequently in natural systems subject to moderate- to harsh abiotic extremes. While this debate is founded in ecological theory, it has important applied implications for restoration management. Sound theoretical predictions about when to expect alternative stable states can only aid more effective restoration if theoretical expectations can be shown to translate into predictable empirical outcomes. If strongly abiotically- or disturbance-structured systems are more likely to exhibit catastrophic phase shifts in community structure that can be resilient to management efforts, then restoration ecologists will need to treat these systems differently in terms of the types of management inputs that are required.     

The iron-sulphur proteins: Evolution of a ubiquitous protein from model systems to higher organisms

Ferredoxins are Fe–S proteins with low molecular weight (6–12000) which act as electron carriers at very low redox potentials eg. –300 to –500 mV, in diverse biochemical processes such as bacterial and plant photosynthesis, N₂ fixation, carbon metabolism, oxidative phosphorylation and steroid hydroxylation. They are found in a wide range of organisms from the primitive obligate anaerobic bacteria, through photosynthetic bacteria, blue-green and green algae, to all higher plants and animals. Three types of ferredoxins are known –8 Fe+8 S, 4 Fe+4 S and 2 Fe+2 S. All three have been found in bacteria while the 2 Fe and some 8 Fe ferredoxins have been found in plants and animals possibly representing an evolutionary sequence. The 8 Fe ferredoxin may all be composed of two 4 Fe units. We have proposed that because of the simplicity of the 8 Fe ferredoxins (only 9 common simple amino acids in clostridia, 6 of which have been detected in the Murchison meteorite) they may have been amongst the earliest proteins formed during the origin of life. A simple peptide of about 27 amino acids could incorporate inorganic Fe+S (or possibly an existing Fe–S complex) into it nonenzymatically under anaerobic conditions to form a protein carrying one or two electrons at the potential of the H₂ electrode. More than ten Fe–S model compounds have been proposed as analogues of the 4 Fe or 2 Fe containing active centres; inorganic, organometallic and peptide complexes have been synthesized. A few have many of the properties of ferredoxins but none as yet fulfills a sufficient number of criteria to substitute for ferredoxins chemically and biologically — a goal which will provide many clues to primitive peptide systems undergoing biological electron transfer reactions.