scholarly journals Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses

2022 ◽  
Vol 119 (3) ◽  
pp. e2115449119
Author(s):  
Hiroyuki D. Sakai ◽  
Naswandi Nur ◽  
Shingo Kato ◽  
Masahiro Yuki ◽  
Michiru Shimizu ◽  
...  
Keyword(s):  
Host Switching ◽  
Biological Functions ◽  
Genome Sequences ◽  
Ecological Functions ◽  
Archaeal Species ◽  
Genomic Analyses ◽  
Culture Independent ◽  
Acidic Environments ◽  
Genome Analyses ◽  
Insight Into

Decades of culture-independent analyses have resulted in proposals of many tentative archaeal phyla with no cultivable representative. Members of DPANN (an acronym of the names of the first included phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Nanoarchaeota), an archaeal superphylum composed of at least 10 of these tentative phyla, are generally considered obligate symbionts dependent on other microorganisms. While many draft/complete genome sequences of DPANN archaea are available and their biological functions have been considerably predicted, only a few examples of their successful laboratory cultivation have been reported, limiting our knowledge of their symbiotic lifestyles. Here, we investigated physiology, morphology, and host specificity of an archaeon of the phylum “Candidatus Micrarchaeota” (ARM-1) belonging to the DPANN superphylum by cultivation. We constructed a stable coculture system composed of ARM-1 and its original host Metallosphaera sp. AS-7 belonging to the order Sulfolobales. Further host-switching experiments confirmed that ARM-1 grew on five different archaeal species from three genera—Metallosphaera, Acidianus, and Saccharolobus—originating from geologically distinct hot, acidic environments. The results suggested the existence of DPANN archaea that can grow by relying on a range of hosts. Genomic analyses showed inferred metabolic capabilities, common/unique genetic contents of ARM-1 among cultivated micrarchaeal representatives, and the possibility of horizontal gene transfer between ARM-1 and members of the order Sulfolobales. Our report sheds light on the symbiotic lifestyles of DPANN archaea and will contribute to the elucidation of their biological/ecological functions.

scholarly journals Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome

2021 ◽  
Vol 22 (15) ◽  
pp. 8012
Author(s):  
Rongxin Zhang ◽  
Yajun Liu ◽  
Xingxing Zhang ◽  
Ke Xiao ◽  
Yue Hou ◽  
...  
Keyword(s):  
Bioinformatics Analysis ◽  
Biological Functions ◽  
Bioinformatics Pipeline ◽  
The Real ◽  
Human Transcriptome ◽  
Gene Sets ◽  
Nucleic Acid Structures ◽  
Regulatory Functions ◽  
Whole Transcriptome ◽  
Insight Into

G-quadruplexes are the non-canonical nucleic acid structures that are preferentially formed in G-rich regions. This structure has been shown to be associated with many biological functions. Regardless of the broad efforts on DNA G-quadruplexes, we still have limited knowledge on RNA G-quadruplexes, especially in a transcriptome-wide manner. Herein, by integrating the DMS-seq and the bioinformatics pipeline, we profiled and depicted the RNA G-quadruplexes in the human transcriptome. The genes that contain RNA G-quadruplexes in their specific regions are significantly related to immune pathways and the COVID-19-related gene sets. Bioinformatics analysis reveals the potential regulatory functions of G-quadruplexes on miRNA targeting at the scale of the whole transcriptome. In addition, the G-quadruplexes are depleted in the putative, not the real, PAS-strong poly(A) sites, which may weaken the possibility of such sites being the real cleaved sites. In brief, our study provides insight into the potential function of RNA G-quadruplexes in post-transcription.

