scholarly journals Distribution and Evolutionary History of Sialic Acid Catabolism in the Phylum Actinobacteria

2022 ◽  
Author(s):  
Yisong Li ◽  
Ying Huang
Keyword(s):  
Sialic Acid ◽  
Evolutionary History ◽  
Sialic Acids ◽  
Free Living ◽  
Evolutionary Pathway ◽  
History Of

Sialic acids play essential roles in the physiology of humans and other metazoan animals, and microbial sialic acid catabolism (SAC) is one of the processes critical for pathogenesis. To date, microbial SAC is studied mainly in commensals and pathogens, while its distribution in free-living microbes and evolutionary pathway remain largely unexplored.

scholarly journals Myxosporea (Myxozoa, Cnidaria) Lack DNA Cytosine Methylation

2020 ◽  
Author(s):  
Ryan Kyger ◽  
Agusto Luzuriaga-Neira ◽  
Thomas Layman ◽  
Tatiana Orli Milkewitz Sandberg ◽  
Devika Singh ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Cytosine Methylation ◽  
Bisulfite Sequencing ◽  
Regulatory Mechanism ◽  
Regulation Of Gene Expression ◽  
Biological Processes ◽  
Free Living ◽  
Genome Bisulfite Sequencing ◽  
History Of ◽  
Dna Cytosine Methylation

Abstract DNA cytosine methylation is central to many biological processes, including regulation of gene expression, cellular differentiation, and development. This DNA modification is conserved across animals, having been found in representatives of sponges, ctenophores, cnidarians, and bilaterians, and with very few known instances of secondary loss in animals. Myxozoans are a group of microscopic, obligate endoparasitic cnidarians that have lost many genes over the course of their evolution from free-living ancestors. Here, we investigated the evolution of the key enzymes involved in DNA cytosine methylation in 29 cnidarians and found that these enzymes were lost in an ancestor of Myxosporea (the most speciose class of Myxozoa). Additionally, using whole-genome bisulfite sequencing, we confirmed that the genomes of two distant species of myxosporeans, Ceratonova shasta and Henneguya salminicola, completely lack DNA cytosine methylation. Our results add a notable and novel taxonomic group, the Myxosporea, to the very short list of animal taxa lacking DNA cytosine methylation, further illuminating the complex evolutionary history of this epigenetic regulatory mechanism.

scholarly journals Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dayana E. Salas-Leiva ◽  
Eelco C. Tromer ◽  
Bruce A. Curtis ◽  
Jon Jerlström-Hultqvist ◽  
Martin Kolisko ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Origin Recognition Complex ◽  
Common Ancestor ◽  
Genomic Analysis ◽  
Free Living ◽  
A Genome ◽  
History Of ◽  
Eukaryotic Dna ◽  
Comparative Genomics Analysis ◽  
Dna Processing

AbstractCells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.

scholarly journals Coral symbiotic algae calcifyex hospitein partnership with bacteria

2015 ◽  
Vol 112 (19) ◽  
pp. 6158-6163 ◽  
Author(s):  
Jörg C. Frommlet ◽  
Maria L. Sousa ◽  
Artur Alves ◽  
Sandra I. Vieira ◽  
David J. Suggett ◽  
...  
Keyword(s):  
Life History ◽  
Coral Reef ◽  
Evolutionary History ◽  
Central Importance ◽  
Free Living ◽  
Algal Communities ◽  
Symbiotic Algae ◽  
Coral Reef Ecosystems ◽  
History Of

Dinoflagellates of the genusSymbiodiniumare commonly recognized as invertebrate endosymbionts that are of central importance for the functioning of coral reef ecosystems. However, the endosymbiotic phase withinSymbiodiniumlife history is inherently tied to a more cryptic free-living (ex hospite) phase that remains largely unexplored. Here we show that free-livingSymbiodiniumspp. in culture commonly form calcifying bacterial–algal communities that produce aragonitic spherulites and encase the dinoflagellates as endolithic cells. This process is driven bySymbiodiniumphotosynthesis but occurs only in partnership with bacteria. Our findings not only place dinoflagellates on the map of microbial–algal organomineralization processes but also point toward an endolithic phase in theSymbiodiniumlife history, a phenomenon that may provide new perspectives on the biology and ecology ofSymbiodiniumspp. and the evolutionary history of the coral–dinoflagellate symbiosis.

