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[Symbiosis in the human gastrointestinal tract].
Guarner, F
Nutricion hospitalaria. 2021;(Spec No2):34-37
Abstract
The human body is a planet populated by myriads of microorganisms all over its surface and in cavities connected to the outside. Experimental and clinical research is showing that microbial colonizers are a functional and essential part of the human organism. The microbial ecosystem, which is housed in the gastrointestinal tract, provides a "metagenome": genes and additional functions to the genetic resources of the species, which are involved in multiple physiological processes (somatic development, nutrition, immunity, etc.). The human intestine houses lymphoid structures specialized in the induction and regulation of adaptive immunity, and the interaction of the intestinal microbiota with the immune system of the digestive mucosa plays a key role for the individual's homeostasis with the outside world. Some chronic non-communicable inflammatory diseases in developed society are associated with dysbiosis: loss of species richness in the gut microbiota and deviation from the ancestral microbial environment. Generating and maintaining diversity in the gut microbiota is a new clinical goal for health promotion and disease prevention.
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Mechanistic concepts of iron-sulfur protein biogenesis in Biology.
Braymer, JJ, Freibert, SA, Rakwalska-Bange, M, Lill, R
Biochimica et biophysica acta. Molecular cell research. 2021;(1):118863
Abstract
Iron-sulfur (Fe/S) proteins are present in virtually all living organisms and are involved in numerous cellular processes such as respiration, photosynthesis, metabolic reactions, nitrogen fixation, radical biochemistry, protein synthesis, antiviral defense, and genome maintenance. Their versatile functions may go back to the proposed role of their Fe/S cofactors in the origin of life as efficient catalysts and electron carriers. More than two decades ago, it was discovered that the in vivo synthesis of cellular Fe/S clusters and their integration into polypeptide chains requires assistance by complex proteinaceous machineries, despite the fact that Fe/S proteins can be assembled chemically in vitro. In prokaryotes, three Fe/S protein biogenesis systems are known; ISC, SUF, and the more specialized NIF. The former two systems have been transferred by endosymbiosis from bacteria to mitochondria and plastids, respectively, of eukaryotes. In their cytosol, eukaryotes use the CIA machinery for the biogenesis of cytosolic and nuclear Fe/S proteins. Despite the structural diversity of the protein constituents of these four machineries, general mechanistic concepts underlie the complex process of Fe/S protein biogenesis. This review provides a comprehensive and comparative overview of the various known biogenesis systems in Biology, and summarizes their common or diverging molecular mechanisms, thereby illustrating both the conservation and diverse adaptions of these four machineries during evolution and under different lifestyles. Knowledge of these fundamental biochemical pathways is not only of basic scientific interest, but is important for the understanding of human 'Fe/S diseases' and can be used in biotechnology.
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Prebiotic peptides, their formation, fermentation in the gut, and health implications.
Ashaolu, TJ, Ashaolu, JO
Biotechnology progress. 2021;(3):e3142
Abstract
Prebiotics can be synthesized from sources other than dietary fibers, such as proteins. The proteins, when processed into peptides have healthful or deleterious effects on the host. Outside living systems, prebiotic peptides (PP) are formed via preformation of amino acids or related monomeric building blocks, resulting in nonenzymatic polymerization/ligation to produce peptides. Whereas, inside living systems like the human gut, many metabolic pathways are involved in PP production, and mostly involve host-microbiota interactions. The interplay is responsible for PP activities and their implications on host amino acid balance and metabolism. Similar to carbohydrates fermentation, PP will yield short chain fatty acids (SCFA), but also branched chain fatty acids (BCFAs), phenols, indole, hydrogen sulfide, amines, and ammonia, capable of biologically mediating molecular signals. This holistic review considers a brief description of prebiotics, and tracks down prebiotic peptides formation processes, interactions with gut microbes, and health outcomes.
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Extracellular Metabolism Sets the Table for Microbial Cross-Feeding.
Fritts, RK, McCully, AL, McKinlay, JB
Microbiology and molecular biology reviews : MMBR. 2021;(1)
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Abstract
The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.
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Regulators of commensal and pathogenic life-styles of an opportunistic fungus-Candida albicans.
Rai, LS, Wijlick, LV, Bougnoux, ME, Bachellier-Bassi, S, d'Enfert, C
Yeast (Chichester, England). 2021;(4):243-250
Abstract
The yeast Candida albicans is primarily a commensal of humans that colonizes the mucosal surfaces of the gastrointestinal and genital tracts. Yet, C. albicans can under certain circumstances undergo a shift from commensalism to pathogenicity. This transition is governed by fungal factors such as morphological transitions, environmental cues for instance relationships with gut microbiota and the host immune system. C. albicans utilizes distinct sets of regulatory programs to colonize or infect its host and to evade the host defense systems. Moreover, an orchestrated iron acquisition mechanism operates to adapt to specific niches with variable iron availability. Studies on regulatory networks and morphogenesis of these two distinct modes of C. albicans growth, suggest that both yeast and hyphal forms exist in both growth patterns and the regulatory circuits are inter-connected. Here, we summarize current knowledge about C. albicans commensal-to-pathogen shift, its regulatory elements and their contribution to human disease.
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Perception of lipo-chitooligosaccharides by the bioenergy crop Populus.
