Fine Mapping of ui6.1, a Gametophytic Factor Controlling Pollen-Side Unilateral Incompatibility in Interspecific Solanum Hybrids

Unilateral incompatibility (UI) is a prezygotic reproductive barrier in plants that prevents fertilization by foreign (interspecific) pollen through the inhibition of pollen tube growth. Incompatibility occurs in one direction only, most often when the female is a self-incompatible species and the male is self-compatible (the “SI × SC rule”). Pistils of the wild tomato relative Solanum lycopersicoides (SI) reject pollen of cultivated tomato (S. lycopersicum, SC), but accept pollen of S. pennellii (SC accession). Expression of pistil-side UI is weakened in S. lycopersicum × S. lycopersicoides hybrids, as pollen tube rejection occurs lower in the style. Two gametophytic factors are sufficient for pollen compatibility on allotriploid hybrids: ui1.1 on chromosome 1 (near the S locus), and ui6.1 on chromosome 6. We report herein a fine-scale map of the ui6.1 region. Recombination around ui6.1 was suppressed in lines containing a short S. pennellii introgression, but less so in lines containing a longer introgression. More recombinants were obtained from female than male meioses. A high-resolution genetic map of this region delineated the location of ui6.1 to ∼0.128 MU, or 160 kb. Identification of the underlying gene should elucidate the mechanism of interspecific pollen rejection and its relationship to self-incompatibility.FLOWERING plants have evolved several reproductive barriers for preventing illegitimate hybridization with related species. These barriers may be expressed prefertilization and/or postfertilization. Unilateral incompatibility or incongruity (UI) is a prefertilization barrier that occurs when pollen of one species is rejected on pistils of a related species, while no rejection occurs in the reciprocal cross (De Nettancourt 1977). In theory, unilateral incompatibility should reinforce species identity in natural, sympatric populations of related taxa. This barrier also impedes the efforts of plant breeders to transfer traits from wild species into related crop plants. For example, the transfer of cytoplasmic traits from species with maternally inherited chloroplasts and mitochondria may be prevented by unilateral crossing barriers. Nuclear-encoded traits may also be inaccessible if F₁ interspecific hybrids are both male sterile and incompatible as female parents.In the Solanaceae, unilateral incompatibility is observed in crosses between cultivated tomato (Solanum lycopersicum, formerly Lycopersicon esculentum) and some related wild species. In general, pistils of the cultivated tomato act as a “universal acceptor,” in that they fail to recognize and reject pollen of other tomato species. In the reciprocal crosses, pollen of S. lycopersicum is rejected on styles of virtually all of the green-fruited species, but not on styles of other red or orange-fruited species (reviewed by Mutschler and Liedl 1994). This pattern is mostly consistent with the “SI × SC” rule, wherein pollen of self-compatible (SC) species (including cultivated tomato) are rejected on pistils of self-incompatible (SI) species, but not in the reverse direction (Lewis and Crowe 1958). Exceptions to the SI × SC rule in the tomato clade include species or populations that have lost self-incompatibility but retain the ability to reject pollen of tomato. This is the case for the facultative outcrossing species S. chmielewskii, the autogamous S. neorickii (formerly L. parviflorum), as well as marginal SC populations of normally SI species such as S. pennellii and S. habrochaites (formerly L. hirsutum). An SC accession of S. pennellii, LA0716, is exceptional in having lost the ability to reject self pollen, while retaining the ability to serve as pollen parent on styles of SI accessions of this species (and other SI species, including S. peruvianum and S. lycopersicoides) (Hardon 1967; Rick 1979; Quiros et al. 1986). In this regard, S. pennellii LA0716 conforms to the Lewis and Crowe (1958) model in that it behaves like a transitional form lacking SI function in the pistil but not in the pollen.Unilateral incompatibility may also occur in crosses between populations or races of a single species. In S. habrochaites for example, pollen from SC biotypes located at the northern or southern margins of its geographic range is rejected on pistils of the central, SI populations (Martin 1961, 1963). Furthermore, pollen from the northern SC group is rejected by styles of the southern SC populations. Yet pistils of both SC biotypes are able to reject pollen of cultivated tomato. Thus there appear to be at least three distinct unilateral crossing barriers, just within S. habrochaites, possibly indicating different pollen tube recognition and rejection systems. The F₁ N × S hybrid is SC, as expected, but SI plants are recovered in the F₂ generation, suggesting that the loss of SI occurred via independent mutations in the north and the south (Rick and Chetelat 1991).Interspecific F₁ hybrids between SI wild species and SC cultivated tomato are self-incompatible and reject pollen of cultivated tomato, indicating both traits are at least partially dominant (McGuire and Rick 1954; Martin 1963; Hardon 1967). Interestingly, pollen of the F₁ hybrids is incompatible on pistils of the wild species parent (i.e., including other individuals of the same accessions, but with nonmatching S alleles). This observation suggests that there are dominant factors from cultivated tomato that lead to pollen rejection on styles of the wild species, regardless of the pollen genotype. This apparent sporophytic effect contrasts with the purely gametophytic nature of pollen SI specificity in the Solanaceae (De Nettancourt 1977).Early studies of the inheritance of unilateral incompatibility in tomato suggested the involvement of several genes controlling the pistil response; however, the genetics of pollen responses have received little attention. In F₂ S. habrochaites (northern SC accession) × S. habrochaites (central SI accession), the rejection of pollen from the SC parent segregated as if controlled by one to two dominant genes from the SI accession (Martin 1964). In crosses of S. lycopersicum to both SI and SC accessions of S. pennellii, the intra- and interspecific crossing relations were largely consistent with the Lewis and Crowe (1958) model of stepwise mutation at the S locus (Hardon 1967); there was also evidence of a second barrier in the SC S. pennellii accession. In F₁ and BC₁ hybrids of S. lycopersicum × S. habrochaites, the segregation of unilateral and self-incompatibilities was consistent with the action of two major genes, with minor polygenes indicated as well (Martin 1967). More recently, several QTL underlying pistil-side unilateral and self-incompatibilities were mapped in BC₁ S. lycopersicum × S. habrochaites (Bernacchi and Tanksley 1997); the major QTL for both forms of pollen rejection was located at or near the S locus on chromosome 1, which controls SI specificity (Tanksley and Loaiza-Figueroa 1985).There are little data on pollen-side unilateral incompatibility factors in the tomato clade, or any other system. Our previous work identified two to three genetic loci from S. pennellii that are required for pollen to overcome incompatibility on pistils of S. lycopersicum × S. lycopersicoides or S. lycopersicum × S. sitiens hybrids (Chetelat and Deverna 1991; Pertuze et al. 2003). One of these factors mapped to the S locus, the other two were on chromosomes 6 and 10. In this system the female tester stocks were either diploid or allotriploid hybrids, the latter containing one genome of the wild, SI parent, plus two genomes of cultivated tomato; both types of hybrids reject pollen of cultivated tomato. The pollen parents were either F₁ S. lycopersicum × S. pennellii or bridging lines developed by backcrossing the F₁ to cultivated tomato and selecting for the ability to overcome stylar incompatibility. In the progeny, distorted segregation ratios were observed in which the S. pennellii alleles were preferentially transmitted, indicating linkage to gametophytic factors required forcompatibility.This experimental system has several advantages for detecting pollen (gametophytic) unilateral incompatibility genes. First, pollen-expressed factors are readily distinguished from pistil factors because only the former show linkage to S. pennellii specific markers. Second, pollen rejection is by unilateral, not self-incompatibility, since both species contributing to the pollen genotype, S. lycopersicum and S. pennellii, are SC. Finally, as we describe herein, the rejection of tomato pollen by pistils of the interspecific hybrids is weakened by the decreasing dosage of the S. lycopersicoides genome, which reduces the number of pollen factors required for compatibility. Thus, the gametophytic factors on chromosomes 1 and 6 (denoted hereinafter ui1.1 and ui6.1), when present in the same pollen, are sufficient for full compatibility on pistils of allotriploid interspecific hybrids, whereas they confer only partial compatibility on diploid hybrids.Our overall objectives are to identify the genes underlying both the chromosome 1 and chromosome 6 pollen-specific unilateral incompatibility factors from S. pennellii and to determine the nature of their interaction. Toward this goal, we report herein the high-resolution genetic and physical mapping of the ui6.1 region.     