scholarly journals Specificity in the symbiotic association between fungus-growing ants and protective Pseudonocardia bacteria

2010 ◽  
Vol 278 (1713) ◽  
pp. 1814-1822 ◽  
Author(s):  
Matías J. Cafaro ◽  
Michael Poulsen ◽  
Ainslie E. F. Little ◽  
Shauna L. Price ◽  
Nicole M. Gerardo ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Diversity ◽  
Antibiotic Production ◽  
Symbiotic Association ◽  
Free Living ◽  
Ant Colonies ◽  
History Of ◽  
Fungus Growing Ants ◽  
Related Fungus

Fungus-growing ants (tribe Attini) engage in a mutualism with a fungus that serves as the ants' primary food source, but successful fungus cultivation is threatened by microfungal parasites (genus Escovopsis ). Actinobacteria (genus Pseudonocardia ) associate with most of the phylogenetic diversity of fungus-growing ants; are typically maintained on the cuticle of workers; and infection experiments, bioassay challenges and chemical analyses support a role of Pseudonocardia in defence against Escovopsis through antibiotic production. Here we generate a two-gene phylogeny for Pseudonocardia associated with 124 fungus-growing ant colonies, evaluate patterns of ant– Pseudonocardia specificity and test Pseudonocardia antibiotic activity towards Escovopsis . We show that Pseudonocardia associated with fungus-growing ants are not monophyletic: the ants have acquired free-living strains over the evolutionary history of the association. Nevertheless, our analysis reveals a significant pattern of specificity between clades of Pseudonocardia and groups of related fungus-growing ants. Furthermore, antibiotic assays suggest that despite Escovopsis being generally susceptible to inhibition by diverse Actinobacteria, the ant-derived Pseudonocardia inhibit Escovopsis more strongly than they inhibit other fungi, and are better at inhibiting this pathogen than most environmental Pseudonocardia strains tested. Our findings support a model that many fungus-growing ants maintain specialized Pseudonocardia symbionts that help with garden defence.

scholarly journals Origin Recognition Complex (ORC) Evolution Is Influenced by Global Gene Duplication/Loss Patterns in Eukaryotic Genomes

2020 ◽  
Vol 12 (2) ◽  
pp. 3878-3889 ◽  
Author(s):  
Eduard Ocaña-Pallarès ◽  
Zaida Vergara ◽  
Bénédicte Desvoyes ◽  
Manuel Tejada-Jimenez ◽  
Ainoa Romero-Jurado ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Origin Recognition Complex ◽  
Free Living ◽  
Data Set ◽  
Genome Duplications ◽  
History Of ◽  
Eukaryotic Genomes ◽  
Eukaryotic Feature ◽  
Origin Recognition

Abstract The conservation of orthologs of most subunits of the origin recognition complex (ORC) has served to propose that the whole complex is common to all eukaryotes. However, various uncertainties have arisen concerning ORC subunit composition in a variety of lineages. Also, it is unclear whether the ancestral diversification of ORC in eukaryotes was accompanied by the neofunctionalization of some subunits, for example, role of ORC1 in centriole homeostasis. We have addressed these questions by reconstructing the distribution and evolutionary history of ORC1-5/CDC6 in a taxon-rich eukaryotic data set. First, we identified ORC subunits previously undetected in divergent lineages, which allowed us to propose a series of parsimonious scenarios for the origin of this multiprotein complex. Contrary to previous expectations, we found a global tendency in eukaryotes to increase or decrease the number of subunits as a consequence of genome duplications or streamlining, respectively. Interestingly, parasites show significantly lower number of subunits than free-living eukaryotes, especially those with the lowest genome size and gene content metrics. We also investigated the evolutionary origin of the ORC1 role in centriole homeostasis mediated by the PACT region in human cells. In particular, we tested the consequences of reducing ORC1 levels in the centriole-containing green alga Chlamydomonas reinhardtii. We found that the proportion of centrioles to flagella and nuclei was not dramatically affected. This, together with the PACT region not being significantly more conserved in centriole-bearing eukaryotes, supports the notion that this neofunctionalization of ORC1 would be a recent acquisition rather than an ancestral eukaryotic feature.

