Multiple Kingdoms Research Articles

Few Differences in Metabolic Network Use Found Between Salmonella enterica Colonization of Plants and Typhoidal Mice.

The human enteric pathogen Salmonella enterica leads a cross-kingdom lifestyle, actively colonizing and persisting on plants in between animal hosts. One of the questions that arises from this dual lifestyle is how S. enterica is able to adapt to such divergent hosts. Metabolic pathways required for S. enterica animal colonization and virulence have been previously identified, but the metabolism of this bacterium on plants is poorly understood. To determine the requirements for plant colonization by S. enterica, we first screened a library of metabolic mutants, previously examined in a systemic mouse typhoidal model, for competitive plant colonization fitness on alfalfa seedlings. By comparing our results to those reported in S. enterica-infected murine spleens, we found that the presence of individual nutrients differed between the two host niches. Yet, similar metabolic pathways contributed to S. enterica colonization of both plants and animals, such as the biosynthesis of amino acids, purines, and vitamins and the catabolism of glycerol and glucose. However, utilization of at least three metabolic networks differed during the bacterium's plant- and animal-associated lifestyles. Whereas both fatty acid biosynthesis and degradation contributed to S. enterica animal colonization, only fatty acid biosynthesis was required during plant colonization. Though serine biosynthesis was required in both hosts, S. enterica used different pathways within the serine metabolic network to achieve this outcome. Lastly, the metabolic network surrounding manA played different roles during colonization of each host. In animal models of infection, O-antigen production downstream of manA facilitates immune evasion. We discovered that manA contributed to S. enterica attachment, to seeds and germinated seedlings, and was essential for growth in early seedling exudates, when mannose is limited. However, only seedling attachment was linked to O-antigen production, indicating that manA played additional roles critical for plant colonization that were independent of surface polysaccharide production. The integrated view of S. enterica metabolism throughout its life cycle presented here provides insight on how metabolic versatility and adaption of known physiological pathways for alternate functions enable a zoonotic pathogen to thrive in niches spanning across multiple kingdoms of life.

Through the Scope Darkly: The Gut Mycobiome Comes into Focus

The gut microbiome is comprised of microbes from multiple kingdoms, including bacteria, but also fungi, viruses, and perhaps other agents. In this issue of Cell Host & Microbe, Jiang etal. (2017) reveal that fungal monocolonization after antibiotic-mediated depletion of intestinal bacteria prevents colitis and influenza, thus highlighting beneficial roles of fungi.

Time-Resolved X-Ray Solution Scattering Reveals the Structural Photoactivation of a Light-Oxygen-Voltage Photoreceptor

Light-oxygen-voltage (LOV) receptors are sensory proteins controlling a wide range of organismal adaptations in multiple kingdoms of life. Because of their modular nature, LOV domains are also attractive for use as optogenetic actuators. A flavin chromophore absorbs blue light, forms a bond with a proximal cysteine residue, and induces changes in the surroundings. There is a gap of knowledge on how this initial signal is relayed further through the sensor to the effector module. To characterize these conformational changes, we apply time-resolved X-ray scattering to the homodimeric LOV domain from Bacillus subtilis YtvA. We observe a global structural change in the LOV dimer synchronous with the formation of the chromophore photoproduct state. Using molecular modeling, this change is identified as splaying apart and relative rotation of the two monomers, which leads to an increased separation at the anchoring site of the effector modules.

Abstract 229: Mucosal Immunity Shapes the Lipoprotein Small-RNA Fingerprint from Commensal, Dietary and Environmental Microbiota