Aging in a Long-Lived Clonal Tree

From bacteria to multicellular animals, most organisms exhibit declines in survivorship or reproductive performance with increasing age (“senescence”) [1],[2]. Evidence for senescence in clonal plants, however, is scant [3],[4]. During asexual growth, we expect that somatic mutations, which negatively impact sexual fitness, should accumulate and contribute to senescence, especially among long-lived clonal plants [5],[6]. We tested whether older clones of Populus tremuloides (trembling aspen) from natural stands in British Columbia exhibited significantly reduced reproductive performance. Coupling molecular-based estimates of clone age with male fertility data, we observed a significant decline in the average number of viable pollen grains per catkin per ramet with increasing clone age in trembling aspen. We found that mutations reduced relative male fertility in clonal aspen populations by about 5.8×10⁻⁵ to 1.6×10⁻³ per year, leading to an 8% reduction in the number of viable pollen grains, on average, among the clones studied. The probability that an aspen lineage ultimately goes extinct rises as its male sexual fitness declines, suggesting that even long-lived clonal organisms are vulnerable to senescence.     

The “Domestication Syndrome” in Mammals: A Unified Explanation Based on Neural Crest Cell Behavior and Genetics

Charles Darwin, while trying to devise a general theory of heredity from the observations of animal and plant breeders, discovered that domesticated mammals possess a distinctive and unusual suite of heritable traits not seen in their wild progenitors. Some of these traits also appear in domesticated birds and fish. The origin of Darwin’s “domestication syndrome” has remained a conundrum for more than 140 years. Most explanations focus on particular traits, while neglecting others, or on the possible selective factors involved in domestication rather than the underlying developmental and genetic causes of these traits. Here, we propose that the domestication syndrome results predominantly from mild neural crest cell deficits during embryonic development. Most of the modified traits, both morphological and physiological, can be readily explained as direct consequences of such deficiencies, while other traits are explicable as indirect consequences. We first show how the hypothesis can account for the multiple, apparently unrelated traits of the syndrome and then explore its genetic dimensions and predictions, reviewing the available genetic evidence. The article concludes with a brief discussion of some genetic and developmental questions raised by the idea, along with specific predictions and experimental tests.A major gap in Charles Darwin’s theory of evolution, as presented in the first edition of The Origin of Species (Darwin 1859), was the absence of a theory of heredity. As Darwin knew, his theory of evolution required a distinct idea of how biological heredity worked, but in 1859 he was not prepared to offer one. His attempt to fill this gap came subsequently, in his massive, detailed study of inheritance, The Variation of Plants and Animals under Domestication (Darwin 1868). Written decades before there was a science of genetics, it relied primarily on the data produced by animal and plant breeders, hence on observations of domesticated animals and plants.Darwin’s encyclopedic investigation of domesticated species revealed an intriguing phenomenon. From his survey of the animal breeding work, he found that domesticated mammals in general exhibit a suite of behavioral, physiological, and morphological traits not observed in their wild forebears. Today, the full set of these characteristics is known to include: increased docility and tameness, coat color changes, reductions in tooth size, changes in craniofacial morphology, alterations in ear and tail form (e.g., floppy ears), more frequent and nonseasonal estrus cycles, alterations in adrenocorticotropic hormone levels, changed concentrations of several neurotransmitters, prolongations in juvenile behavior, and reductions in both total brain size and of particular brain regions. The consistency of this extremely diverse set of phenotypic changes in domesticated mammals presents a major puzzle, as Darwin recognized. The suite seems to reflect something about the process of domestication per se, a conclusion strengthened by the finding that domesticated birds and even fish share some components of this spectrum of traits. Because Darwin published these findings just a few years after Mendel published his work, the hereditary basis of this phenomenon constitutes one of the oldest problems in genetics.The general combination of traits in domesticated mammals is an ensemble that we will refer to as the “domestication syndrome” (DS) (adopting a term used for domesticated crop plants, e.g., Brown et al. 2008). We list its core components in Table 1List of traits modified in the “domestication syndrome” in mammals^*     

