Are all domains of life satisfaction equal? Differential associations with health and well-being in older adults.

PURPOSE: Growing evidence documents strong associations between overall life satisfaction and favorable health and well-being outcomes. However, because most previous studies have assessed satisfaction with one's life as a whole, we know little about whether specific domains of life satisfaction (e.g., satisfaction with family life, income) might be responsible for longitudinally driving better health and well-being. METHODS: Data were from 13,752 participants in the Health and Retirement Study-a prospective and nationally representative cohort of US adults aged > 50. We evaluated if positive changes in seven individual domains of life satisfaction (between t0; 2008/2010 and t1; 2012/2014) were associated with 35 indicators of physical, behavioral, and psychosocial health and well-being (at t2; 2016/2018). RESULTS: Most domains of life satisfaction were associated with psychological outcomes: satisfaction with family and non-work activities showed the largest associations (sometimes double in magnitude) with subsequent psychological factors, followed by satisfaction with financial situation and income. Further, some domains showed associations with specific physical health outcomes (e.g., mortality, number of chronic conditions, physical functioning limitations), health behaviors (e.g., sleep problems), and social factors (e.g., loneliness). CONCLUSIONS: As countries seek innovative and cost-effective methods of enhancing the health and well-being of our rapidly aging populations, findings from our study suggest that some domains of life satisfaction have a substantially larger influence on health and well-being outcomes than others. Individual domains of life satisfaction might be novel targets for interventions and policies seeking to enhance specific facets of health and well-being.

On the occurrence of cytochrome P450 in viruses.

Genes encoding cytochrome P450 (CYP; P450) enzymes occur widely in the Archaea, Bacteria, and Eukarya, where they play important roles in metabolism of endogenous regulatory molecules and exogenous chemicals. We now report that genes for multiple and unique P450s occur commonly in giant viruses in the Mimiviridae, Pandoraviridae, and other families in the proposed order Megavirales. P450 genes were also identified in a herpesvirus (Ranid herpesvirus 3) and a phage (Mycobacterium phage Adler). The Adler phage P450 was classified as CYP102L1, and the crystal structure of the open form was solved at 2.5 Å. Genes encoding known redox partners for P450s (cytochrome P450 reductase, ferredoxin and ferredoxin reductase, and flavodoxin and flavodoxin reductase) were not found in any viral genome so far described, implying that host redox partners may drive viral P450 activities. Giant virus P450 proteins share no more than 25% identity with the P450 gene products we identified in Acanthamoeba castellanii, an amoeba host for many giant viruses. Thus, the origin of the unique P450 genes in giant viruses remains unknown. If giant virus P450 genes were acquired from a host, we suggest it could have been from an as yet unknown and possibly ancient host. These studies expand the horizon in the evolution and diversity of the enormously important P450 superfamily. Determining the origin and function of P450s in giant viruses may help to discern the origin of the giant viruses themselves.

Diversification of Ferredoxins across Living Organisms.

Ferredoxins, iron-sulfur (Fe-S) cluster proteins, play a key role in oxidoreduction reactions. To date, evolutionary analysis of these proteins across the domains of life have been confined to observing the abundance of Fe-S cluster types (2Fe-2S, 3Fe-4S, 4Fe-4S, 7Fe-8S (3Fe-4s and 4Fe-4S) and 2[4Fe-4S]) and the diversity of ferredoxins within these cluster types was not studied. To address this research gap, here we propose a subtype classification and nomenclature for ferredoxins based on the characteristic spacing between the cysteine amino acids of the Fe-S binding motif as a subtype signature to assess the diversity of ferredoxins across the living organisms. To test this hypothesis, comparative analysis of ferredoxins between bacterial groups, Alphaproteobacteria and Firmicutes and ferredoxins collected from species of different domains of life that are reported in the literature has been carried out. Ferredoxins were found to be highly diverse within their types. Large numbers of alphaproteobacterial species ferredoxin subtypes were found in Firmicutes species and the same ferredoxin subtypes across the species of Bacteria, Archaea, and Eukarya, suggesting shared common ancestral origin of ferredoxins between Archaea and Bacteria and lateral gene transfer of ferredoxins from prokaryotes (Archaea/Bacteria) to eukaryotes. This study opened new vistas for further analysis of diversity of ferredoxins in living organisms.

Climate sensitivity across marine domains of life: limits to evolutionary adaptation shape species interactions.