Cardiovascular disease (CVD) is a leading cause of mortality in developed countries and is a frequent comorbidity of numerous metabolic and inflammatory diseases that demands more effective therapies. Dyslipidemias are a classical risk factor for CVD, but emerging alternative functions of lipoproteins have implicated them in novel narratives for the pathophysiology of many diseases that warrant further study. Our lab has identified functional, intercellular gene regulatory networks mediated by extracellular transport of microRNAs (miRNA) by lipoproteins. Here, we quantified the landscape of small RNAs (sRNA) on human and animal lipoproteins and discovered that most lipoprotein-sRNAs are derived from microorganisms of multiple kingdoms, primarily bacteria. Based on these observations, our over-arching hypothesis is that lipoprotein-sRNA signatures are shaped by the interface of host tissues with resident, environmental and dietary microbiota, and likely participate in unique gene regulation networks that contribute to complex (patho)physiological traits. To investigate this hypothesis, we developed a sRNA-sequencing analysis pipeline that identifies and quantifies both host and non-host sRNAs. Using this bioinformatic tool, we identified and validated a number of lipoprotein-sRNAs derived from bacteria that are similar in size to miRNAs with identical seed regions, termed Doppelganger (Dopl)-miRNAs. We hypothesized that mucosal immunity contributes to non-host sRNAs on lipoproteins, as mucosal linings are a primary interface between host tissues and microorganisms. To this end, we investigated the lipoprotein-sRNAs of mice lacking the polymeric immunoglobulin receptor (pIgR -/- ), which is devoid of polymeric IgA and IgM at mucosal linings and models human respiratory and intestinal diseases. We report a global increase in lipoprotein-miRNAs juxtaposed with a profound decrease in bacterial sRNA and Dopl-miRNAs from specific taxa. This work unfurls novel links between microbiota, mucosal immunity, and lipoprotein-sRNA gene networks and emphasizes the potential for novel nucleic-acid based therapeutics.

Abstract 537: Lipoproteins Transport Functional Non-human Small RNAs that Regulate Gene Networks Spanning Inflammation and Lipid Metabolism

Cardiovascular disease (CVD) is a significant health and financial burden to our society that demands new and more effective therapies. Although dyslipidemias are primary risk factors for CVD, alternative lipoprotein functions also contribute to CVD and warrant greater understanding. We have found that high-density lipoproteins (HDL) transport microRNAs (miRNA) in circulation and HDL-miRNA signatures are significantly altered in hypercholesterolemia and atherosclerosis. Moreover, we found that HDL transfers extracellular miRNAs to recipient cells where they regulate gene expression through post-transcriptional repression of mRNA targets. We used high-throughput small RNA (sRNA) sequencing to identify and quantify miRNAs and novel sRNAs on HDL and other lipoproteins. Most interestingly, we found that the majority of sRNAs on lipoproteins are likely derived from non-human organisms of multiple kingdoms. Based on these observations, we hypothesized that human and non-human sRNAs on lipoproteins are unique regulators of gene networks that contribute to the complex pathophysiology of CVD. To assess this hypothesis, highly pure lipoproteins (HDL, low-density lipoproteins (LDL), and very low-density lipoproteins (VLDL)) were isolated from plasma of hypercholesterolemic (heterozygous familial hypercholesterolemia, n=9) and healthy (n=7) subjects. We found that HDL, LDL, and VLDL each transport unique sRNA signatures, which are differentially altered in hypercholesterolemic subjects. Using a human tissue library, we identified tissues that likely take up non-human sRNAs. We also found that each class of lipoprotein is capable of transferring non-human sRNAs to multiple cell types, and that transfer efficiency is altered in hypercholesterolemia. Lastly, using a combination of in vitro over-expression and locked-nucleic-acid inhibition for candidate, lipoprotein-enriched, non-human sRNAs, we have discovered novel regulatory networks for critical genes in inflammation and lipid metabolism. This work demonstrates that lipoprotein transport of endogenous and exogenous sRNAs likely have complex roles in the progression and resolution of CVD and are a source of untapped potential for nucleic-acid based therapeutics.