Mechanotransduction by Membrane Proteins: Worms find PEZO-1’s function easy to swallow

JGP study finds that the C. elegans orthologue of the PIEZO family is a mechanosensitive ion channel that regulates pharyngeal pumping and food sensation.

The PIEZO family of mechanosensitive cation channels has been implicated in a wide variety of physiological processes in mammals and is also associated with human disease. Mammalian genomes encode two family members, known as Piezo1 and Piezo2, but invertebrates such as the nematode Caenorhabditis elegans only possess a single Piezo-related gene (1). The function of the C. elegans orthologue, known as pezo-1, has largely remained obscure, but, in this issue of JGP, Millet et al. reveal that it encodes a bona fide mechanosensitive ion channel that regulates pharyngeal activity (2).Jonathan Millet (left), Valeria Vásquez (center), and colleagues reveal that pezo-1, the sole PIEZO family member in C. elegans, is a mechanosensitive ion channel that regulates pharyngeal pumping and food sensation, particularly when worms are fed with large and stiff bacterial filaments that are difficult to swallow (graphic created with BioRender.com).In 2020, an elegant study demonstrated that pezo-1 controls C. elegans ovulation and fertilization (3). However, explains Valeria Vásquez from the University of Tennessee Health Science Center, whether pezo-1 encodes for a mechanosensitive ion channel was unknown. “PEZO-1 is expressed in many tissues, including the pharynx, which is the organ we decided to concentrate on in our study,” Vásquez says.Muscle cells in the C. elegans pharynx rhythmically contract and relax to pump food into the worm’s intestine. Vásquez and colleagues, including first author Jonathan Millet, found that PEZO-1 is expressed in several different pharyngeal cell types (2), including the gland cells whose secretions lubricate the pharynx, and the proprioceptive NSM neurons that are thought to sense the presence of food within the pharynx lumen and release serotonin to increase the rate of pharyngeal pumping.Millet et al. analyzed pharyngeal pumping in worms lacking pezo-1, as well as in animals expressing a pezo-1 point mutant that, in human Piezo1, increases channel function by slowing channel deactivation and inactivation. Loss or gain of pezo-1 function had surprisingly little effect on pharyngeal activity, causing only mild alterations in the duration and frequency of pumping induced by serotonin, and more obvious effects when challenged with high osmolarity solutions.Worms cultured in the laboratory are usually fed a diet of small, easily ingested Escherichia coli cells and, both loss and gain of pezo-1 function increased the pharynx’s response to this type of food. In their natural habitat, however, C. elegans encounter bacteria of various shapes and sizes, some of which might be harder to swallow. “It occurred to me that it might make a difference if we fed the worms with bacteria that were stiffer and longer,” Vásquez says.The researchers therefore provided their pezo-1 mutants with E. coli treated with cephalexin, an antibiotic that inhibits cell separation and causes the bacteria to form long, spaghetti-like filaments. Compared with wild-type worms fed with this diet, pharyngeal activity was markedly enhanced by the gain-of-function pezo-1 mutant, but substantially reduced in the absence of pezo-1, almost as if the worms were “choking” on the bacterial filaments.Crucially, by performing patch-clamp experiments on both cultured C. elegans cells and insect cells expressing recombinant pezo-1, Millet et al. confirmed that PEZO-1 is, indeed, a mechanosensitive ion channel. However, it remains to be seen exactly how PEZO-1 helps the pharynx sense the physical parameters of food and adjust its pumping activity accordingly. One possibility is that the channel acts within the proprioceptive neurons to regulate the release of serotonin.Intriguingly, the Drosophila PIEZO orthologue controls feeding behavior in flies (4). “However, it’s not known which mechanosensitive channels are important in the pharyngeal system of mammals,” Vásquez says. “Our studies in C. elegans could therefore open an opportunity to understand food sensation in humans.”     

Analysis of the Fine-Scale Population Structure of “Candidatus Accumulibacter phosphatis” in Enhanced Biological Phosphorus Removal Sludge,Using Fluorescence In Situ Hybridization and Flow Cytometric Sorting

