Functional adaptation of mercuric reductases from the deep brine environment of Atlantis II in the Red Sea to high temperature

The lower convective layer (LCL) of the Atlantis II (ATII) brine pool of the red sea is a unique environment characterized by high salinity of around 4 Molar, temperature of 68οC, and very high concentrations of heavy metals. We have previously described a metagenome-derived mercuric reductase, ATII-LCL MerA, from the LCL of the ATII brine pool that is thermo-stable at 60oC and retain more than 70% of its activity after 10 minutes incubation at 70oC. One of the structural characteristics of this enzyme, that distinguish it from a thermo-sensitive ortholog, is the limited substitutions of amino acids, less than 9%, including the presence of 4 aspartic acids at positions 414 to 417 replacing 4 alanine in the thermo-sensitive MerA. In this work, we identified a metagenome-derived MerA from the ATII-LCL environment, ATII-LCL-NH, that is lacking all the substitutions observed in ATII-LCL MerA. Site-directed mutagenesis replacing alanine 415 and 416 found in ATII-LCL-NH with the corresponding aspartic acids present in ATII-LCL increased the thermo-stability of the enzyme. However, substituting the 4 alanine, 415 to 417, with the corresponding four aspartic acids present in ATII-LCL decreased tremendously the thermal stability of the enzyme. Three-dimensional modeling of the MerA with the substituted Aspartic acids 415/416 revealed newly formed salt-bridge with arginine residue at position 420 and hydrogen bonds that may explain the enhanced thermal stability of this ATII-LCL-NH with the substituted Aspartic 415/416. Please click Additional Files below to see the full abstract

Unique prokaryotic consortia in geochemically distinct sediments from Red Sea Atlantis II and Discovery Deep brine pools

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e42872, doi:10.1371/journal.pone.0042872.The seafloor is a unique environment, which allows insights into how geochemical processes affect the diversity of biological life. Among its diverse ecosystems are deep-sea brine pools - water bodies characterized by a unique combination of extreme conditions. The ‘polyextremophiles’ that constitute the microbial assemblage of these deep hot brines have not been comprehensively studied. We report a comparative taxonomic analysis of the prokaryotic communities of the sediments directly below the Red Sea brine pools, namely, Atlantis II, Discovery, Chain Deep, and an adjacent brine-influenced site. Analyses of sediment samples and high-throughput pyrosequencing of PCR-amplified environmental 16S ribosomal RNA genes (16S rDNA) revealed that one sulfur (S)-rich Atlantis II and one nitrogen (N)-rich Discovery Deep section contained distinct microbial populations that differed from those found in the other sediment samples examined. Proteobacteria, Actinobacteria, Cyanobacteria, Deferribacteres, and Euryarchaeota were the most abundant bacterial and archaeal phyla in both the S- and N-rich sections. Relative abundance-based hierarchical clustering of the 16S rDNA pyrotags assigned to major taxonomic groups allowed us to categorize the archaeal and bacterial communities into three major and distinct groups; group I was unique to the S-rich Atlantis II section (ATII-1), group II was characteristic for the N-rich Discovery sample (DD-1), and group III reflected the composition of the remaining sediments. Many of the groups detected in the S-rich Atlantis II section are likely to play a dominant role in the cycling of methane and sulfur due to their phylogenetic affiliations with bacteria and archaea involved in anaerobic methane oxidation and sulfate reduction.This work was supported by King Abdullah University for Science and Technology Global Collaborative Partners (GCR) program

Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses

Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.This work was supported by King Abdullah University for Science and Technology Global Collaborative Partners (GCR) program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea

