scholarly journals Ubiquitousness of Haloferax and Carotenoid Producing Genes in Arabian Sea Coastal Biosystems of India

Marine Drugs ◽  
2021 ◽  
Vol 19 (8) ◽  
pp. 442
Author(s):  
Jamseel Moopantakath ◽  
Madangchanok Imchen ◽  
Ranjith Kumavath ◽  
Rosa María Martínez-Espinosa
Keyword(s):  
Multidrug Resistance ◽  
Comparative Analysis ◽  
Pure Culture ◽  
Arabian Sea ◽  
Halophilic Archaea ◽  
Carotenoid Pigment ◽  
Extreme Halophiles ◽  
Open Sea ◽  
Whole Genomes ◽  
Public Repositories

This study presents a comparative analysis of halophiles from the global open sea and coastal biosystems through shotgun metagenomes (n = 209) retrieved from public repositories. The open sea was significantly enriched with Prochlorococcus and Candidatus pelagibacter. Meanwhile, coastal biosystems were dominated by Marinobacter and Alcanivorax. Halophilic archaea Haloarcula and Haloquandratum, predominant in the coastal biosystem, were significantly (p < 0.05) enriched in coastal biosystems compared to the open sea. Analysis of whole genomes (n = 23,540), retrieved from EzBioCloud, detected crtI in 64.66% of genomes, while cruF was observed in 1.69% Bacteria and 40.75% Archaea. We further confirmed the viability and carotenoid pigment production by pure culture isolation (n = 1351) of extreme halophiles from sediments (n = 410 × 3) sampling at the Arabian coastline of India. All red-pigmented isolates were represented exclusively by Haloferax, resistant to saturated NaCl (6 M), and had >60% G + C content. Multidrug resistance to tetracycline, gentamicin, ampicillin, and chloramphenicol were also observed. Our study showed that coastal biosystems could be more suited for bioprospection of halophiles rather than the open sea.

scholarly journals Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

2021 ◽  
Author(s):  
Grayson L Chadwick ◽  
Connor T Skennerton ◽  
Rafael Laso-Perez ◽  
Andy O Leu ◽  
Daan R Speth ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Comparative Analysis ◽  
Comparative Genomics ◽  
Pure Culture ◽  
Methanogenic Archaea ◽  
Anaerobic Oxidation Of Methane ◽  
Genomic Features ◽  
Sulfate Reducing ◽  
Oxidation Of Methane ◽  
Reducing Bacteria

The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features which separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well-distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.

scholarly journals Multidrug Resistance Dynamics in Salmonella in Food Animals in the United States: An Analysis of Genomes from Public Databases

2021 ◽  
Author(s):  
João Pires ◽  
Jana S. Huisman ◽  
Sebastian Bonhoeffer ◽  
Thomas P. Van Boeckel
Keyword(s):  
United States ◽  
Multidrug Resistance ◽  
Next Generation Sequencing ◽  
Antimicrobial Resistance ◽  
The United States ◽  
Next Generation ◽  
Exponential Increase ◽  
Food Animals ◽  
Public Repositories ◽  
Generation Sequencing

Next-generation sequencing has led to an exponential increase in the number of genomes deposited in public repositories. This growing volume of information presents opportunities to track the prevalence of genes conferring antimicrobial resistance (AMR), a growing threat to the health of humans and animals.

scholarly journals Species Widely Distributed in Halophilic Archaea Exhibit Opsin-Mediated Inhibition of Bacterioruberin Biosynthesis

2018 ◽  
Vol 201 (2) ◽  
Author(s):  
Ronald F. Peck ◽  
Serena M. Graham ◽  
Abby M. Gregory
Keyword(s):  
Regulatory Mechanism ◽  
Halophilic Archaea ◽  
Halobacterium Salinarum ◽  
Efficient Production ◽  
Carotenoid Pigment ◽  
Prosthetic Group ◽  
Content Type ◽  
Genes Encoding ◽  
The Common ◽  
Insight Into