To investigate the fine-scale diversity of the polyphosphate-accumulating organisms (PAO) “Candidatus Accumulibacter phosphatis” (henceforth referred to as “Ca. Accumulibacter”), two laboratory-scale sequencing batch reactors (SBRs) for enhanced biological phosphorus removal (EBPR) were operated with sodium acetate as the sole carbon source. During SBR operations, activated sludge always contained morphologically different “Ca. Accumulibacter” strains showing typical EBPR performances, as confirmed by the combined technique of fluorescence in situ hybridization (FISH) and microautoradiography (MAR). Fragments of “Ca. Accumulibacter” 16S rRNA genes were retrieved from the sludge. Phylogenetic analyses together with sequences from the GenBank database showed that “Ca. Accumulibacter” 16S rRNA genes of the EBPR sludge were clearly differentiated into four “Ca. Accumulibacter” clades, Acc-SG1, Acc-SG2, Acc-SG3, and Acc-SG4. The specific FISH probes Acc444, Acc184, Acc72, and Acc119 targeting these clades and some helpers and competitors were designed by using the ARB program. Microbial characterization by FISH analysis using specific FISH probes also clearly indicated the presence of different “Ca. Accumulibacter” cell morphotypes. Especially, members of Acc-SG3, targeted by probe Acc72, were coccobacillus-shaped cells with a size of approximately 2 to 3 μm, while members of Acc-SG1, Acc-SG2, and Acc-SG4, targeted by Acc444, Acc184, and Acc119, respectively, were coccus-shaped cells approximately 1 μm in size. Subsequently, cells targeted by each FISH probe were sorted by use of a flow cytometer, and their polyphosphate kinase 1 (ppk1) gene homologs were amplified by using a ppk1-specific PCR primer set for “Ca. Accumulibacter.” The phylogenetic tree based on sequences of the ppk1 gene homologs was basically congruent with that of the 16S rRNA genes, but members of Acc-SG3 with a distinct morphology comprised two different ppk1 genes. These results suggest that “Ca. Accumulibacter” strains may be diverse physiologically and ecologically and represent distinct populations with genetically determined adaptations in EBPR systems.Enhanced biological phosphorus removal (EBPR) has been applied in many wastewater treatment plants to reduce the phosphorus that causes eutrophication in surface waters. EBPR employs polyphosphate-accumulating organisms (PAOs), which are enriched through alternating aerobic-anaerobic cycles (34). Since PAOs are essential for an understanding of EBPR, many candidates have been proposed as potential PAOs, such as Acinetobacter spp. (11), Tetrasphaera spp. (31), Microlunatus phosphovorus (36), Lampropedia spp. (40), and Gram-positive Actinobacteria (24). However, those organisms do not exhibit all of the characteristics of the EBPR biochemistry model. Recently developed culture-independent approaches such as PCR-clone libraries, fluorescence in situ hybridization (FISH), and microautoradiography (MAR) have highlighted an uncultured Rhodocyclus-related bacterium, “Candidatus Accumulibacter phosphatis” (henceforth referred to as “Ca. Accumulibacter”), as one of the most important PAO candidates (2, 5, 16, 22, 23, 27, 28, 47).Numerous studies have sought to investigate uncultured “Ca. Accumulibacter” and have shown the presence of genetically and physiologically different members with a global geographic distribution (3, 9, 22, 27, 39). For example, Kong et al. (22) identified two morphologically different “Ca. Accumulibacter” cells of small cocci and large coccobacilli labeled with PAOmix (PAO462, PAO651, and PAO846) in laboratory-scale EBPR reactors. Additional results showing phenotypic and morphological diversities of “Ca. Accumulibacter” cells also existed with respect to the different roles of denitrifying PAO (DPAO) in the EBPR process (3, 9, 23). Carvalho et al. (3) detected two different morphotypes of “Ca. Accumulibacter” with different nitrate reduction capabilities. The presence of other “Ca. Accumulibacter” strains with 15% genome sequence divergence from the dominant strains in metagenomic analyses is likely to explain these morphological and phenotypic differences (12). McMahon et al. (33) suggested the use of the polyphosphate kinase (ppk) gene, which is involved in the production of polyphosphate, for a finer elucidation of “Ca. Accumulibacter” diversity. He et al. (15) grouped “Ca. Accumulibacter” strains into five distinct clades, designated clades I, IIA, IIB, IIC, and IID, using ppk gene sequence information. Flowers and colleagues (9) previously reported that “Ca. Accumulibacter” cells of clade IA had nitrate reduction activity with phosphorus uptake but that “Ca. Accumulibacter” cells of clade IIA did not.FISH-fluorescence activated cell sorting (FACS) techniques have been used for the separation of specific microbial cells from complex microbial consortia and their metabolic gene analysis (14, 46). For example, Miyauchi et al. (35) sorted PAOmix probe-labeled “Ca. Accumulibacter” cells from EBPR sludge and analyzed their nitrite reductase gene (nirS) diversity. In the current study, we found that four different “Ca. Accumulibacter” clades (Acc-SG1, Acc-SG2, Acc-SG3, and Acc-SG4) were present in the EBPR sludge of laboratory-scale reactors supplied with acetate as the sole carbon source. We analyzed their morphological characteristics and ppk gene sequence information using a suite of FISH and FACS approaches and linked fine-scale phylogenetic diversities of “Ca. Accumulibacter” strains with their morphological characteristics and metabolic genes. This study will be useful for further genetic and physiological studies of different “Ca. Accumulibacter” clades.     

Outcomes for patients with the same disease treated inside and outside of randomized trials: a systematic review and meta-analysis

Background:

It is unclear whether participation in a randomized controlled trial (RCT), irrespective of assigned treatment, is harmful or beneficial to participants. We compared outcomes for patients with the same diagnoses who did (“insiders”) and did not (“outsiders”) enter RCTs, without regard to the specific therapies received for their respective diagnoses.

Methods:

By searching the MEDLINE (1966–2010), Embase (1980–2010), CENTRAL (1960–2010) and PsycINFO (1880–2010) databases, we identified 147 studies that reported the health outcomes of “insiders” and a group of parallel or consecutive “outsiders” within the same time period. We prepared a narrative review and, as appropriate, meta-analyses of patients’ outcomes.

Results:

We found no clinically or statistically significant differences in outcomes between “insiders” and “outsiders” in the 23 studies in which the experimental intervention was ineffective (standard mean difference in continuous outcomes −0.03, 95% confidence interval [CI] −0.1 to 0.04) or in the 7 studies in which the experimental intervention was effective and was received by both “insiders” and “outsiders” (mean difference 0.04, 95% CI −0.04 to 0.13). However, in 9 studies in which an effective intervention was received only by “insiders,” the “outsiders” experienced significantly worse health outcomes (mean difference −0.36, 95% CI −0.61 to −0.12).