Organisms in all domains, Archaea, Bacteria, and Eukarya will respond to climate change with differential vulnerabilities resulting in shifts in species distribution, coexistence, and interactions. The identification of unifying principles of organism functioning across all domains would facilitate a cause and effect understanding of such changes and their implications for ecosystem shifts. For example, the functional specialization of all organisms in limited temperature ranges leads us to ask for unifying functional reasons. Organisms also specialize in either anoxic or various oxygen ranges, with animals and plants depending on high oxygen levels. Here, we identify thermal ranges, heat limits of growth, and critically low (hypoxic) oxygen concentrations as proxies of tolerance in a meta-analysis of data available for marine organisms, with special reference to domain-specific limits. For an explanation of the patterns and differences observed, we define and quantify a proxy for organismic complexity across species from all domains. Rising complexity causes heat (and hypoxia) tolerances to decrease from Archaea to Bacteria to uni- and then multicellular Eukarya. Within and across domains, taxon-specific tolerance limits likely reflect ultimate evolutionary limits of its species to acclimatization and adaptation. We hypothesize that rising taxon-specific complexities in structure and function constrain organisms to narrower environmental ranges. Low complexity as in Archaea and some Bacteria provide life options in extreme environments. In the warmest oceans, temperature maxima reach and will surpass the permanent limits to the existence of multicellular animals, plants and unicellular phytoplankter. Smaller, less complex unicellular Eukarya, Bacteria, and Archaea will thus benefit and predominate even more in a future, warmer, and hypoxic ocean.

Carl Woese's vision of cellular evolution and the domains of life.

In a series of conceptual articles published around the millennium, Carl Woese emphasized that evolution of cells is the central problem of evolutionary biology, that the three-domain ribosomal tree of life is an essential framework for reconstructing cellular evolution, and that the evolutionary dynamics of functionally distinct cellular systems are fundamentally different, with the information processing systems "crystallizing" earlier than operational systems. The advances of evolutionary genomics over the last decade vindicate major aspects of Woese's vision. Despite the observations of pervasive horizontal gene transfer among bacteria and archaea, the ribosomal tree of life comes across as a central statistical trend in the "forest" of phylogenetic trees of individual genes, and hence, an appropriate scaffold for evolutionary reconstruction. The evolutionary stability of information processing systems, primarily translation, becomes ever more striking with the accumulation of comparative genomic data indicating that nearly all of the few universal genes encode translation system components. Woese's view on the fundamental distinctions between the three domains of cellular life also withstand the test of comparative genomics, although his non-acceptance of symbiogenetic scenarios for the origin of eukaryotes might not. Above all, Woese's key prediction that understanding evolution of microbes will be the core of the new evolutionary biology appears to be materializing.

Origin, Diversity, and Multiple Roles of Enzymes with Metallo-ß-Lactamase Fold from Different Organisms.

ß-lactamase enzymes have generated significant interest due to their ability to confer resistance to the most commonly used family of antibiotics in human medicine. Among these enzymes, the class B ß-lactamases are members of a superfamily of metallo-ß-lactamase (MßL) fold proteins which are characterised by conserved motifs (i.e., HxHxDH) and are not only limited to bacteria. Indeed, as the result of several barriers, including low sequence similarity, default protein annotation, or untested enzymatic activity, MßL fold proteins have long been unexplored in other organisms. However, thanks to search approaches which are more sensitive compared to classical Blast analysis, such as the use of common ancestors to identify distant homologous sequences, we are now able to highlight their presence in different organisms including Bacteria, Archaea, Nanoarchaeota, Asgard, Humans, Giant viruses, and Candidate Phyla Radiation (CPR). These MßL fold proteins are multifunctional enzymes with diverse enzymatic or non-enzymatic activities of which, at least thirteen activities have been reported such as ß-lactamase, ribonuclease, nuclease, glyoxalase, lactonase, phytase, ascorbic acid degradation, anti-cancer drug degradation, or membrane transport. In this review, we (i) discuss the existence of MßL fold enzymes in the different domains of life, (ii) present more suitable approaches to better investigating their homologous sequences in unsuspected sources, and (iii) report described MßL fold enzymes with demonstrated enzymatic or non-enzymatic activities.

Errors of the ancestral translation, LUCA, and nature of its direct descendants.