The deep-sea brines of the Red Sea include some of the most extreme and unique environments on Earth. They combine high salinities with increases in temperature, heavy metals, hydrostatic pressure, and anoxic conditions, creating unique settings for thriving populations of novel extremophiles. Despite a recent increase of studies focusing on these unusual biotopes, their viral communities remain unexplored. The current survey explores four metagenomic datasets obtained from different brine–seawater interface samples, focusing specifically on the diversity of their viral communities. Data analysis confirmed that the particle-attached viral communities present in the brine–seawater interfaces were diverse and generally dominated by Caudovirales, yet appearing distinct from sample to sample. With a level of caution, we report the unexpected finding of Phycodnaviridae, which infects algae and plants, and trace amounts of insect-infecting Iridoviridae. Results from Kebrit Deep revealed stratification in the viral communities present in the interface: the upper-interface was enriched with viruses associated with typical marine bacteria, while the lower-interface was enriched with haloviruses and halophages. These results provide first insights into the unexplored viral communities present in deep-sea brines of the Red Sea, representing one of the first steps for ongoing and future sampling efforts and studies

Hamza El Dorry Oral History

Hamza El Dorry was a faculty member in the Biology Department at the American University in Cairo (AUC) from 2005 to 2017. He provides background on his family, and describes his move from Egypt to Brazil in the 1960s for doctoral studies in biochemistry, his later study in the United States, and his career in biochemistry and molecular biology in both countries over several decades. He discusses joining AUC upon his return to Egypt in 2005, and setting up a biotechnology laboratory at AUC’s Yousef Jameel Science and Technology Research Center. He tells of how the Biology Department’s focus developed while he was Chair, through introduction of personnel and research facilities in genomics and computational biology and connection with the PhD program in biotechnology. El Dorry also speaks about AUC’s collaboration with Saudi Arabia’s King Abdullah University for Science and Technology {KAUST}, including a project related to the Red Sea. The leadership style of administrators like Dean of School of Sciences and Engineering (and later Provost) Medhat Haroun are also covered, as well as the upper administration’s relationship with the faculty in 2016 and 2017, including contention over the Faculty Handbook

Subunits of aldolase Fructose-1,6-diphosphate striated muscle of rabbit (EC 4.1.2.13)

Foi levado a efeito estudo sobre formas múltiplas de aldolase de músculo de coelho. A enzima foi purificada a pH 7,5 por eluição com substrato a partir de coluna de fosfocelulose. A enzima foi ainda cristalizada por diálise dessas preparações contra solução saturada de sulfato de amônio. Formas múltiplas de aldolase foram obtidas por fracionamento a diferentes pI por eletrofocalização em gradiente de Ampholine na faixa de pH entre 7,0 a 10,0. Nessas condições foram separados cinco híbridos resultantes da associação ao acaso das sub-unidades α e β, os quais foram analisados em estado de dissociação a partir de proteínas carboximetiladas e separadas por eletroforese em gel de poliacrilamida na presença de uréia 8M. Foi também estudado o aparecimento de sub-unidade α e β em músculo de coelhos de idades que variavam de 1 a 240 dias, verificando-se que em coelhos de 1 dia existia apenas a proteína α4, surgindo sub-unidades β já em animais de 10 dias.Not available

Subunits of aldolase Fructose-1,6-diphosphate striated muscle of rabbit (EC 4.1.2.13)

Foi levado a efeito estudo sobre formas múltiplas de aldolase de músculo de coelho. A enzima foi purificada a pH 7,5 por eluição com substrato a partir de coluna de fosfocelulose. A enzima foi ainda cristalizada por diálise dessas preparações contra solução saturada de sulfato de amônio. Formas múltiplas de aldolase foram obtidas por fracionamento a diferentes pI por eletrofocalização em gradiente de Ampholine na faixa de pH entre 7,0 a 10,0. Nessas condições foram separados cinco híbridos resultantes da associação ao acaso das sub-unidades α e β, os quais foram analisados em estado de dissociação a partir de proteínas carboximetiladas e separadas por eletroforese em gel de poliacrilamida na presença de uréia 8M. Foi também estudado o aparecimento de sub-unidade α e β em músculo de coelhos de idades que variavam de 1 a 240 dias, verificando-se que em coelhos de 1 dia existia apenas a proteína α4, surgindo sub-unidades β já em animais de 10 dias.Not available