Author Correction: Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist

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.

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Genomic analysis reveals depression due to both individual and maternal inbreeding in a free‐living mammal population

Molecular Ecology ◽

10.1111/mec.13681 ◽

2016 ◽

Vol 25 (13) ◽

pp. 3152-3168 ◽

Cited By ~ 38

Author(s):

Camillo Bérénos ◽

Philip A. Ellis ◽

Jill G. Pilkington ◽

Josephine M. Pemberton

Keyword(s):

Genomic Analysis ◽

Free Living

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Symbiotic Burkholderia Species Show Diverse Arrangements of nif/fix and nod Genes and Lack Typical High-Affinity Cytochrome cbb3 Oxidase Genes

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-05-16-0091-r ◽

2016 ◽

Vol 29 (8) ◽

pp. 609-619 ◽

Cited By ~ 28

Author(s):

Sofie E. De Meyer ◽

Leah Briscoe ◽

Pilar Martínez-Hidalgo ◽

Christina M. Agapakis ◽

Paulina Estrada de-los Santos ◽

...

Keyword(s):

16S Rrna ◽

Gene Sequencing ◽

Genomic Analysis ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Free Living ◽

Nod Genes ◽

Electron Transport Chains ◽

Rrna Gene Sequencing ◽

Fix Genes

Genome analysis of fourteen mimosoid and four papilionoid beta-rhizobia together with fourteen reference alpha-rhizobia for both nodulation (nod) and nitrogen-fixing (nif/fix) genes has shown phylogenetic congruence between 16S rRNA/MLSA (combined 16S rRNA gene sequencing and multilocus sequence analysis) and nif/fix genes, indicating a free-living diazotrophic ancestry of the beta-rhizobia. However, deeper genomic analysis revealed a complex symbiosis acquisition history in the beta-rhizobia that clearly separates the mimosoid and papilionoid nodulating groups. Mimosoid-nodulating beta-rhizobia have nod genes tightly clustered in the nodBCIJHASU operon, whereas papilionoid-nodulating Burkholderia have nodUSDABC and nodIJ genes, although their arrangement is not canonical because the nod genes are subdivided by the insertion of nif and other genes. Furthermore, the papilionoid Burkholderia spp. contain duplications of several nod and nif genes. The Burkholderia nifHDKEN and fixABC genes are very closely related to those found in free-living diazotrophs. In contrast, nifA is highly divergent between both groups, but the papilionoid species nifA is more similar to alpha-rhizobia nifA than to other groups. Surprisingly, for all Burkholderia, the fixNOQP and fixGHIS genes required for cbb3 cytochrome oxidase production and assembly are missing. In contrast, symbiotic Cupriavidus strains have fixNOQPGHIS genes, revealing a divergence in the evolution of two distinct electron transport chains required for nitrogen fixation within the beta-rhizobia.

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Redox Chemistry in the Genome: Emergence of the [4Fe4S] Cofactor in Repair and Replication

Annual Review of Biochemistry ◽

10.1146/annurev-biochem-013118-110644 ◽

2019 ◽

Vol 88 (1) ◽

pp. 163-190 ◽

Cited By ~ 18

Author(s):

Jacqueline K. Barton ◽

Rebekah M.B. Silva ◽

Elizabeth O'Brien

Keyword(s):

Charge Transport ◽

Fold Increase ◽

Redox Signaling ◽

Processing Enzymes ◽

Dna Charge Transport ◽

Eukaryotic Dna ◽

Redox Switch ◽

Signaling Interactions ◽

Dna Electrochemistry ◽

Dna Processing

Many DNA-processing enzymes have been shown to contain a [4Fe4S] cluster, a common redox cofactor in biology. Using DNA electrochemistry, we find that binding of the DNA polyanion promotes a negative shift in [4Fe4S] cluster potential, which corresponds thermodynamically to a ∼500-fold increase in DNA-binding affinity for the oxidized [4Fe4S]3+cluster versus the reduced [4Fe4S]2+cluster. This redox switch can be activated from a distance using DNA charge transport (DNA CT) chemistry. DNA-processing proteins containing the [4Fe4S] cluster are enumerated, with possible roles for the redox switch highlighted. A model is described where repair proteins may signal one another using DNA-mediated charge transport as a first step in their search for lesions. The redox switch in eukaryotic DNA primases appears to regulate polymerase handoff, and in DNA polymerase δ, the redox switch provides a means to modulate replication in response to oxidative stress. We thus describe redox signaling interactions of DNA-processing [4Fe4S] enzymes, as well as the most interesting potential players to consider in delineating new DNA-mediated redox signaling networks.

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The hidden pangenome: comparative genomics reveals pervasive diversity in symbiotic and free-living sulfur-oxidizing bacteria

10.1101/2020.12.11.421487 ◽

2020 ◽

Author(s):

Rebecca Ansorge ◽

Stefano Romano ◽

Lizbeth Sayavedra ◽

Maxim Rubin-Blum ◽

Harald Gruber-Vodicka ◽

...

