Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome

Saccharibacteria are a group of widespread and genetically diverse ultrasmall bacteria with highly reduced genomes that belong to the Candidate Phyla Radiation. Comparative genomic analyses suggest convergent evolution of key functions enabling the adaptation of environmental Saccharibacteria to mammalian microbiomes. Currently, our understanding of this environment-to-mammal niche transition within Saccharibacteria and their obligate episymbiotic association with host bacteria is limited. Here, we identified a complete arginine deiminase system (ADS), found in further genome streamlined mammal-associated Saccharibacteria but missing in their environmental counterparts, suggesting acquisition during environment-to-mammal niche transition. Using TM7x, the first cultured Saccharibacteria strain from the human oral microbiome and its host bacterium Actinomyces odontolyticus, we experimentally tested the function and impact of the ADS. We demonstrated that by catabolizing arginine and generating adenosine triphosphate, the ADS allows metabolically restrained TM7x to maintain higher viability and infectivity when disassociated from the host bacterium. Furthermore, the ADS protects TM7x and its host bacterium from acid stress, a condition frequently encountered within the human oral cavity due to bacterial metabolism of dietary carbohydrates. Intriguingly, with a restricted host range, TM7x forms obligate associations with Actinomyces spp. lacking the ADS but not those carrying the ADS, suggesting the acquired ADS may also contribute to partner selection for cooperative episymbiosis within a mammalian microbiome. These data present experimental characterization of a mutualistic interaction between TM7x and their host bacteria, and illustrate the benefits of acquiring a novel pathway in the transition of Saccharibacteria to mammalian microbiomes.

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Structural characterization of NrnC identifies unifying features of dinucleotidases

eLife ◽

10.7554/elife.70146 ◽

2021 ◽

Vol 10 ◽

Author(s):

Justin D Lormand ◽

Soo-Kyoung Kim ◽

George A Walters-Marrah ◽

Bryce A Brownfield ◽

J Christopher Fromme ◽

...

Keyword(s):

Cell Growth ◽

Convergent Evolution ◽

Specific Activity ◽

Structural Features ◽

Rna Degradation ◽

Comparative Genomic ◽

Quantitative Structure ◽

Unique Role ◽

Genomic Analyses

RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses, we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC and Orn employ similar structural features that distinguish these two classes of dinucleotidases from other exonucleases, the key determinants for dinucleotidase activity are realized through distinct structural scaffolds. The structures, together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases, indicate convergent evolution as the mechanism of how dinucleotidase activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinucleotidase activity further underlines the important role these analogous proteins play for cell growth.

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The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition

Open Biology ◽

10.1098/rsob.200359 ◽

2021 ◽

Vol 11 (2) ◽

pp. 200359

Author(s):

Núria Ros-Rocher ◽

Alberto Pérez-Posada ◽

Michelle M. Leger ◽

Iñaki Ruiz-Trillo

Keyword(s):

Gene Regulation ◽

Cell Communication ◽

Regulatory Mechanisms ◽

Comparative Genomic ◽

Ancestral Reconstruction ◽

Genomic Analyses ◽

Gene Regulatory ◽

Key Events ◽

Early Developmental

How animals evolved from a single-celled ancestor, transitioning from a unicellular lifestyle to a coordinated multicellular entity, remains a fascinating question. Key events in this transition involved the emergence of processes related to cell adhesion, cell–cell communication and gene regulation. To understand how these capacities evolved, we need to reconstruct the features of both the last common multicellular ancestor of animals and the last unicellular ancestor of animals. In this review, we summarize recent advances in the characterization of these ancestors, inferred by comparative genomic analyses between the earliest branching animals and those radiating later, and between animals and their closest unicellular relatives. We also provide an updated hypothesis regarding the transition to animal multicellularity, which was likely gradual and involved the use of gene regulatory mechanisms in the emergence of early developmental and morphogenetic plans. Finally, we discuss some new avenues of research that will complement these studies in the coming years.

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Towards artificial methanogenesis: biosynthesis of the [Fe]-hydrogenase cofactor and characterization of the semi-synthetic hydrogenase

Faraday Discussions ◽

10.1039/c6fd00209a ◽

2017 ◽

Vol 198 ◽

pp. 37-58 ◽

Cited By ~ 12

Author(s):

Liping Bai ◽

Takashi Fujishiro ◽

Gangfeng Huang ◽

Jürgen Koch ◽

Atsushi Takabayashi ◽

...