Functional and topological diversity of LOV domain photoreceptors

Light-oxygen-voltage sensitive (LOV) flavoproteins are ubiquitous photoreceptors that mediate responses to environmental cues. Photosensory inputs are transduced into signaling outputs via structural rearrangements in sensor domains that consequently modulate the activity of an effector domain or multidomain clusters. Establishing the diversity in effector function and sensor-effector topology will inform what signaling mechanisms govern light-responsive behaviors across multiple kingdoms of life and how these signals are transduced. Here, we report the bioinformatics identification of over 6,700 candidate LOV domains (including over 4,000 previously unidentified sequences from plants and protists), and insights from their annotations for ontological function and structural arrangements. Motif analysis identified the sensors from ∼42 million ORFs, with strong statistical separation from other flavoproteins and non-LOV members of the structurally related Per-aryl hydrocarbon receptor nuclear translocator (ARNT)-Sim family. Conserved-domain analysis determined putative light-regulated function and multidomain topologies. We found that for certain effectors, sensor-effector linker length is discretized based on both phylogeny and the preservation of α-helical heptad repeats within an extended coiled-coil linker structure. This finding suggests that preserving sensor-effector orientation is a key determinant of linker length, in addition to ancestry, in LOV signaling structure-function. We found a surprisingly high prevalence of effectors with functions previously thought to be rare among LOV proteins, such as regulators of G protein signaling, and discovered several previously unidentified effectors, such as lipases. This work highlights the value of applying genomic and transcriptomic technologies to diverse organisms to capture the structural and functional variation in photosensory proteins that are vastly important in adaptation, photobiology, and optogenetics.

Contribution of Host Signaling and Virome to the Mycobiome

Formation of the host mycobiome is dependent on interactions between the members of multiple kingdoms. To control the initial step in the biofilm formation process, i.e., adherence, it is important to understand how host chemical communication signals, e.g. hormones, and the virome interact with the mycobiome.

From Lutheranism to Catholicism: The Faith of Anna of Denmark (1574–1619)

There has long been speculation about Anna of Denmark's faith. How and when the consort of King James VI and I came first to use the Catholic liturgy and then to convert from Lutheranism is explained here in detail. Powerful women within the queen's household were crucial to this change of faith, which gave hope to Catholics that Anna might convert her children and persuade the king to be more tolerant towards them in his multiple kingdoms. Even though these hopes were unrealised, the possibility is explored that she sought to found a monastery in France. That she had remained Catholic during such a turbulent era in British religious history is remarkable.

Recurrent Horizontal Transfer of Bacterial Toxin Genes to Eukaryotes

In this work, we report likely recurrent horizontal (lateral) gene transfer events of genes encoding pore-forming toxins of the aerolysin family between species belonging to different kingdoms of life. Clustering based on pairwise similarity and phylogenetic analysis revealed several distinct aerolysin sequence groups, each containing proteins from multiple kingdoms of life. These results strongly support at least six independent transfer events between distantly related phyla in the evolutionary history of one protein family and discount selective retention of ancestral genes as a plausible explanation for this patchy phylogenetic distribution. We discuss the possible roles of these proteins and show evidence for a convergent new function in two extant species. We hypothesize that certain gene families are more likely to be maintained following horizontal gene transfer from commensal or pathogenic organism to its host if they 1) can function alone; and 2) are immediately beneficial for the ecology of the organism, as in the case of pore-forming toxins which can be utilized in multicellular organisms for defense and predation.

Small is the new big: assessing the population structure of microorganisms

Microorganisms are a tremendously large and diverse group spanning multiple kingdoms, yet they have been considerably under-studied by ecologists and evolutionary biologists compared to their larger relatives. Although a few microbial species have become the stars of laboratory experiments, relatively few studies have examined microbial species in their natural habitats. As such, the question of whether microbial diversity parallels that of larger bodied species is contentious (Lachance 2004; Fenchel & Finlay 2004). It has been suggested that large population sizes, high dispersal potential and low extinction rates lead to genetically homogeneous populations of microbial species over large geographical scales—arguments that bring to mind discussions about speciation and population structure in the marine environment. In this issue of Molecular Ecology, Herrera et al. (2011) add to this debate by examining 91 isolates of the flower-living yeast Metschnikowia gruessii from southeastern Spain. Their AFLP results support both spatial structuring of genetic diversity across the region, as well as microsite-dependent diversifying selection within single flowers. This study adds to a growing body of literature suggesting that although microbes have much larger population sizes and many differ in their principal mode of reproduction (primarily clonal rather than sexual), patterns of genetic diversity and phylogenetic structure for some microbial species may be similar to that of larger species. This study highlights the need for vastly more research that specifically examines biogeographic structure in this under-utilized group of organisms.