I analyzed the implications of the observation that the methyltransferases, Trm5 and TrmD, which perform the methylation of the 37th base (m1G37) in tRNAs of bacteria and archaea respectively, are not homologous proteins. The first implication is that these methyltransferases originated very late only when the fundamental lineages leading to bacteria and archaea had separated, otherwise the two methyltransferases would have been homologous enzymes, which they are not. The conclusion that Trm5 and TrmD originated only when the main lineages were defined would imply that at least some aspects of the translation, such as +1 frameshifting, were still in rapid and progressive evolution, that is, they were still originating. This would in itself imply a high rate of translation errors because the absence of m1G37 from tRNAs could have determined a high rate of +1 translational frameshifting in the reading of mRNAs, identifying this stage as that of a phase of the origin of the genetic code. Furthermore, the observation that the frameshifting mechanism was still in rapid and progressive evolution in such an advanced evolutionary stage would imply that other mechanisms concerning translation were still rapidly evolving simply because it would be very unique if only the frameshifting mechanism were the only one still originating. Importantly, the observation that in archaea m1G37 also acts as a determinant of the identity of the tRNACysGCA would imply in itself that some aspects of the origin of the genetic code were still originating, greatly strengthening the hypothesis that other aspects of the translation apparatus were still in rapid and progressive evolution. Then, all this would imply a status of progenote for LUCA and ancestors of archaea and bacteria because a high rate of translation errors would fall within the definition of progenote.

Influence of the cold bottom water on taxonomic and functional composition and complexity of microbial communities in the southern Yellow Sea during the summer.

The formation and presence of the cold bottom water (Yellow Sea Cold Water Mass, YSCWM) is a striking hydrological phenomenon in the southern Yellow Sea during the summer and has important effects on the marine ecosystem. To better understand its influence on microbial community structure and function, we compared the bacterial, archaeal and microeukaryotic communities in the cold water mass area (CWMA) and the southern area (SA) during the summer using amplicon and metagenomic sequencings. The habitat environment in the deep waters of the CWMA was characterized by higher salinity/DO/PO4-P, greater depth/distance to the coast, and lower levels of temperature/chlorophyll a/DIN/SiO3-Si/N:P ratio compared to that of the SA. Pure depth or distance to the coast explained a small portion of the microbial community variance, while environment explained a significant fraction of the variance when partialling the effects of depth and distance to the coast. Oligotrophic taxa (e.g. SAR11 clade Ia, Nitrosopumilus, Chloropicophyceae) dominated the deep water communities in the CWMA, while the common coastal taxa (e.g. Roseobacter strain HIMB11, Bacillariophyta, Noctilucophyceae) were more dominant in the deep waters of the SA, suggesting the great impact of the oligotrophic condition in the YSCWM on microbial communities. The microbial co-occurrence networks in the CWMA were less complex but contained a higher proportion of mutual exclusion relationship among prokaryotes; the prokaryotic α-diversity in the CWMA was significantly lower than in the SA while the microeukaryotic α-diversity was significantly higher in the CWMA, implying that prokaryotes and microeukaryotes respond to the cold water mass differently and the competition among prokaryotes was intensified under the impact of the YSCWM. Genes that relate to replication and repair accounted for a significantly lower proportion in the CWMA, which was likely an adaptation to the low carbon environment.

Information theory unveils the evolution of tRNA identity elements in the three domains of life.

We determined the identity elements of each tRNA isoacceptor for the three domains of life: Eubacteria, Archaea, and Eukarya. Our analyses encompass the most updated and curated available databases using an information theory approach. We obtained a collection of identity clusters for each of the isoacceptors of the 20 canonical amino acids for the three major domains of life. The identity clusters for all isoacceptors are compared within and among the three domains to determine their pattern of differentiation and to shed light on the evolution of the identity elements.

LUCA as well as the ancestors of archaea, bacteria and eukaryotes were progenotes: Inference from the distribution and diversity of the reading mechanism of the AUA and AUG codons in the domains of life.