Interpretation:

We found no evidence to support clinically important overall harm or benefit arising from participation in RCTs. This conclusion refutes earlier claims that trial participants are at increased risk of harm.When people are asked to participate in a randomized controlled trial (RCT), it is natural for them to ask several questions in return. How safe are these treatments? How many extra visits and tests must I undergo? Will the researchers keep my family doctor informed about what’s going on? What outcomes are to be measured, and do they include ones that are of interest to me as a patient?These multiple questions can be summarized as follows: Would I fare better being treated within the trial (as an “insider”) or in routine clinical care outside it (as an “outsider”)? Patients may ask this question in 1 of 2 ways. The first is highly specific: “Am I better off receiving this specific treatment as an insider or as an outsider?” Alternatively, they might ask a more general question: “Am I better off having my illness managed, regardless of the specific treatment I would receive, as an insider or as an outsider?” These questions are highly appropriate, and both deserve to be asked and answered,^1,2 especially given that nonsystematic reviews have suggested a possible “inclusion benefit” from participating in trials.³These 2 specific patient questions are analogous to those posed by researchers asking whether treatments do more good than harm when applied under “ideal” circumstances (in explanatory trials) or in the “real world” of routine health care (in pragmatic trials). Vist and colleagues answered the explanatory question when their earlier review⁴ found no advantage or disadvantage from receiving the same treatment inside or outside an RCT. Left unanswered, however, was the broader, more pragmatic question. In our experience, trial participants are often offered new, as-yet-untested treatments that would not be available to them outside the trial. This review looks at the dilemma faced by these patients, which needs to be addressed before general conclusions can be drawn about trial safety.     

COVID‐19 Disease Map,a computational knowledge repository of virus‐host interaction mechanisms

The authors requested to correct the spelling of Egon Willighagen and Andrea Senff‐Ribeiro''s names, as well as the following affiliations: Charles Auffray to: “European Institute for Systems Biology and Medicine (EISBM), Vourles, France”; Noriko Hiori to: “Graduate School of Media and Governance, Keio Research Institute at SFC, Keio University, Kanagawa, Japan”; and Leonard Schmeister to: “Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Garching, Germany and Helmholtz Zentrum München – German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany”.     

Impact of Temperature on Ladderane Lipid Distribution in Anammox Bacteria

Anaerobic ammonium-oxidizing (anammox) bacteria have the unique ability to synthesize fatty acids containing linearly concatenated cyclobutane rings, termed “ladderane lipids.” In this study we investigated the effect of temperature on the ladderane lipid composition and distribution in anammox enrichment cultures, marine particulate organic matter, and surface sediments. Under controlled laboratory conditions we observed an increase in the amount of C₂₀ [5]-ladderane fatty acids compared with the amount of C₁₈ [5]-ladderane fatty acids with increasing temperature and also an increase in the amount of C₁₈ [5]-ladderane fatty acids compared with the amount of C₂₀ [5]-ladderane fatty acids with decreasing temperature. Combining these data with results from the natural environment showed a significant (R² = 0.85, P = <0.0001, n = 121) positive sigmoidal relationship between the amounts of C₁₈ and C₂₀ [5]-ladderane fatty acids and the in situ temperature; i.e., there is an increase in the relative abundance of C₁₈ [5]-ladderane fatty acids at lower temperatures and vice versa, particularly at temperatures between 12°C and 20°C. Novel shorter (C₁₆) and longer (C₂₂ to C₂₄) ladderane fatty acids were also identified, but their relative amounts were small and did not change with temperature. The adaptation of ladderane fatty acid chain length to temperature changes is similar to the regulation of common fatty acid composition in other bacteria and may be the result of maintaining constant membrane fluidity under different temperature regimens (homeoviscous adaptation). Our results can potentially be used to discriminate between the origins of ladderane lipids in marine sediments, i.e., to determine if ladderanes are produced in situ in relatively cold surface sediments or if they are fossil remnants originating from the warmer upper water column.Anaerobic ammonium-oxidizing (anammox) bacteria possess the unique ability to oxidize NH₄⁺ with NO₂⁻ to N₂ under anoxic conditions (42). Since the discovery of the anammox process in a wastewater treatment plant in the Netherlands (21), studies have indicated that anammox bacteria are omnipresent in low-oxygen environments around the world. Anammox therefore forms an important link in both the oceanic (4, 7, 17, 18, 31) and freshwater (14, 33) nitrogen cycles. Unlike other Planctomycetes, anammox bacteria contain a unique “organelle” called the anammoxosome (19, 37, 44-46). The membrane of this compartment contains unusual “ladderane” lipids (37). The core ladderane lipids consist of C₁₈ and C₂₀ fatty acids containing either 3 or 5 linearly concatenated cyclobutane rings, which are ester bound to a glycerol backbone or ether bound as alkyl chains (35). In addition, the intact polar lipids containing the core lipid structures may have different types of polar head groups, including phosphatidylcholine (PC), phosphatidylethanolamine (PE), or phosphatidylglycerol (PG) (1, 22). In silico density simulation modeling experiments with a ladderane lipid-containing membrane (glycerol-bound mixed ether-ester containing both ladderane moieties) have indicated that ladderane lipids could provide a denser cell membrane than conventional membrane lipids (37). Since the anammoxosome appears to be impenetrable to fluorophores, the ladderane membrane could function in cell energy conservation (37, 44).Experimental evidence has shown that anammox bacteria isolated from wastewater treatment reactors grow over a wide range of temperatures (20 to 43°C) and have an optimum temperature of about 35°C (39). In the natural environment the anammox process has been reported to occur at temperatures as low as −2.5°C in sea ice (5, 26) and as high as 70°C in hot springs and hydrothermal vent areas (3, 12). Furthermore, “Candidatus Scalindua spp.” has been successfully enriched from marine sediment (Gullmarsfjord, Sweden) in sequencing batch reactors at temperatures of 15 and 20°C (43). In other bacteria containing common fatty acids temperature adaptation can be achieved by (among other things) modifying the composition of the membrane bilayers to deal with alterations in membrane viscosity due to changes in temperature. This process has been well documented and is termed “homeoviscous adaptation”; i.e., the fatty acid composition is changed to maintain membrane fluidity (23, 27, 34, 40). Currently, it is not known how anammox bacteria, with their highly unusual ladderane lipids, react to temperature. To investigate this, we analyzed the ladderane lipid composition of anammox bacteria grown at different temperatures in sequencing batch reactors and in samples from different natural environments covering a wide range of temperatures.     