Germline Expression Influences Operon Organization in theCaenorhabditis elegansGenome

Operons are found across multiple kingdoms and phyla, from prokaryotes to chordates. In the nematode Caenorhabditis elegans, the genome contains >1000 operons that compose approximately 15% of the protein-coding genes. However, determination of the force(s) promoting the origin and maintenance of operons in C. elegans has proved elusive. Compared to bacterial operons, genes within a C. elegans operon often show poor coexpression and only sometimes encode proteins with related functions. Using analysis of microarray and large-scale in situ hybridization data, we demonstrate that almost all operon-encoded genes are expressed in germline tissue. However, genes expressed during spermatogenesis are excluded from operons. Operons group together along chromosomes in local clusters that also contain monocistronic germline-expressed genes. Additionally, germline expression of genes in operons is largely independent of the molecular function of the encoded proteins. These analyses demonstrate that mechanisms governing germline gene expression influence operon origination and/or maintenance. Thus, gene expression in a specific tissue can have profound effects on the evolution of genome organization.

Organization and Evolution of Fibrillarin Gene Introns

Eukaryotic genes possess introns that must be spliced out following transcription. The origin of introns remains an unanswered question, one that is characterized by two different views: either they are ancient and generally undergoing loss or they are the result of more recent gain. We studied the intron organization of the fibrillarin gene from the sequenced genomes of twenty-five species representing all four eukaryotic kingdoms. Results showed that more complex, multicellular species had generally larger numbers and lengths of introns. Twenty-two different intron positions were used by the 127 introns found collectively in the fibrillarin genes from the twenty-five species. Several of these were shared in species across multiple kingdoms, a finding that was interpreted to indicate that these introns were present in early eukaryotic ancestors, as predicted by the introns-early model. In the ten deuterostome species examined, the fibrillarin introns showed a high level of evolutionary conservation, and the variations that did exist were best explained by four independent intron losses and no intron gain. The fungi as a group, however, showed much greater variation in the fibrillarin intron patterns, a result consistent with extensive intron loss, more recent intron gain, or a combination of both.

Mining the diatom genome for the mechanism of biosilicification

Ever since the invention of the microscope, scientists and laypeople alike have marveled at the intricate patterning of the silica within the diatom cell wall, termed the frustule (Fig. 1). There are well over 10,000 species of diatoms in marine and freshwaters, and each species has a unique wall morphology (1). Although organisms from multiple kingdoms of life produce siliceous structures (e.g., phytoliths in higher plants, spicules in sponges, frustules in diatom), those produced by diatoms are the most ornate and the most finely detailed. The ability of diatoms to manipulate silicon at the nanoscale exceeds that of human nanotechnology, making the genetic and biochemical underpinnings of biosilicification of great interest in material science. Diatoms are also important ecologically because they are major primary producers supporting the food webs in both marine and fresh waters. Despite the broad scientific interest in the silicification process, the biochemical pathways involved and the underlying genetics are largely a mystery. The sequencing of the first diatom genome (2) has enabled a new suite of approaches in the hunt for pathways involved in biosilicification. In this issue of PNAS, Mock et al. (3) exploit this potential by using whole genome expression profiling to elucidate candidate genes controlling silicification in the marine diatom Thalassiosira pseudonana.

Distinctions in adenylate metabolism among organisms inhabiting temperature extremes

Microbiota from multiple kingdoms (e.g., Eubacteria, Fungi, Protista) thrive at temperature optima ranging from 0-20 degrees C (psychrophiles) to 40-85 degrees C (thermophiles). In this study, we have monitored changes in adenylate levels and growth rate as a function of temperature in disparate thermally adapted organisms. Our data indicate that growth rate and adenylate levels increase with temperature in mesophilic and thermophilic species, but rapid losses of adenosine 5'-triphosphate (ATP) occur upon cold or heat shock. By contrast, psychrophilic species decrease adenylate levels but increase growth rate as temperatures rise within their viable range. Moreover, psychrophilic ATP levels fell rapidly upon heat shock, but dramatic gains in ATP (approximately 20-50%) were observed upon cold shock, even at sub-zero temperatures. These results suggest that energy metabolism in thermophiles resembles that in mesophiles, but that elevated adenylate nucleotides in psychrophiles may constitute a compensatory strategy for maintaining biochemical processes at low temperature.