Keyword(s):

Sufficient Conditions ◽

Methanogenic Archaea ◽

Crystal Structure Analysis ◽

Guanosine Monophosphate ◽

Comparative Genomic ◽

Enzymatic Reactions ◽

Methanococcus Maripaludis ◽

System P ◽

Genomic Analyses

The greenhouse gas and energy carrier methane is produced on Earth mainly by methanogenic archaea. In the hydrogenotrophic methanogenic pathway the reduction of one CO2 to one methane molecule requires four molecules of H2 containing eight electrons. Four of the electrons from two H2 are supplied for reduction of an electron carrier F420, which is catalyzed by F420-reducing [NiFe]-hydrogenase under nickel-sufficient conditions. The same reaction is catalysed under nickel-limiting conditions by [Fe]-hydrogenase coupled with a reaction catalyzed by F420-dependent methylene tetrahydromethanopterin dehydrogenase. [Fe]-hydrogenase contains an iron-guanylylpyridinol (FeGP) cofactor for H2 activation at the active site. FeII of FeGP is coordinated to a pyridinol-nitrogen, an acyl-carbon, two CO and a cysteine-thiolate. We report here on comparative genomic analyses of biosynthetic genes of the FeGP cofactor, which are primarily located in a hmd-co-occurring (hcg) gene cluster. One of the gene products is HcgB which transfers the guanosine monophosphate (GMP) moiety from guanosine triphosphate (GTP) to a pyridinol precursor. Crystal structure analysis of HcgB from Methanococcus maripaludis and its complex with 6-carboxymethyl-3,5-dimethyl-4-hydroxy-2-pyridinol confirmed the physiological guanylyltransferase reaction. Furthermore, we tested the properties of semi-synthetic [Fe]-hydrogenases using the [Fe]-hydrogenase apoenzyme from several methanogenic archaea and a mimic of the FeGP cofactor. On the basis of the enzymatic reactions involved in the methanogenic pathway, we came up with an idea how the methanogenic pathway could be simplified to develop an artificial methanogenesis system.

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The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

Horticulture Research ◽

10.1038/s41438-021-00544-9 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Josué Barrera-Redondo ◽

Guillermo Sánchez-de la Vega ◽

Jonás A. Aguirre-Liguori ◽

Gabriela Castellanos-Morales ◽

Yocelyn T. Gutiérrez-Guerrero ◽

...

Keyword(s):

Defense Mechanisms ◽

Population Level ◽

Growth Hormones ◽

Comparative Genomic ◽

Structural Variants ◽

Closely Related Species ◽

Level Data ◽

Genomic Analyses ◽

Genotype By Sequencing ◽

Regulation Of Growth

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

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Complete chloroplast genomes of Leptodermis scabrida complex: comparative genomic analyses and phylogenetic relationships

Gene ◽

10.1016/j.gene.2021.145715 ◽

2021 ◽

pp. 145715

Author(s):

Ying Zhang ◽

Zhengfeng Wang ◽

Yanan Guo ◽

Sheng Chen ◽

Xianyi Xu ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Comparative Genomic ◽

Chloroplast Genomes ◽

Genomic Analyses

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Evidence from comparative genomic analyses indicating that Lactobacillus-mediated irritable bowel syndrome alleviation is mediated by the conjugated linoleic acid synthesis

Food & Function ◽

10.1039/d0fo02616f ◽

2021 ◽

Author(s):

Yang Liu ◽

Wei Xiao ◽

Leilei Yu ◽

Fengwei Tian ◽

Gang Wang ◽

...

Keyword(s):

Irritable Bowel Syndrome ◽

Linoleic Acid ◽

Gut Microbiota ◽

Acid Synthesis ◽

Comparative Genomic ◽

Low Grade ◽

Genomic Analyses ◽

Irritable Bowel ◽

Low Grade Inflammation ◽

Gut Microbiota Dysbiosis

Irritable bowel syndrome (IBS) is a chronic intestinal disorder accompanied by low-grade inflammation, visceral hypersensitivity, and gut microbiota dysbiosis. Several studies have indicated that Lactobacillus supplementation can help to alleviate...

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