Endogenous Retroviruses Drive Resistance and Promotion of Exogenous Retroviral Homologs

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Elliott S. Chiu ◽  
Sue VandeWoude
Keyword(s):  
Immune Modulation ◽  
Viral Infections ◽  
Viral Evolution ◽  
Endogenous Retroviruses ◽  
Annual Review ◽  
Publication Date ◽  
Biological Functions ◽  
Self Tolerance ◽  
Vertebrate Hosts ◽  
Insight Into

Endogenous retroviruses (ERVs) serve as markers of ancient viral infections and provide invaluable insight into host and viral evolution. ERVs have been exapted to assist in performing basic biological functions, including placentation, immune modulation, and oncogenesis. A subset of ERVs share high nucleotide similarity to circulating horizontally transmitted exogenous retrovirus (XRV) progenitors. In these cases, ERV–XRV interactions have been documented and include ( a) recombination to result in ERV–XRV chimeras, ( b) ERV induction of immune self-tolerance to XRV antigens, ( c) ERV antigen interference with XRV receptor binding, and ( d) interactions resulting in both enhancement and restriction of XRV infections. Whereas the mechanisms governing recombination and immune self-tolerance have been partially determined, enhancement and restriction of XRV infection are virus specific and only partially understood. This review summarizes interactions between six unique ERV–XRV pairs, highlighting important ERV biological functions and potential evolutionary histories in vertebrate hosts. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Conjugative plasmids: vessels of the communal gene pool

2009 ◽  
Vol 364 (1527) ◽  
pp. 2275-2289 ◽  
Author(s):  
Anders Norman ◽  
Lars H. Hansen ◽  
Søren J. Sørensen
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Significant Contribution ◽  
Prokaryotic Genome ◽  
Whole Genome ◽  
Adaptive Traits ◽  
Conjugative Plasmids ◽  
Environmental Setting ◽  
Genome Analyses ◽  
Insight Into

Comparative whole-genome analyses have demonstrated that horizontal gene transfer (HGT) provides a significant contribution to prokaryotic genome innovation. The evolution of specific prokaryotes is therefore tightly linked to the environment in which they live and the communal pool of genes available within that environment. Here we use the term supergenome to describe the set of all genes that a prokaryotic ‘individual’ can draw on within a particular environmental setting. Conjugative plasmids can be considered particularly successful entities within the communal pool, which have enabled HGT over large taxonomic distances. These plasmids are collections of discrete regions of genes that function as ‘backbone modules’ to undertake different aspects of overall plasmid maintenance and propagation. Conjugative plasmids often carry suites of ‘accessory elements’ that contribute adaptive traits to the hosts and, potentially, other resident prokaryotes within specific environmental niches. Insight into the evolution of plasmid modules therefore contributes to our knowledge of gene dissemination and evolution within prokaryotic communities. This communal pool provides the prokaryotes with an important mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized ‘private genes’.

Archaeal biofilms: widespread and complex

2013 ◽  
Vol 41 (1) ◽  
pp. 393-398 ◽  
Author(s):  
Sabrina Fröls
Keyword(s):  
Biofilm Formation ◽  
Extracellular Polymeric Substances ◽  
Bacterial Species ◽  
Surface Adhesion ◽  
Form Complex ◽  
Abiotic Surfaces ◽  
Archaeal Species ◽  
Physical And Chemical ◽  
Insight Into ◽  
Mixed Communities

Biofilms or multicellular structures become accepted as the dominant microbial lifestyle in Nature, but in the past they were only studied extensively in bacteria. Investigations on archaeal monospecies cultures have shown that many archaeal species are able to adhere on biotic and abiotic surfaces and form complex biofilm structures. Biofilm-forming archaea were identified in a broad range of extreme and moderate environments. Natural biofilms observed are mostly mixed communities composed of archaeal and bacterial species of various abundances. The physiological functions of the archaea identified in such mixed communities suggest a significant impact on the biochemical cycles maintaining the flow and recycling of the nutrients on earth. Therefore it is of high interest to investigate the characteristics and mechanisms underlying the archaeal biofilm formation. In the present review, I summarize and discuss the present investigations of biofilm-forming archaeal species, i.e. their diverse biofilm architectures in monospecies or mixed communities, the identified EPSs (extracellular polymeric substances), archaeal structures mediating surface adhesion or cell–cell connections, and the response to physical and chemical stressors implying that archaeal biofilm formation is an adaptive reaction to changing environmental conditions. A first insight into the molecular differentiation of cells within archaeal biofilms is given.