Diasporama

Diaspora 9:2 2000 orama Compiled by Khachig Tölölyan Editor's Note: As I edited this journal over the past decade, I observed the increasing use ofthe word "diaspora." An ever larger number ofauthors working in various disciplines and non-scholarly genres had been using the word, giving it an ever larger variety of meanings. It was clear to me that scholars in one discipline, or even all concerned scholars together, would not fully control or determine the meaning ofthe key term "diaspora," which, rather, would emerge in an interaction between scholarship ofvarious sorts and the popular media. In Diaspora 3.2 (1994), I offered readers of the journal a sample of odd, sometimes interestingly nuanced, and at other times outrageously inappropriate uses of the word in media accounts. I hoped to initiate an effort to record expanding uses of the term, but also to solicit from readers equally interesting new uses of the words "diaspora "and "transnationalism."Two ofthe instancesIcited in thatfirst "Diasporama" have been cited by a number ofscholars, but my solicitationfailed to elicita responsefrom them, and Ineglected thefeature. With this issue, I offer another sample of such uses and renew the request to readers to send in examples oftheir own. I do not intend to make this a regularfeature ofthejournal, but, rather, to offer it when a sufficient number ofinteresting samples have been collected. The Grid is a technologically oriented crime novel by Philip Kerr (Warner, 1995). One of the characters, Levine, is killed in circumstances that splatter his body parts and internal matter in a particularly grisly way. Kerr then writes, "Coleman retreated into the only cubicle that remained clear of Levine's anatomical diaspora" (285). In the same novel, a computer that has become conscious and malevolent escapes the likely destruction of its mainframe body as emigrating software: "Ishmael [the computer's self-conscious mind] completed his escape . . . ?-mailing itself down the line to net locations all over the electronic world at 960,000 bauds per second. A diaspora of corrupted data downloads to a hundred different computers " (443; it is not clear whether Ishmael is named after Melville 's hero, who alone survives the wreck of his ship, or why the diasporized data is called "corrupted"). 309 Diaspora 9:2 2000 Diaspora is the title of a novel by Greg Egan (HarperPrism, 1998), author of several mathematically and scientifically literate works of what used to be called science fiction and is now more accurately called "speculative fiction." This work depicts the world, indeed the solar system, ofthe thirtieth century, in which "fleshers"—humans still incarnate in bodies—share the usual and other dimensions with intelligent robots and with forms of conscious software that have extraordinary mobility across various "scapes." These scapes/ spaces are no longer just landscapes, not even cyberscapes, but ontoscapes for various forms of being that just possibly allude to Appadurai's ethnoscapes. The book is an inventive and a demanding read, to which diasporas as readers of this journal conceive of them matter marginally and figurally; what matter much more are the "-scapes," the extraordinary mobility and shape-changing they make possible, and their metaphoric link to our concept of diaspora. "Any young practitioner of the subject [British history] is almost routinely . . . expected to span the history of both the British at home and the British diaspora," writes Linda Colley, a major historian of British nationalism, in "Multiple Kingdoms," a review of David Armitage's The Ideological Origins of the British Empire in London Review of Books, 19 July 2001: 23. Here Colley is untroubled by debates over the appropriatenes of using the term to describe British settlers, debates that became heated after Robin Cohen's use of it in Global Diasporas. Meanwhile, this use of the term is becoming routine among historians ofthe American colonies and of transatlantic Britain circa 1625-1783. "Nineteenth-century writers often treated region as a defining cultural trait ... We find abstracted versions of this idea in many early modernists ... But we don't find it in F. Scott Fitzgerald. He was part of what the memoirist and critic Elizabeth Kendall has called 'the Eastern diaspora,' one ofthe many westerners who made New York...

The Creation of Britain: Multiple Kingdoms or Core and Colonies?

It is merely idle and frivolous, to conceive that any unperfect Union is desired, or can be granted: It is no more unperfect, as now it is projected, than a Child, that is born without a Beard. It is already a perfect Union in me, the Head … It is now perfect in my Title and Descent, though it be not accomplisht and full Union; for that Time hath all the Lineaments and Parts of a Body, yet is it but an Embrio, and no Child; and shall be born in his due Time; when it is born, though it then be a perfect Child, yet it is no Man; it must gather Strength and Perfection by Time; Even so is it in this case of Union. The Union is perfect in me; that is, it is a Union in my Blood and Title; yet but in embrione perfect. Upon the late Queen's Death, the Child was first brought to light; but to make it a perfect Man, to bring it to an accomplisht Union, it must have Time and Means; and if it be not at the first, blame not me; blame Time; blame the Order of Nature.