Here I use the rationale assuming that if of a certain trait that exerts its function in some aspect of the genetic code or, more generally, in protein synthesis, it is possible to identify the evolutionary stage of its origin then it would imply that this evolutionary moment would be characterized by a high translational noise because this trait would originate for the first time during that evolutionary stage. That is to say, if this trait had a non-marginal role in the realization of the genetic code, or in protein synthesis, then the origin of this trait would imply that, more generally, it was the genetic code itself that was still originating. But if the genetic code were still originating - at that precise evolutionary stage - then this would imply that there was a high translational noise which in turn would imply that it was in the presence of a protocell, i.e. a progenote that was by definition characterized by high translational noise. I apply this rationale to the mechanism of modification of the base 34 of the anticodon of an isoleucine tRNA that leads to the reading of AUA and AUG codons in archaea, bacteria and eukaryotes. The phylogenetic distribution of this mechanism in these phyletic lineages indicates that this mechanism originated only after the evolutionary stage of the last universal common ancestor (LUCA), namely, during the formation of cellular domains, i.e., at the stage of ancestors of these main phyletic lineages. Furthermore, given that this mechanism of modification of the base 34 of the anticodon of the isoleucine tRNA would result to emerge at a stage of the origin of the genetic code - despite in its terminal phases - then all this would imply that the ancestors of bacteria, archaea and eukaryotes were progenotes. If so, all the more so, the LUCA would also be a progenote since it preceded these ancestors temporally. A consequence of all this reasoning might be that since these three ancestors were of the progenotes that were different from each other, if at least one of them had evolved into at least two real and different cells - basically different from each other - then the number of cellular domains would not be three but it would be greater than three.

Coccolithoviruses: A Review of Cross-Kingdom Genomic Thievery and Metabolic Thuggery.

Coccolithoviruses (Phycodnaviridae) infect and lyse the most ubiquitous and successful coccolithophorid in modern oceans, Emiliania huxleyi. So far, the genomes of 13 of these giant lytic viruses (i.e., Emiliania huxleyi viruses-EhVs) have been sequenced, assembled, and annotated. Here, we performed an in-depth comparison of their genomes to try and contextualize the ecological and evolutionary traits of these viruses. The genomes of these EhVs have from 444 to 548 coding sequences (CDSs). Presence/absence analysis of CDSs identified putative genes with particular ecological significance, namely sialidase, phosphate permease, and sphingolipid biosynthesis. The viruses clustered into distinct clades, based on their DNA polymerase gene as well as full genome comparisons. We discuss the use of such clustering and suggest that a gene-by-gene investigation approach may be more useful when the goal is to reveal differences related to functionally important genes. A multi domain "Best BLAST hit" analysis revealed that 84% of the EhV genes have closer similarities to the domain Eukarya. However, 16% of the EhV CDSs were very similar to bacterial genes, contributing to the idea that a significant portion of the gene flow in the planktonic world inter-crosses the domains of life.

Gender differences in the importance of participation associated with injured workers/persons perceived barriers to returning to work in the context of vocational rehabilitation.

PURPOSE: To investigate gender differences in the importance of participation in core domains of life, and the association to perceived hindrances for return to work (RTW) before (T1) and after (T2) vocational rehabilitation. METHODS: Two hundred-seventy (T1) and 149 (T2) respondents completed the questionnaire. Gender differences in the importance of participation were calculated using t-tests. A principal component analysis was conducted on 21 questions of hindrances for RTW. A four-component structure was chosen. The family care barrier component was kept as an outcome variable in the logistic regression. RESULTS: There were mean gender differences in importance of participation in family prior to chronic pain and at T1. Importance of work changed from prior to pain to rehabilitation. At T1 children, age and importance of participation in work and family contributed to the model for women. For men importance of participation in leisure contributed to the model. The variables which contributed to the model at T2 for women were age and importance of participation in work and for men; children and importance of participation in leisure. CONCLUSION: Understanding gender differences in participation, and the association to hindrances for RTW, can enhance the rehabilitation counsellor's ability to work collaboratively with the clients. Implications for Rehabilitation Participation is a value and context driven process which influences the process of vocational rehabilitation. Understanding the driving forces for participation in important domains of life can illuminate gender differences in the process and outcome of vocational rehabilitation. Understanding gender differences in importance of participation, and the association to perceived hindrances to return to work, facilitates a shared understanding of rehabilitation goals among clients and rehabilitation professionals.

Archaeal viruses: living fossils of the ancient virosphere?

Studies on viruses parasitizing archaea reveal their specific nature and complete the tripartite division of the biosphere, indicating that each of the three domains of life-Archaea, Bacteria, and Eukarya-has its own set of associated DNA viruses. I argue that the remarkable morphotypical diversity of archaea-specific viruses could have originated from diverse viral archetypes that predated the divergence of the three domains of cellular life. It is possible that the descendants of many of these viral archetypes are able to parasitize extant archaea owing to their ability to evade archaea-specific defenses against virus infection, specifically the defenses linked to the evolution of cell envelope structure.