scholarly journals Therapeutic Exosomes in Prognosis and Developments of Coronary Artery Disease

2021 ◽  
Vol 8 ◽  
Author(s):  
Ai-Qun Chen ◽  
Xiao-Fei Gao ◽  
Zhi-Mei Wang ◽  
Feng Wang ◽  
Shuai Luo ◽  
...  
Keyword(s):  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Cell Types ◽  
Biological Functions ◽  
Stent Restenosis ◽  
Artery Disease ◽  
Almost All ◽  
Different Cell Types ◽  
Insight Into ◽  
Systematic Knowledge

Exosomes, with an diameter of 30~150 nm, could be released from almost all types of cells, which contain diverse effective constituent, such as RNAs, proteins, lipids, and so on. In recent years, exosomes have been verified to play an important role in mechanism, diagnosis, treatment, and prognosis of cardiovascular disease, especially coronary artery disease (CAD). Moreover, it has also been shown that exosomes derived from different cell types have various biological functions based on the cell stimulation and microenvironment. However, therapeutic exosomes are currently far away from clinical translation, despite it is full of hope. In this review, we summarize an update of the recent studies and systematic knowledge of therapeutic exosomes in atherosclerosis, myocardial infarction, and in-stent restenosis, which might provide a novel insight into the treatment of CAD and promote the potential clinical application of therapeutic exosomes.

scholarly journals Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Brianna J. Klein ◽  
Suk Min Jang ◽  
Catherine Lachance ◽  
Wenyi Mi ◽  
Jie Lyu ◽  
...  
Keyword(s):  
Posttranslational Modification ◽  
Memory Impairment ◽  
Target Genes ◽  
Epigenetic Mark ◽  
Mechanistic Insight ◽  
Genomic Analyses ◽  
Insight Into

Abstract Acetylation of histone H3K23 has emerged as an essential posttranslational modification associated with cancer and learning and memory impairment, yet our understanding of this epigenetic mark remains insufficient. Here, we identify the native MORF complex as a histone H3K23-specific acetyltransferase and elucidate its mechanism of action. The acetyltransferase function of the catalytic MORF subunit is positively regulated by the DPF domain of MORF (MORFDPF). The crystal structure of MORFDPF in complex with crotonylated H3K14 peptide provides mechanistic insight into selectivity of this epigenetic reader and its ability to recognize both histone and DNA. ChIP data reveal the role of MORFDPF in MORF-dependent H3K23 acetylation of target genes. Mass spectrometry, biochemical and genomic analyses show co-existence of the H3K23ac and H3K14ac modifications in vitro and co-occupancy of the MORF complex, H3K23ac, and H3K14ac at specific loci in vivo. Our findings suggest a model in which interaction of MORFDPF with acylated H3K14 promotes acetylation of H3K23 by the native MORF complex to activate transcription.

scholarly journals Pyruvate Substitutions on Glycoconjugates

2019 ◽  
Vol 20 (19) ◽  
pp. 4929 ◽  
Author(s):  
Hager ◽  
Sützl ◽  
Stefanović ◽  
Blaukopf ◽  
Schäffer
Keyword(s):  
Cell Wall ◽  
Cell Surface ◽  
Early Stage ◽  
Ring Structure ◽  
Genome Sequences ◽  
Cell Wall Component ◽  
Cellular Physiology ◽  
Associated Functions ◽  
Acid Labile ◽  
Insight Into