scholarly journals New endosymbiotic relationships between Mucoromycota and Burkholderiaceae representatives

2021 ◽  
Author(s):  
Alicja Okrasińska ◽  
Aleksandra Bokus ◽  
Katarzyna Duk ◽  
Aleksandra Gęsiorska ◽  
Blanka Sokołowska ◽  
...  
Keyword(s):  
Intimate Relationships ◽  
Evolutionary History ◽  
Free Living ◽  
16S Rdna Gene ◽  
Fungal Strains ◽  
The Family ◽  
Alternative Hypotheses ◽  
History Of ◽  
Terrestrial Fungi ◽  
Fungal Kingdom

Mucoromycota representatives are known to harbour two types of endohyphal bacteria (EHB) – Burkholderia related endobacteria (BRE) and Mycoplasma related endobacteria (MRE). While both BRE and MRE occur in fungi representing all subphyla of Mucoromycota, their distribution is not well studied. Therefore, it is difficult to resolve the evolutionary history of these associations in favour of one of the two alternative hypotheses explaining their origin: “early invasion” and “late invasion”. Our main goal was to fill this knowledge gap by surveying Mucoromycota fungi for presence of EHB. We screened 196 fungal strains from 16 genera using PCR-based approach to detect bacterial 16S rDNA gene, complemented with FISH imaging to confirm presence of bacteria within the hyphae. We detected Burkholderiaceae in ca. 20% of fungal strains. Some of these bacteria clustered phylogenetically with previously described BRE clades whereas others grouped with free-living Paraburkholderia. Importantly, the latter were detected in Umbelopsidales, which previously were not known to harbour endobacteria. Our results suggest that this group of EHB is recruited from the environment, supporting the late invasion scenario. This pattern complements the early invasion scenario apparent in the BRE clade of EHB. IMPORTANCE Bacteria living within fungal hyphae present an example of one of the most intimate relationships between fungi and bacteria. Even though there are several well-described examples of such partnerships, their prevalence within fungal kingdom remains unknown. Our study focused on early divergent terrestrial fungi in the phylum Mucoromycota. We found that ca. 20% of the strains tested, harboured bacteria from the family Burkholderiaceae. Not only did we confirm the presence of bacteria from previously described endosymbiont clades, we also identified new group of endohyphal Burkholderiaceae representing the genus Paraburkholderia. We established that more than half of the screened Umbelopsis strains were positive for bacteria from this new group. We also determined that, while previously described BRE codiverged with their fungal hosts, Paraburkholderia symbionts did not.

scholarly journals Extreme Genomic Makeover: Evolutionary History of Maternally-transmitted Clam Symbionts

2020 ◽  
Author(s):  
M Perez ◽  
C Breusing ◽  
B Angers ◽  
YJ Won ◽  
CR Young
Keyword(s):  
Genome Evolution ◽  
Evolutionary History ◽  
Free Living ◽  
Genome Wide ◽  
A Genome ◽  
Chemosynthetic Bacteria ◽  
History Of ◽  
Vesicomyid Clam ◽  
Do So

AbstractGiven their recent switch to a vertically-transmitted intracellular lifestyle, the chemosynthetic bacteria associated with deep-sea vesicomyid clams are an excellent model system to study the processes underlying reductive genome evolution. In this study, we provide the first estimates of the relative contributions of drift, recombination and selection in shaping the ongoing reductive genome evolution in these symbionts. To do so, we compared the genomes of endosymbionts associated with 11 vesicomyid clam species to that of closely related free-living bacteria and their respective hosts’ mitochondria. Our investigation confirmed that neutral evolutionary processes were the dominant driver of reductive genome evolution in this group and highlighted the important role of horizontal gene transfer in mitigating genome erosion. Finally, a genome-wide screen for episodic positive selection across the symbiont phylogeny revealed the pervasive role of selective processes in maintaining symbiont functional integrity.