Posttranscriptional regulation of colonic epithelial repair by RNA binding protein IMP1/IGF2BP1

Correction to: EMBO Reports (2019) 20: e47074. DOI 10.15252/embr.201847074 | Published online 6 May 2019The authors noticed that the control and disease labels had been inverted in their data analysis resulting in publication of incorrect data in Figure 1C. The corrected figure is displayed below. This change affects the conclusions as detailed below. The authors apologize for this error and any confusion it may have caused.In the legend of 1C, change from, “Differential gene expression analysis of pediatric ileal CD patient samples (n = 180) shows increased (> 4‐fold) IMP1 expression as compared to non‐inflammatory bowel disease (IBD) pediatric samples (n = 43)”.Open in a separate windowFigure 1CCorrected Open in a separate windowFigure 1COriginal To, "Differential gene expression analysis of pediatric ileal CD patient samples (n = 180) shows decreased (> 4‐fold) IMP1 expression as compared to non‐inflammatory bowel disease (IBD) pediatric samples (n = 43)”.In abstract, change from, “Here, we report increased IMP1 expression in patients with Crohn''s disease and ulcerative colitis”.To, “Here, we report increased IMP1 expression in adult patients with Crohn''s disease and ulcerative colitis”.In results, change from, “Consistent with these findings, analysis of published the Pediatric RISK Stratification Study (RISK) cohort of RNA‐sequencing data 38 from pediatric patients with Crohn''s disease (CD) patients revealed that IMP1 is upregulated significantly compared to control patients and that this effect is specific to IMP1 (i.e., other distinct isoforms, IMP2 and IMP3, are not changed; Fig 1C)”.To, “Contrary to our findings in colon tissue from adults, analysis of published RNA‐sequencing data from the Pediatric RISK Stratification Study (RISK) cohort of ileal tissue from children with Crohn’s disease (CD) 38 revealed that IMP1 is downregulated significantly compared to control patients in the RISK cohort and that this effect is specific to IMP1 (i.e., other distinct isoforms, IMP2 and IMP3, are not changed; Fig 1C)”.In discussion, change from, “Indeed, we report that IMP1 is upregulated in patients with Crohn''s disease and ulcerative colitis and that mice with Imp1 loss exhibit enhanced repair following DSS‐mediated damage”.To “Indeed, we report that IMP1 is upregulated in adult patients with Crohn''s disease and ulcerative colitis and that mice with Imp1 loss exhibit enhanced repair following DSS‐mediated damage”.     

Characterization of an ATP Translocase Identified in the Destructive Plant Pathogen “Candidatus Liberibacter asiaticus”

ATP/ADP translocases transport ATP across a lipid bilayer, which is normally impermeable to this molecule due to its size and charge. These transport proteins appear to be unique to mitochondria, plant plastids, and obligate intracellular bacteria. All bacterial ATP/ADP translocases characterized thus far have been found in endosymbionts of protozoa or pathogens of higher-order animals, including humans. A putative ATP/ADP translocase was uncovered during the genomic sequencing of the intracellular plant pathogen “Candidatus Liberibacter asiaticus,” the causal agent of citrus huanglongbing. Bioinformatic analysis of the protein revealed 12 transmembrane helices and predicted an isoelectric point of 9.4, both of which are characteristic of this family of proteins. The “Ca. Liberibacter asiaticus” gene (nttA) encoding the translocase was subsequently expressed in Escherichia coli and shown to enable E. coli to import ATP directly into the cell. Competition assays with the heterologous E. coli system demonstrated that the translocase was highly specific for ATP and ADP but that other nucleotides, if present in high concentrations, could also be taken up and/or block the ability of the translocase to import ATP. In addition, a protein homologous to NttA was identified in “Ca. Liberibacter solanacearum,” the bacterium associated with potato zebra chip disease. This is the first reported characterization of an ATP translocase from “Ca. Liberibacter asiaticus,” indicating that some intracellular bacteria of plants also have the potential to import ATP directly from their environment.Citrus huanglongbing (HLB), also known as citrus greening, is a disease of citrus that was first reported in China in the early 20th century (33) and identified in the United States in August 2005 in South Florida (22). As it spread rapidly across Florida, HLB has caused substantial economic losses to the citrus industry, and now other citrus-producing states may be in danger as well. The effects of this disease range from mild to severe and include symptoms such as yellow shoots, blotchy mottles on leaves, vein yellowing and corking, lopsided fruit with aborted seeds, early fruit dropping, and limb dieback, which can ultimately lead to the total loss of the infected tree. The disease has been associated with three species of bacteria known as “Candidatus Liberibacter” species. Each of the three “Ca. Liberibacter” species was discovered and named based on its presumptive origin, with “Ca. Liberibacter asiaticus” being found in Asia, “Ca. Liberibacter africanus” in Africa (13), and “Ca. Liberibacter americanus” in South America (24). A fourth species, known as “Ca. Liberibacter solanacearum,” is genetically related, although it is not naturally associated with HLB in citrus plants (16). “Ca. Liberibacter solanacearum” is associated with the emerging zebra chip disease of potatoes and tomatoes (15). “Ca. Liberibacter” species are Gram-negative, fastidious alphaproteobacteria (13) that reside in the sieve tube elements of infected plants (23). The same bacteria found in citrus plants have also been found in two phloem-feeding insects, the Asian citrus psyllid (Diaphorina citri) and the African citrus psyllid (Trioza erytreae), which act as vectors for the disease (for recent reviews, see references 3 and 9). Since insects that carry the pathogen do not have a shortened life span or other adverse effects (12), “Ca. Liberibacter” is thought to act more as an endosymbiont than as a pathogen in insects. There is no known cure for HLB, and current management strategies include elimination of infected trees and methods aimed at vector control. Because of the rapid spread and devastating consequences of infection with “Ca. Liberibacter,” understanding this obligate intracellular pathogen will be critical for the survival of the citrus industry.Recently, the complete genome sequence of “Ca. Liberibacter asiaticus” was obtained via metagenomics (5). Within this “Ca. Liberibacter asiaticus” genome, an open reading frame encoding a putative ATP/ADP translocase was found. Translocases are enzymes that aid in the transport of molecules, in this case adenosine phosphate, across a cell membrane. These adenylate transporters can be placed into one of three groups based upon where they reside. The first group was discovered in mitochondria and is involved in transporting the ATP synthesized in the mitochondrial matrix to the cytosol of the cell (28). The second type of transporter is found in plant plastids (19, 21, 31). In contrast to the mitochondrial transporters, which transport ATP to the cytosol, this set of transporters import ATP from the cytosol. Their function is to provide the stroma with a supply of cytosolic ATP in order to facilitate many of the anabolic reactions that take place there. The third set of transporters was originally discovered in the obligate intracellular bacterium Rickettsia prowazekii (30). Similar to their plastid counterparts, these transporters import ATP from the host cell''s cytosol and translocate it into the bacterial cell. Bacteria that posses this enzyme can act as “energy parasites” and import ATP directly from their hosts.Since its discovery in Rickettsia, the ATP/ADP translocase has been identified in other obligate intracellular parasites of animals, such as Chlamydia psittaci and Lawsonia intracellularis (11, 20), in addition to some protist endosymbionts, such as Caedibacter caryophilus and “Protochlamydia amoebophila” (4, 10). Analyses of the translocase proteins in these bacteria have demonstrated that certain translocase homologs can be used by the cell to import nucleotides other than ATP (2, 4, 10, 26), and thus, the family of proteins has come to be known more generally as nucleotide transporters. In spite of all of the previous research in this area, an ATP/ADP translocase from a bacterial plant pathogen has yet to be characterized. Here, we present the first characterization of a nucleotide transport protein (NttA) from the obligate intracellular plant pathogen “Ca. Liberibacter asiaticus.”     