Keyword(s):

Defense Mechanisms ◽

Hydrothermal Vents ◽

Driving Forces ◽

Genetic Material ◽

Genomic Analysis ◽

Comparative Genomic ◽

Free Living ◽

Bacterial Populations ◽

Genomic Studies ◽

Sulfur Oxidizing

AbstractSulfur-oxidizing Thioglobaceae, often referred to as SUP05 and Arctic96BD clades, are widespread and common to hydrothermal vents and oxygen minimum zones. They impact global biogeochemical cycles and exhibit a variety of host-associated and free-living lifestyles. The evolutionary driving forces that led to the versatility, adoption of multiple lifestyles and global success of this family are largely unknown. Here, we perform an in-depth comparative genomic analysis using all available and newly generated Thioglobaceae genomes. Gene content variation was common, throughout taxonomic ranks and lifestyles. We uncovered a pool of variable genes within most Thioglobaceae populations in single environmental samples and we referred to this as the ‘hidden pangenome’. The ‘hidden pangenome’ is often overlooked in comparative genomic studies and our results indicate a much higher intra-specific diversity within environmental bacterial populations than previously thought. Our results show that core-community functions are different from species core genomes suggesting that core functions across populations are divided among the intra-specific members within a population. Defense mechanisms against foreign DNA and phages were enriched in symbiotic lineages, indicating an increased exchange of genetic material in symbioses. Our study suggests that genomic plasticity and frequent exchange of genetic material drives the global success of this family by increasing its evolvability in a heterogeneous environment.

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The Many Lives of Nontuberculous Mycobacteria

Journal of Bacteriology ◽

10.1128/jb.00739-17 ◽

2018 ◽

Vol 200 (11) ◽

Cited By ~ 33

Author(s):

Tiffany A. Claeys ◽

Richard T. Robinson

Keyword(s):

Biofilm Formation ◽

Nontuberculous Mycobacteria ◽

Genomic Analysis ◽

Mycobacterium Abscessus ◽

Aquatic Environments ◽

Free Living ◽

Content Type ◽

As Species ◽

Acquired Immunodeficiency ◽

The Many

ABSTRACTNontuberculous mycobacteria (NTM) include species that colonize human epithelia, as well as species that are ubiquitous in soil and aquatic environments. NTM that primarily inhabit soil and aquatic environments include theMycobacterium aviumcomplex (MAC) (M. aviumandMycobacterium intracellulare) and theMycobacterium abscessuscomplex (MABSC) (M. abscessussubsp.abscessus,M. abscessussubsp.massiliense, andM. abscessussubsp.bolletii) and can be free living, biofilm associated, or amoeba associated. Although NTM are rarely pathogenic in immunocompetent individuals, individuals who are immunocompromised, due to either an inherited or acquired immunodeficiency, are highly susceptible to NTM infection (NTMI). Several characteristics, such as biofilm formation and the ability of select NTM species to form distinct colony morphotypes, all may play a role in pathogenesis that is not observed in the related, well-characterized pathogenMycobacterium tuberculosis. Different morphotypes of NTM have been recognized and characterized since the 1950s, but the mechanisms that underlie colony phenotype change and subsequent differences in pathogenicity are just beginning to be explored. Advances in genomic analysis have led to progress in identifying genes important to the pathogenesis and persistence of MAC disease as well as in illuminating genetic aspects of different colony morphotypes. Here we review recent literature regarding NTM ecology and transmission, as well as the factors which regulate colony morphotype and pathogenicity.

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Ultrastructure of neuromuscular relationships in the canine heartworm (dirofilaria immitis)

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100143018 ◽

1986 ◽

Vol 44 ◽

pp. 278-279

Author(s):

W. L. Steffens ◽

Nancy B. Roberts ◽

J. M. Bowen

Keyword(s):

Dirofilaria Immitis ◽

Domestic Dogs ◽

Structural Description ◽

Pharmacological Effects ◽

Free Living ◽

Canine Heartworm ◽

The World ◽

Synaptic Region ◽

Muscle Innervation ◽

Insight Into

The canine heartworm is a common and serious nematode parasite of domestic dogs in many parts of the world. Although nematode neuroanatomy is fairly well documented, the emphasis has been on sensory anatomy and primarily in free-living soil species and ascarids. Lee and Miller reported on the muscular anatomy in the heartworm, but provided little insight into the peripheral nervous system or myoneural relationships. The classical fine-structural description of nematode muscle innervation is Rosenbluth's earlier work in Ascaris. Since the pharmacological effects of some nematacides currently being developed are neuromuscular in nature, a better understanding of heartworm myoneural anatomy, particularly in reference to the synaptic region is warranted.

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Genomic analysis of C-type lectins

Biochemical Society Symposium ◽

10.1042/bss0690059 ◽

2002 ◽

Vol 69 ◽

pp. 59-72 ◽

Cited By ~ 85

Author(s):

Kurt Drickamer ◽

Andrew J. Fadden

Keyword(s):

Biological Effects ◽

Cell Signalling ◽

Genomic Analysis ◽

Binding Activity ◽

Immunoglobulin Superfamily ◽

Carbohydrate Binding ◽

Carbohydrate Recognition ◽

Calcium Dependent ◽

Binding Domains ◽

Carbohydrate Recognition Domains

Many biological effects of complex carbohydrates are mediated by lectins that contain discrete carbohydrate-recognition domains. At least seven structurally distinct families of carbohydrate-recognition domains are found in lectins that are involved in intracellular trafficking, cell adhesion, cell–cell signalling, glycoprotein turnover and innate immunity. Genome-wide analysis of potential carbohydrate-binding domains is now possible. Two classes of intracellular lectins involved in glycoprotein trafficking are present in yeast, model invertebrates and vertebrates, and two other classes are present in vertebrates only. At the cell surface, calcium-dependent (C-type) lectins and galectins are found in model invertebrates and vertebrates, but not in yeast; immunoglobulin superfamily (I-type) lectins are only found in vertebrates. The evolutionary appearance of different classes of sugar-binding protein modules parallels a development towards more complex oligosaccharides that provide increased opportunities for specific recognition phenomena. An overall picture of the lectins present in humans can now be proposed. Based on our knowledge of the structures of several of the C-type carbohydrate-recognition domains, it is possible to suggest ligand-binding activity that may be associated with novel C-type lectin-like domains identified in a systematic screen of the human genome. Further analysis of the sequences of proteins containing these domains can be used as a basis for proposing potential biological functions.

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