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1. Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki - and Thorarchaeota

   https://doi.org/10.1128/mBio.02039-19  

   Manoharan, Lokeshwaran; Kozlowski, Jessica A.; Murdoch, Robert W.; Löffler, Frank E.; Sousa, Filipa L.; Schleper, Christa; Hug, Laura; Gribaldo, Simonetta (October 2019, mBio)

   Moran, Mary Ann (Ed.)

   ABSTRACT The genomes of Asgard Archaea , a novel archaeal proposed superphylum, share an enriched repertoire of eukaryotic signature genes and thus promise to provide insights into early eukaryote evolution. However, the distribution, metabolisms, cellular structures, and ecology of the members within this superphylum are not well understood. Here we provide a meta-analysis of the environmental distribution of the Asgard archaea, based on available 16S rRNA gene sequences. Metagenome sequencing of samples from a salt-crusted lagoon on the Baja California Peninsula of Mexico allowed the assembly of a new Thorarchaeota and three Lokiarchaeota genomes. Comparative analyses of all known Lokiarchaeota and Thorarchaeota genomes revealed overlapping genome content, including central carbon metabolism. Members of both groups contained putative reductive dehalogenase genes, suggesting that these organisms might be able to metabolize halogenated organic compounds. Unlike the first report on Lokiarchaeota , we identified genes encoding glycerol-1-phosphate dehydrogenase in all Loki - and Thorarchaeota genomes, suggesting that these organisms are able to synthesize bona fide archaeal lipids with their characteristic glycerol stereochemistry. IMPORTANCE Microorganisms of the superphylum Asgard Archaea are considered to be the closest living prokaryotic relatives of eukaryotes (including plants and animals) and thus promise to give insights into the early evolution of more complex life forms. However, very little is known about their biology as none of the organisms has yet been cultivated in the laboratory. Here we report on the ecological distribution of Asgard Archaea and on four newly sequenced genomes of the Lokiarchaeota and Thorarchaeota lineages that give insight into possible metabolic features that might eventually help to identify these enigmatic groups of archaea in the environment and to culture them. 

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2. Archaeal roots of intramembrane aspartyl protease siblings signal peptide peptidase and presenilin

   https://doi.org/10.1002/prot.26009  

   Raut, Priyam; Glass, Jennifer B.; Lieberman, Raquel L. (October 2020, Proteins: Structure, Function, and Bioinformatics)

   Abstract Signal peptides help newly synthesized proteins reach the cell membrane or be secreted. As part of a biological process key to immune response and surveillance in humans, and associated with diseases, for example, Alzheimer, remnant signal peptides and other transmembrane segments are proteolyzed by the intramembrane aspartyl protease (IAP) enzyme family. Here, we identified IAP orthologs throughout the tree of life. In addition to eukaryotes, IAPs are encoded in metabolically diverse archaea from a wide range of environments. We found three distinct clades of archaeal IAPs: (a)Euryarchaeota(eg, halophilicHalobacteriales, methanogenicMethanosarcinalesandMethanomicrobiales, marinePoseidoniales, acidophilicThermoplasmatales, hyperthermophilicArchaeoglobusspp.), (b) DPANN, and (c)Bathyarchaeota,Crenarchaeota, andAsgard. IAPs were also present in bacterial genomes from uncultivated members of Candidate Phylum Radiation, perhaps due to horizontal gene transfer from DPANN archaeal lineages. Sequence analysis of the catalytic motif YD…GXGD (where X is any amino acid) in IAPs from archaea and bacteria reveals WD inLokiarchaeotaand many residue types in the X position. Gene neighborhood analysis in halophilic archaea shows IAP genes near corrinoid transporters (btuCDFgenes). In marineEuryarchaeota, a putative BtuF‐like domain is found in N‐terminus of the IAP gene, suggesting a role for these IAPs in metal ion cofactor or other nutrient scavenging. Interestingly, eukaryotic IAP family members appear to have evolved either fromEuryarchaeotaor fromAsgardarchaea. Taken together, our phylogenetic and bioinformatics analysis should prompt experiments to probe the biological roles of IAPs in prokaryotic secretomes. 