Evolution and Diversity of Facultative Symbionts from the Aphid Subfamily Lachninae

Many aphids harbor a variety of endosymbiotic bacteria. The functions of these symbionts can range from an obligate nutritional role to a facultative role in protecting their hosts against environmental stresses. One such symbiont is “Candidatus Serratia symbiotica,” which is involved in defense against heat and potentially also in aphid nutrition. Lachnid aphids have been the focus of several recent studies investigating the transition of this symbiont from a facultative symbiont to an obligate symbiont. In a phylogenetic analysis of Serratia symbionts from 51 lachnid hosts, we found that diversity in symbiont morphology, distribution, and function is due to multiple independent origins of symbiosis from ancestors belonging to Serratia and possibly also to evolution within distinct symbiont clades. Our results do not support cocladogenesis of “Ca. Serratia symbiotica” with Cinara subgenus Cinara species and weigh against an obligate nutritional role. Finally, we show that species belonging to the subfamily Lachninae have a high incidence of facultative symbiont infection.Many insect species harbor heritable endosymbiotic bacteria. Among the best studied of these species are aphids. Almost all aphids are infected with the obligate nutritional symbiont Buchnera aphidicola, which is generally required for the survival of aphids and provides essential amino acids that are rare in their phloem sap diet (32). Many aphids also possess additional symbionts that may be facultative from the host''s perspective and that coexist with Buchnera (20).Three lineages of facultative symbionts that are prevalent in aphids belong to the Enterobacteriaceae. Two of these lineages (“Candidatus Hamiltonella defensa” and “Candidatus Regiella insecticola”) form well-defined clades distinct from free-living bacterial species (4, 20) and confer clear advantages to their hosts by protecting them against natural enemies. “Ca. Hamiltonella defensa” prevents wasp parasitism by arresting development of wasp larvae in pea aphids, and “Ca. Regiella insecticola” provides resistance against the fungal pathogen Pandora neoaphidis (24, 31). The third lineage, “Candidatus Serratia symbiotica,” is closely related to free-living members of the genus Serratia. This symbiont is distributed sporadically among aphid species and has been proposed to have a variety of effects on hosts. In pea aphids (Acyrthosiphon pisum; Macrosiphini), “Ca. Serratia symbiotica” ameliorates the deleterious fitness effects of heat shock by protecting symbiont-harboring bacteriocyte cells (2, 19, 29). Additionally, a strain of “Ca. Serratia symbiotica” provided some resistance to parasitoid wasp attack (24). “Ca. Serratia symbiotica” has been proposed to play a role in nutrition by producing amino acids for its aphid host and by decreasing its host''s reliance on Buchnera (10, 15, 16, 26). In contrast to most Buchnera strains, Buchnera strains from Cinara cedri (Lachnini) have lost the genes for biosynthesis of the essential amino acid tryptophan, while “Ca. Serratia symbiotica” in the same host possesses at least part of the pathway, suggesting that it has a mutualistic role in the nutrition of aphids (26).In A. pisum, “Ca. Serratia symbiotica” cells are rod-shaped bacteria that are present in the sheath cells, hemolymph, and bacteriocytes of some individuals. In contrast, in C. cedri “Ca. Serratia symbiotica” occurs in all individuals, and its cells are large, round, and pleomorphic, similar to the cells of many obligate bacterial aphid endosymbionts, including Buchnera (10, 26). Furthermore, “Ca. Serratia symbiotica” has consistently been present in other Cinara species sampled (28). Both the rod-shaped and pleomorphic forms are assigned to “Ca. Serratia symbiotica” based on phylogenetic analyses of several gene sequences, but they fall into two distinct sister clades of symbiont lineages that seem to coincide with bacterial morphology (17, 20).This diversity in “Ca. Serratia symbiotica” morphology, distribution, and functions may represent evolution of different features within lineages of a single symbiont clade. If “Ca. Serratia symbiotica” is an obligate nutritional symbiont in Cinara hosts, it is expected that Cinara-associated symbionts would form a clade in which the intraclade relationships mirror those of the hosts (cocladogenesis), as observed for Buchnera and other obligate nutritional symbionts of insects (13, 21, 38). Indeed, Lamelas et al. postulated that, based on their similar phylogenies, Serratia symbionts from aphids belonging to the subgenus Cinara have had a long-term relationship with their hosts (17).In addition to the three most common facultative symbiont types found in aphids described above, several other symbiont lineages with unknown functions have been identified by amplification of bacterial 16S rRNA gene sequences from various aphid species (10, 28, 39). Here we examine the diversity of Serratia and other facultative symbionts in aphids belonging to the subfamily Lachninae. We investigated the distribution of symbionts in aphid species and geographic locations and looked for coevolutionary patterns that may correspond to the functions of facultative symbionts within their hosts.     