ABSTRACT Halophilic Archaea are a distinctive pink color due to a carotenoid pigment called bacterioruberin. To sense or utilize light, many halophilic Archaea also produce rhodopsins, complexes of opsin proteins with a retinal prosthetic group. Both bacterioruberin and retinal are synthesized from isoprenoid precursors, with lycopene as the last shared intermediate. We previously described a regulatory mechanism by which Halobacterium salinarum bacterioopsin and Haloarcula vallismortis cruxopsin inhibit bacterioruberin synthesis catalyzed by lycopene elongase. In this work, we found that opsins in all three major Halobacteria clades inhibit bacterioruberin synthesis, suggesting that this regulatory mechanism existed in the common Halobacteria ancestor. Halophilic Archaea, which are generally heterotrophic and aerobic, likely evolved from an autotrophic, anaerobic methanogenic ancestor by acquiring many genes from Bacteria via lateral gene transfer. These bacterial “imports” include genes encoding opsins and lycopene elongases. To determine if opsins from Bacteria inhibit bacterioruberin synthesis, we tested bacterial opsins and found that an opsin from Curtobacterium, in the Actinobacteria phylum, inhibits bacterioruberin synthesis catalyzed by its own lycopene elongase, as well as that catalyzed by several archaeal enzymes. We also determined that the lycopene elongase from Halococcus salifodinae, a species from a family of Halobacteria lacking opsin homologs, retained the capacity to be inhibited by opsins. Together, our results indicate that opsin-mediated inhibition of bacterioruberin biosynthesis is a widely distributed mechanism found in both Archaea and Bacteria, possibly predating the divergence of the two domains. Further analysis may provide insight into the acquisition and evolution of the genes and their host species. IMPORTANCE All organisms use a variety of mechanisms to allocate limited resources to match their needs in their current environment. Here, we explore how halophilic microbes use a novel mechanism to allow efficient production of rhodopsin, a complex of an opsin protein and a retinal prosthetic group. We previously demonstrated that Halobacterium salinarum bacterioopsin directs available resources toward retinal by inhibiting synthesis of bacterioruberin, a molecule that shares precursors with retinal. In this work, we show that this mechanism can be carried out by proteins from halophilic Archaea that are not closely related to H. salinarum and those in at least one species of Bacteria. Therefore, opsin-mediated inhibition of bacterioruberin synthesis may be a highly conserved, ancient regulatory mechanism.

Comparative Analysis of Chlorophyll-aDistribution from SeaWiFS, MODIS-Aqua, MODIS-Terra and MERIS in the Arabian Sea

2014 ◽  
Vol 38 (1) ◽  
pp. 40-57 ◽  
Author(s):  
S. V. V. Arun Kumar ◽  
K. N. Babu ◽  
A. K. Shukla
Keyword(s):  
Comparative Analysis ◽  
Arabian Sea

scholarly journals Complete Genome Sequences of the Probiotic Lactic Acid BacteriaLactobacillus helveticusD75 and D76

2018 ◽  
Vol 6 (11) ◽  
Author(s):  
V. A. Toropov ◽  
T. Y. Vakhitov ◽  
O. N. Shalaeva ◽  
E. K. Roshchina ◽  
S. I. Sitkin
Keyword(s):  
Lactic Acid ◽  
Comparative Analysis ◽  
Healthy Child ◽  
Complete Genome ◽  
Intestinal Tract ◽  
Lactobacillus Helveticus ◽  
Genome Sequences ◽  
Whole Genomes

ABSTRACTLactobacillus helveticusD75 and D76 were isolated from the intestinal tract of a healthy child. Both strains possess symbiotic, probiotic, and antagonistic activities. We have sequenced and annotated the whole genomes ofL. helveticusD75 and D76 and have conducted a preliminary genome comparative analysis.

scholarly journals Unique and Universal Proteins in Human Genome

2020 ◽  
Vol 16 (11) ◽  
pp. 45
Author(s):  
Essam Al-Daoud ◽  
Ghadeer Albesani
Keyword(s):  
Comparative Analysis ◽  
Amino Acid ◽  
Human Genome ◽  
Reference Genome ◽  
Amino Acid Sequences ◽  
The Other ◽  
Entire Genome ◽  
Whole Genomes ◽  
The Common ◽  
Similar Amino Acid

<span>One of the major troubles with a comparative analysis between human and other species is that only similar amino acid sequences are selected for analysis. To find the connection among the species and find out the unique, the common and the universal proteins, the entire genome of 40 species are compared with the human genome which is utilized as reference genome. More than 11 billion pairwise alignments are performed using blastp. Several findings are introduced in this study, for example, we found 330 unique proteins in human genome and have insignificant hits in all tested genomes, the number of universal proteins in human genome and conserved in all tested species is 82, and there are 180 proteins common in vertebrates genomes, but have insignificant hits in the other tested species. In contrary to the previous studies which use selected set of the genes and do not consider the whole genomes, this study proves that the similarity between human and chimpanzee is only 94.8.</span>

scholarly journals Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

PLoS Biology ◽  
2022 ◽  
Vol 20 (1) ◽  
pp. e3001508
Author(s):  
Grayson L. Chadwick ◽  
Connor T. Skennerton ◽  
Rafael Laso-Pérez ◽  
Andy O. Leu ◽  
Daan R. Speth ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Comparative Analysis ◽  
Comparative Genomics ◽  
Pure Culture ◽  
Methanogenic Archaea ◽  
Anaerobic Oxidation Of Methane ◽  
Genomic Features ◽  
Sulfate Reducing ◽  
Oxidation Of Methane ◽  
Reducing Bacteria

The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.

Sign in / Sign up

Export Citation Format

Share Document