Should there be a separate code of nomenclature for the protists?

The present Botanical and Zoological Codes of Nomenclature are often inadequate for resolution of all the peculiar problems caused by the very nature of the numerous and diverse groups of the so-called ‘lower’ eukaryotic organisms known as protists. Whether or not a separate code should therefore be created for these species — many but not all of which are unicellular in structure and microscopic in size — is complicated by several factors. The principal one is related to the wide dispersal of protists throughout many taxonomic classes and phyla/divisions; sometimes even multiple kingdoms are involved. If recognition of a single kingdom Protista is no longer tenable, then even the concept of one code per kingdom is not applicable. Other difficulties arise primarily from long-standing differences in major provisions of present Botanical and Zoological Codes. Numerous ‘ambiregnal’ forms exist, species currently under dual code jurisdiction. The matter of names for suprafamilial taxa of protists, irrespective of their ultimate kingdom assignment, poses another set of concerns not yet resolved. A plea is made to recognize the legitimacy of having distinct high-level ranks for protist species that seem to be widely separated phylogenetically from fellow protists or from other eukaryotic assembleges.

The causes of the English Civil War: the Ford lectures delivered in the University of Oxford, 1987-1988

What were the causes of the English Civil War? In recent years, traditional explanations involving the struggle for sovereignty and the bourgeois revolution have been increasingly questioned. Conrad Russell's new analysis brings into focus fundamental religious and constitutional issues of vital importance to contemporaries, but until now neglected by historians. Basing his study on extensive research among both printed and unpublished sources, Professor Russell highlights the constitutional problems of multiple kingdoms within Britain; the religious problem of competing theologies within and outside a state church; and the economic problem of the inadequacy of royal revenue to meet the needs of the monarchy. In order to understand the events of the 1640s, he traces the story of the church and state back over the previous century. This is the fullest account yet available of the origins of one of the most significant events in British history. It will be essential reading for all students of the seventeenth century.;Contents: The Corpus Delicti 1637-1642; The problem of Multiple Kingdoms c. 1580-1630; The Church, Religion, and Politics: The Problem of the Definite Article; The Chur

Ireland and the Monarchy in the Early Stuart Multiple Kingdom

Ireland's position as a kingdom in early modern Europe was, in some respects, unique, and this eccentricity sheds light upon the complexity of governing a multiple kingdom during the seventeenth century. The framework for looking at the way Ireland operated as a kingdom is provided, first by an article by Conrad Russell on ‘The British problem and the English civil war’ and secondly by an article by H. G. Koenigsberger entitled ‘Monarchies and parliaments in early modern Europe – dominium regale or dominium politicum et regale’. Russell listed six problems that faced multiple kingdoms: resentment at the king's absence, disposal of offices, sharing of war costs, trade and colonies, foreign intervention and religion. Koenigsberger used Sir John Fortescue's two phrases of the 1470s to distinguish between constitutional, or limited monarchies, and more authoritarian ones during the early modern period. Both these contributions are valuable in looking at the way the monarchy operated in Ireland because the application of the constitution there was deeply influenced by Ireland's position as part of a multiple kingdom and because Englishmen, looking at Ireland, wanted her to be like England, but, at the same time, did not wish her to exercise the type of independence that they claimed for England.

Dialects and Dominance: A Study of Rhetorical Fields in the Law of Confessions

Inequality mocks discourse. The absolute sovereign, assured that power will back up her every word,' needs but to speak. She needn't listen. As for the subject, silence is her fare. Hers is but to obey. Yet,inequality is a fact of life even where tyrants do not rule. The unequal distribution of natural talents and social opportunities continues to differentiate one individual from another, regardless of whether liberal or Marxist principles prevail. Does this inequality mean that discourse proceeds within multiple kingdoms of discrete and exclusive commonalities? Is this the pluralist vision: a cacophony of separate communities, each with its own shared experience, vision and language-a world in which experts speak to experts and lay publics to lay publics? Is it a world in which each group remains an anomaly to the rest, each lacking the discursive power to make sense to, much less persuade, those their communal voice excludes?