Comparison of Arctic and Antarctic teleost haemoglobins: primary structure, function and phytogeny

2004 ◽  
Vol 16 (1) ◽  
pp. 59-69 ◽  
Author(s):  
CINZIA VERDE ◽  
ELIO PARISI ◽  
GUIDO DI PRISCO
Keyword(s):  
Structure Function ◽  
Cold Adaptation ◽  
Evolutionary History ◽  
The Arctic ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Root Effect ◽  
Evolutionary Pathway ◽  
History Of ◽  
The Antarctic

Organisms living in the Arctic and Antarctic are exposed to strong environmental constraints, especially temperature. Consequently, haemoglobin evolution has included adaptations with implications at the biochemical, physiological and molecular levels. The northern and southern polar oceans have very different oceanographic characteristics. Within the study of the molecular bases of cold adaptation in fish inhabiting polar habitats, and taking advantage of the information available on haemoglobin structure and function, we analysed the evolutionary history of the α and β globins of Antarctic and Arctic haemoglobins, under the assumption of the molecular-clock hypothesis, as a basis for reconstructing the phylogenetic relationships between species. Temperate fish, including two non-Antarctic notothenioids of special evolutionary interest, were also considered. Phylogenetic analysis was performed on the multiple sequence alignments constructed with the programme Clustal X. Tree topologies indicate that the chains of Antarctic major and minor haemoglobins cluster in two well separated groups and diverged prior to cold adaptation, forming a monophyletic group. In Arctic haemoglobins, the structure/function relationship reveals important differences in comparison with Antarctic ones, indicating a distinct evolutionary pathway. The Arctic ichthyofauna (unlike the Antarctic, dominated by one taxonomically uniform group) is characterized by high diversity, reflected in the phylogeny of a given trait. The constant physico-chemical conditions of the Antarctic waters are matched by a clear grouping of fish globin sequences, whereas the variability typical of the Arctic Ocean corresponds to high sequence variation, reflected in the trees by scattered intermediate positions between the Antarctic and non-Antarctic clades. The evolutionary history of the Root effect, an important physiological feature of fish haemoglobin, was investigated. Analysis of the fate of the residues of the β chains suggested to be correlated with the Root effect indicate that they should rather be regarded as ancestral characters, inherited by some species but not by others.

Systematics of the Gracilariales (Rhodophyta) including new subfamilies, tribes, subgenera, and two new genera, Agarophyton gen. nov. and Crassa gen. nov.

Phytotaxa ◽  
2018 ◽  
Vol 374 (1) ◽  
pp. 1 ◽  
Author(s):  
CARLOS FREDERICO D. GURGEL ◽  
JAMES N. NORRIS ◽  
WILLIAM E. SCHMIDT ◽  
HAU NHU LE ◽  
SUZANNE FREDERICQ
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
New Genera ◽  
New Classification ◽  
Free Living ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Evolutionary Lineages ◽  
Stable Classification

The Gracilariales is a red macroalgal order and the main global source of the economically important agar, a marine phycocolloid. Independent comparative morphological and molecular phylogenetic studies over the last 20 years have revealed the existence of seven major clades recognizable as distinct genera. Of these major clades only four free-living genera have been widely accepted taxonomically: Curdiea, Melanthalia, Gracilariopsis, and Gracilaria. Three other clades comprise the reinstatement of the genus Hydropuntia and the proposal of two new genera, Agarophyton and Crassa, described herein. Based on new rbcL DNA sequences, and along with a reassessment of published comparative morphological and molecular phylogenetic studies, we argue that the latter three genera represent distinct evolutionary lineages in the Gracilariaceae, and propose a new classification for the order Gracilariales. Our new proposal incorporates the most current understanding of the evolutionary history of the order, establishes a natural and stable classification system, and provides the basis for the recognization of intra-family ranks. Our classification scheme reconciles all molecular phylogenetic studies published to date.

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