Glycoconjugates are the most diverse biomolecules of life. Mostly located at the cell surface, they translate into cell-specific “barcodes” and offer a vast repertoire of functions, including support of cellular physiology, lifestyle, and pathogenicity. Functions can be fine-tuned by non-carbohydrate modifications on the constituting monosaccharides. Among these modifications is pyruvylation, which is present either in enol or ketal form. The most commonly best-understood example of pyruvylation is enol-pyruvylation of N-acetylglucosamine, which occurs at an early stage in the biosynthesis of the bacterial cell wall component peptidoglycan. Ketal-pyruvylation, in contrast, is present in diverse classes of glycoconjugates, from bacteria to algae to yeast—but not in humans. Mild purification strategies preventing the loss of the acid-labile ketal-pyruvyl group have led to a collection of elucidated pyruvylated glycan structures. However, knowledge of involved pyruvyltransferases creating a ring structure on various monosaccharides is scarce, mainly due to the lack of knowledge of fingerprint motifs of these enzymes and the unavailability of genome sequences of the organisms undergoing pyruvylation. This review compiles the current information on the widespread but under-investigated ketal-pyruvylation of monosaccharides, starting with different classes of pyruvylated glycoconjugates and associated functions, leading to pyruvyltransferases, their specificity and sequence space, and insight into pyruvate analytics.

scholarly journals The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Lisong Hu ◽  
Zhongping Xu ◽  
Maojun Wang ◽  
Rui Fan ◽  
Daojun Yuan ◽  
...  
Keyword(s):  
Reference Genome ◽  
Gene Families ◽  
Black Pepper ◽  
Piper Nigrum ◽  
Comparative Genomic ◽  
Specific Gene ◽  
Phylogenomic Analysis ◽  
Genomic Analyses ◽  
Species Specific ◽  
Insight Into

Abstract Black pepper (Piper nigrum), dubbed the ‘King of Spices’ and ‘Black Gold’, is one of the most widely used spices. Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, BioNano DLS optical mapping, and Hi-C mapping technologies. The 761.2 Mb sequences (45 scaffolds with an N50 of 29.8 Mb) are assembled into 26 pseudochromosomes. A phylogenomic analysis of representative plant genomes places magnoliids as sister to the monocots-eudicots clade and indicates that black pepper has diverged from the shared Laurales-Magnoliales lineage approximately 180 million years ago. Comparative genomic analyses reveal specific gene expansions in the glycosyltransferase, cytochrome P450, shikimate hydroxycinnamoyl transferase, lysine decarboxylase, and acyltransferase gene families. Comparative transcriptomic analyses disclose berry-specific upregulated expression in representative genes in each of these gene families. These data provide an evolutionary perspective and shed light on the metabolic processes relevant to the molecular basis of species-specific piperine biosynthesis.

scholarly journals Venom Function of a New Species of Megalomyrmex Forel, 1885 (Hymenoptera: Formicidae)

Toxins ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 679
Author(s):  
Kyle Sozanski ◽  
Lívia Pires do Prado ◽  
Andrew J. Mularo ◽  
Victoria A. Sadowski ◽  
Tappey H. Jones ◽  
...  
Keyword(s):  
New Species ◽  
Solenopsis Invicta ◽  
Pest Species ◽  
Ecological Functions ◽  
Free Living ◽  
Great Insight ◽  
Ant Venom ◽  
And Function ◽  
A New Species ◽  
Insight Into

Alkaloids are important metabolites found across a variety of organisms with diverse ecological functions. Of particular interest are alkaloids found in ants, organisms well known for dominating the ecosystems they dwell in. Within ants, alkaloids are found in venom and function as potent weapons against heterospecific species. However, research is often limited to pest species or species with parasitic lifestyles and thus fails to address the broader ecological function of ant venom alkaloids. Here we describe a new species of free-living Megalomyrmex ant: Megalomyrmex peetersi sp. n. In addition, we identify its singular venom alkaloid (trans-2-butyl-5-heptylpyrrolidine) and elucidate the antibiotic and insecticidal functions of its venom. Our results show that Megalomyrmex peetersi sp. n. venom is an effective antibiotic and insecticide. These results are comparable to venom alkaloids found in other ant species, such as Solenopsis invicta. This research provides great insight into venom alkaloid function, and it is the first study to explore these ideas in the Megalomyrmex system.

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