Welcome to pandoraviruses at the 'Fourth TRUC' club.

Nucleocytoplasmic large DNA viruses, or representatives of the proposed order Megavirales, belong to families of giant viruses that infect a broad range of eukaryotic hosts. Megaviruses have been previously described to comprise a fourth monophylogenetic TRUC (things resisting uncompleted classification) together with cellular domains in the universal tree of life. Recently described pandoraviruses have large (1.9-2.5 MB) and highly divergent genomes. In the present study, we updated the classification of pandoraviruses and other reported giant viruses. Phylogenetic trees were constructed based on six informational genes. Hierarchical clustering was performed based on a set of informational genes from Megavirales members and cellular organisms. Homologous sequences were selected from cellular organisms using TimeTree software, comprising comprehensive, and representative sets of members from Bacteria, Archaea, and Eukarya. Phylogenetic analyses based on three conserved core genes clustered pandoraviruses with phycodnaviruses, exhibiting their close relatedness. Additionally, hierarchical clustering analyses based on informational genes grouped pandoraviruses with Megavirales members as a super group distinct from cellular organisms. Thus, the analyses based on core conserved genes revealed that pandoraviruses are new genuine members of the 'Fourth TRUC' club, encompassing distinct life forms compared with cellular organisms.

Pithovirus sibericum, a new bona fide member of the "Fourth TRUC" club.

Nucleocytoplasmic large DNA viruses, or representatives of the proposed order Megavirales, include giant viruses of Acanthamoeba that were discovered over the last 12 years and are bona fide microbes. Phylogenies based on a few genes conserved amongst these megaviruses and shared by microbes classified as Eukarya, Bacteria, and Archaea, allowed for delineation of a fourth monophylogenetic group or "TRUC" (Things Resisting Uncompleted Classification) composed of the Megavirales representatives. A new Megavirales member named Pithovirus sibericum was isolated from a >30,000-year-old dated Siberian permafrost sample. This virion is as large as recently described pandoraviruses but has a genome that is approximately three to four times shorter. Our objective was to update the classification of P. sibericum as a new member of the "Fourth TRUC" club. Phylogenetic trees were constructed based on four conserved ancient genes and a phyletic analysis was concurrently conducted based on the presence/absence patterns of a set of informational genes from members of Megavirales, Bacteria, Archaea, and Eukarya. Phylogenetic analyses based on the four conserved genes revealed that P. sibericum is part of the fourth TRUC composed of Megavirales members, and is closely related to the families Marseilleviridae and Ascoviridae/Iridoviridae. Additionally, hierarchical clustering delineated four branches, and showed that P. sibericum is part of this fourth TRUC. Overall, phylogenetic and phyletic analyses using informational genes clearly indicate that P. sibericum is a new bona fide member of the "Fourth TRUC" club composed of representatives of Megavirales, alongside Bacteria, Archaea, and Eukarya.

PVC bacteria: variation of, but not exception to, the Gram-negative cell plan.

Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacteria have features that differentiate them from classical Gram-negative (G-) bacteria. One such feature is their complex endomembrane system. Based on the difference of membrane organization and compartment identity, PVC bacteria were proposed to form an exception to the bacterial G- cell plan. Here I argue that all PVC membranes are derived from G- membranes, and that their organization and the compartments they form are similar to those of G- bacteria. I suggest that PVC membrane organization should be evaluated within a G- framework and as a variation of it.

DNA-dependent RNA polymerase detects hidden giant viruses in published databanks.

Environmental metagenomic studies show that there is a "dark matter," composed of sequences not linked to any known organism, as determined mainly using ribosomal DNA (rDNA) sequences, which therefore ignore giant viruses. DNA-dependent RNA polymerase (RNAP) genes are universal in microbes and conserved in giant viruses and may replace rDNA for identifying microbes. We found while reconstructing RNAP subunit 2 (RNAP2) phylogeny that a giant virus sequenced together with the genome of a large eukaryote, Hydra magnipapillata, has been overlooked. To explore the dark matter, we used viral RNAP2 and reconstructed putative ancestral RNAP2, which were significantly superior in detecting distant clades than current sequences, and we revealed two additional unknown mimiviruses, misclassified as an euryarchaeote and an oomycete plant pathogen, and detected unknown putative viral clades. We suggest using RNAP systematically to decipher the black matter and identify giant viruses.