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3. The supragenic organization of glycoside hydrolase encoding genes reveals distinct strategies for carbohydrate utilization in bacteria

   https://doi.org/10.3389/fmicb.2023.1179206  

   Berlemont, Renaud (June 2023, Frontiers in Microbiology)

   Obulisamy Parthiba Karthikeyan (Ed.)

   Glycoside hydrolases (GHs) are carbohydrate-active enzymes essential for many environmental (e.g., carbon cycling) and biotechnological (e.g., biofuels) processes. The complete processing of carbohydrates by bacteria requires many enzymes acting synergistically. Here, I investigated the clustered or scattered distribution of 406,337 GH-genes and their association with transporter genes identified in 15,640 completely sequenced bacterial genomes. Different bacterial lineages displayed conserved levels of clustered or scattered GH-genes, but overall, the GH-genes clustering was generally higher than in randomized genomes. In lineages with highly clustered GH-genes (e.g.,Bacteroides, Paenibacillus), clustered genes shared the same orientation. These codirectional gene clusters potentially facilitate the genes' co-expression by allowing transcriptional read-through and, at least in some cases, forming operons. In several taxa, the GH-genes clustered with distinct types of transporter genes. The type of transporter genes and the distribution of the so-called GH:TR-genes clusters were conserved in selected lineages. Globally, the phylogenetically conserved clustering of the GH-genes with transporter genes highlights the central function of carbohydrate processing across bacterial lineages. In addition, in bacteria with the most identified GH-genes, the genomic adaptations for carbohydrate processing also mirrored the broad environmental origin of the sequenced strains (e.g., soil and mammal gut) suggesting that a combination of evolutionary history and the environment selects for the specific supragenic organization of the GH-genes supporting the carbohydrate processing in bacterial genomes. 

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4. The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria

   https://doi.org/10.3390/genes10030233  

   Fullmer, Matthew S.; Ouellette, Matthew; Louyakis, Artemis S.; Papke, R. Thane; Gogarten, Johann Peter (March 2019, Genes)

   Restriction–modification (RM) systems in bacteria are implicated in multiple biological roles ranging from defense against parasitic genetic elements, to selfish addiction cassettes, and barriers to gene transfer and lineage homogenization. In bacteria, DNA-methylation without cognate restriction also plays important roles in DNA replication, mismatch repair, protein expression, and in biasing DNA uptake. Little is known about archaeal RM systems and DNA methylation. To elucidate further understanding for the role of RM systems and DNA methylation in Archaea, we undertook a survey of the presence of RM system genes and related genes, including orphan DNA methylases, in the halophilic archaeal class Halobacteria. Our results reveal that some orphan DNA methyltransferase genes were highly conserved among lineages indicating an important functional constraint, whereas RM systems demonstrated patchy patterns of presence and absence. This irregular distribution is due to frequent horizontal gene transfer and gene loss, a finding suggesting that the evolution and life cycle of RM systems may be best described as that of a selfish genetic element. A putative target motif (CTAG) of one of the orphan methylases was underrepresented in all of the analyzed genomes, whereas another motif (GATC) was overrepresented in most of the haloarchaeal genomes, particularly in those that encoded the cognate orphan methylase. 

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5. Discovering regulators in post transcriptional control of the biological clock of Neurospora crassa using Variable Topology Ensemble Methods on GPUs

   https://doi.org/10.1109/ACCESS.2018.2871876  

   Al-Omari, A.; Griffith, J.; Caranica, C.; Taha, T.; Schuttler, H.-B.; Arnold, J. (October 2018, IEEE access)

   In previous work we reconstructed the entire transcriptional network for all 2,418 clock-associated genes in the model filamentous fungus, N. crassa. Several authors have suggested that there is extensive post-transcriptional control in the genome-wide clock network (IEEE 3: 27, 2015). Here we have successfully reconstructed the entire clock network in N. crassa with a Variable Topology Ensemble Method (VTENS), assigning each clock-associated gene to the regulation of one or more of 5 transcription factors as well as to 6 RNA operons. The resulting network provides a unifying framework to explore the clock’s linkage to metabolism through post-transcriptional regulation, in which ~850 genes are predicted to fall under the regulatory control of an RNA operon. A unique feature of all of the RNA operons inferred is their functional connection to genes connected to the ribosome. We have been successful in distinguishing several hypotheses about regulatory topologies of the clock network through protein profiling of the regulators. 

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