Modeling the Effect of Abrupt Acid and Osmotic Shifts within the Growth Region and across Growth Boundaries on Adaptation and Growth of Listeria monocytogenes

This study aims to model the effects of acid and osmotic shifts on the intermediate lag time of Listeria monocytogenes at 10°C in a growth medium. The model was developed from data from a previous study (C. I. A. Belessi, Y. Le Marc, S. I. Merkouri, A. S. Gounadaki, S. Schvartzman, K. Jordan, E. H. Drosinos, and P. N. Skandamis, submitted for publication) on the effects of osmotic and pH shifts on the kinetics of L. monocytogenes. The predictive ability of the model was assessed on new data in milk. The effects of shifts were modeled through the dependence of the parameter h₀ (“work to be done” prior to growth) induced on the magnitude of the shift and/or the stringency of the new environmental conditions. For shifts across the boundary, the lag time was found to be affected by the length of time for which the microorganisms were kept at growth-inhibiting conditions. The predicted concentrations of L. monocytogenes in milk were overestimated when the effects of this shift were not taken into account. The model proved to be suitable to describe the effects of osmotic and acid shifts observed both within the growth domain and across the growth boundaries of L. monocytogenes.The lag phase of a microorganism is usually seen as a period of transition from an initial physiological state to the state of balanced growth. The duration of the lag phase, denoted by lag in what follows, depends on the amount of work to be carried out by the cells prior to exponential growth and the rate at which this work is undertaken (6, 13). According to Baranyi and Roberts (2), the “work to be done” is proportional to h₀, the product of the lag time and the rate at which the work is carried out. Robinson et al. (13) pointed out that there is no direct way to measure this rate, and it is often assumed that it is equal to the specific growth rate characteristic of the growth conditions (2). Some authors use the relative lag time (RLT) (7, 8) as a replacement for the “work to be done” h₀ parameter. In fact the two concepts appear to be very similar, RLT and h₀ being proportional to each other.The transient phase following inoculation is commonly called the initial lag phase. Many authors (6, 7, 14, 17) observed that subsequent abrupt changes in the environmental conditions (temperature, pH, and water activity [a_w]) during the growth phase were able to induce a so-called “intermediate” lag phase. In other words, abrupt changes cause extra “work to be done” that cells have to perform before reinitiating their growth. Most of the studies on intermediate lag times have focused on abrupt thermal changes. For example, some authors have proposed models for the effects of temperature shifts on the lag time of Escherichia coli (14) and Lactobacillus plantarum (17). Using the data of Whiting and Bagi (15), for Listeria monocytogenes, Delignette-Muller et al. (3) highlighted a linear relationship between the “work to be done” and the magnitude and direction of the temperature shifts. Less attention has been given to the effects of acid and osmotic shifts, although such shifts pose a higher energetic burden to the cells than temperature shifts, especially around the growth boundaries (C. I. A. Belessi, Y. Le Marc, S. I. Merkouri, A. S. Gounadaki, S. Schvartzman, K. Jordan, E. H. Drosinos, and P. N. Skandamis, submitted for publication). Generally, the “work to be done” increases with the magnitude of the shifts applied (3, 7) and the cells in exponential phase are more sensitive to abrupt shifts than those in stationary phase (7). Muñoz-Cuevas et al. (9) proposed a model for the lag time of L. monocytogenes induced by temperature and water activity downshifts within the growth region. For osmotic shifts, the authors found that the “work to be done” was related not only to the magnitude of the shift and but also to the level of the environmental factors (temperature and water activity) after the shift.In most of the available modeling packages, predictions in dynamic environments are based on the assumption that when the environmental conditions change, the specific growth rate changes instantaneously relative to the new conditions. The intermediate lag times caused by abrupt changes in the environmental conditions are commonly neglected in the models. Besides, the models usually ignore the effects of shifts across the growth boundary and the duration of the period the cells spend above the growth/no-growth boundary on the physiological state of the cells. However, such abrupt shifts are important, as they may occur for example during fermentation and ripening of dairy products (10, 11) or during cross-contamination (e.g., when L. monocytogenes is accidently transferred to a different environment). The aim of this work was to develop a model to describe the effects of such abrupt shifts (within the growth range or across the growth boundary) on the possibly induced intermediate lag time of L. monocytogenes. The analysis here is based on the data from a previous study (Belessi et al., submitted) on the effects of acid and osmotic shifts on the kinetics of L. monocytogenes at 10°C. We also used new data in milk to explore the possibility of integrating the proposed approach in a generic growth model.