R Cope, K, B Irving, T, Chakraborty, S, Ané, JM
Plant signaling & behavior. 2021;(6):1903758
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Abstract
Populus sp. is a developing feedstock for second-generation biofuel production. To ensure its success as a sustainable biofuel source, it is essential to capitalize on the ability of Populus sp. to associate with beneficial plant-associated microbes (e.g., mycorrhizal fungi) and engineer Populus sp. to associate with non-native symbionts (e.g., rhizobia). Here, we review recent research into the molecular mechanisms that control ectomycorrhizal associations in Populus sp. with particular emphasis on the discovery that ectomycorrhizal fungi produce lipochitooligosaccharides capable of activating the common symbiosis pathway. We also present new evidence that lipo-chitooligosaccharides produced by both ectomycorrhizal fungi and various species of rhizobia that do not associate with Populus sp. can induce nuclear calcium spiking in the roots of Populus sp. Thus, we argue Populus sp. already possesses the molecular machinery necessary for perceiving rhizobia, and the next step in engineering symbiosis with rhizobia should be focused on inducing bacterial accommodation and nodule organogenesis. The gene Nodule INception is central to these processes, and several putative orthologs are present in Populus sp. Manipulating the promoters of these genes to match that of plants in the nitrogen-fixing clade may be sufficient to introduce nodulation in Populus sp.
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A roadmap of plant membrane transporters in arbuscular mycorrhizal and legume-rhizobium symbioses.
Banasiak, J, Jamruszka, T, Murray, JD, Jasiński, M
Plant physiology. 2021;(4):2071-2091
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Abstract
Most land plants live in close contact with beneficial soil microbes: the majority of land plant species establish symbiosis with arbuscular mycorrhizal fungi, while most legumes, the third largest plant family, can form a symbiosis with nitrogen-fixing rhizobia. These microbes contribute to plant nutrition via endosymbiotic processes that require modulating the expression and function of plant transporter systems. The efficient contribution of these symbionts involves precisely controlled integration of transport, which is enabled by the adaptability and plasticity of their transporters. Advances in our understanding of these systems, driven by functional genomics research, are rapidly filling the gap in knowledge about plant membrane transport involved in these plant-microbe interactions. In this review, we synthesize recent findings associated with different stages of these symbioses, from the pre-symbiotic stage to nutrient exchange, and describe the role of host transport systems in both mycorrhizal and legume-rhizobia symbioses.
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Dynamics of miRNA mediated regulation of legume symbiosis.
Tiwari, M, Pandey, V, Singh, B, Bhatia, S
Plant, cell & environment. 2021;(5):1279-1291
Abstract
Symbiotic nitrogen fixation in legume nodules is important in soils with low nitrogen availability. The initiation and sustainability of symbiosis require cellular reprogramming that involves the miRNA-mediated inhibition or activation of specific nodulation genes. The high-throughput sequencing of small RNA libraries has identified miRNAs and their targets, which are the major players in the post-transcriptional gene regulation (PTGS) of the different stages of legume-rhizobia symbiosis ranging from bacterial colonization and organogenesis to symbiotic nitrogen fixation. Here, we present an overview of information obtained from the miRNA libraries from nodulating tissues that have been sequenced to date. The functional analysis of miRNAs has revealed roles in phytohormone homeostasis and spatio-temporal regulation, as well as the mobility of miRNAs and their functions in shoot to root signalling that affects diverse functions, including bacterial entry, meristem division and differentiation, nitrogen fixation and senescence. Furthermore, small RNA fragments of rhizobial origin repress complementary plant mRNAs. We also consider the roles of miRNAs in determinate or indeterminate nodules. Taken together, this overview confirms that miRNAs are master regulators of the legume-rhizobia symbiosis.
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A Roadmap toward Engineered Nitrogen-Fixing Nodule Symbiosis.
Huisman, R, Geurts, R
Plant communications. 2020;(1):100019
Abstract
In the late 19th century, it was discovered that legumes can establish a root nodule endosymbiosis with nitrogen-fixing rhizobia. Soon after, the question was raised whether it is possible to transfer this trait to non-leguminous crops. In the past century, an ever-increasing amount of knowledge provided unique insights into the cellular, molecular, and genetic processes controlling this endosymbiosis. In addition, recent phylogenomic studies uncovered several genes that evolved to function specifically to control nodule formation and bacterial infection. However, despite this massive body of knowledge, the long-standing objective to engineer the nitrogen-fixing nodulation trait on non-leguminous crop plants has not been achieved yet. In this review, the unsolved questions and engineering strategies toward nitrogen-fixing nodulation in non-legume plants are discussed and highlighted.
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Direct and indirect influence of arbuscular mycorrhizae on enhancing metal tolerance of plants.
Janeeshma, E, Puthur, JT
Archives of microbiology. 2020;(1):1-16
Abstract
The acerbic elevation of toxic metal ions in arable lands, enhance the risk of their accumulation and biomagnification in crops as well as in humans. Phytoremediation is an eco-friendly approach to clear metal-contaminated lands by making use of metal accumulation potential of plants; which are referred to as hyperaccumulators. This phytoremediation potential can be enhanced with the symbiotic association between the root of hyperaccumulators and arbuscular mycorrhizae. Modification of root morphology, enhancement of antioxidants biosynthesis, and the increase in shoot biomass are the changes observed in plants as a result of indirect influence of arbuscular mycorrhizae. Direct influence of arbuscular mycorrhizae on enhancing metal tolerance of plants includes immobilization strategies, adsorption of metals on to the hyphal wall and glomalin exudation. Furthermore, we have discussed arbuscular mycorrhizal induced increment in the metal tolerance potential of plants through the alteration in various metabolic processes with special emphasis to the phenylpropanoid pathway.