Microbial siderophores: a mini review

Endophytes as producers of peptides: an overview about the recently discovered peptides from endophytic microbes

An endophyte is a fungus or bacterium that lives within a plant in a symbiotic relationship. Extensive colonization of the plant tissue by endophytes creates a barrier effect, where they outcompete and prevent pathogenic organisms from taking hold. This happens by producing secondary metabolites that inhibit the growth of the competitors or pathogens. In this way they play a very important role in the plant defence mechanisms. The metabolites produced by these endophytes fall within a wide range of classes of compounds that include peptides which are the focus of this review. Peptides are increasingly being selected for drug development because they are specific for their targets and have a higher degree of interactions. There have been quite a number of endophytic peptides reported in the recent past indicating that endophytes can be used for the production of peptide based drugs. Molecular screening for NRPS, which shows peptide producing capability, has also shown that endophytes are potential producers of peptides. The presence of NRPS also offers the possibility of genetic modifications which may generate peptides with high pharmacological activities. This review, therefore, aims to show the current status of peptides isolated from endophytic bacteria and fungi in the recent decade. Endophytes as potential sources of peptides according to NRPS studies will also be discussed.

Nitrogen signalling in plant interactions with associative and endophytic diazotrophic bacteria

Some beneficial plant-interacting bacteria can biologically fix N2 to plant-available ammonium. Biological nitrogen fixation (BNF) is an important source of nitrogen (N) input in agriculture and represents a promising substitute for chemical N fertilizers. Diazotrophic bacteria have the ability to develop different types of root associations with different plant species. Among the highest rates of BNF are those measured in legumes nodulated by endosymbionts, an already very well documented model of plant-diazotrophic bacterial association. However, it has also been shown that economically important crops, especially monocots, can obtain a substantial part of their N needs from BNF by interacting with associative and endophytic diazotrophic bacteria, that either live near the root surface or endophytically colonize intercellular spaces and vascular tissues of host plants. One of the best reported outcomes of this association is the promotion of plant growth by direct and indirect mechanisms. Besides fixing N, these bacteria can also produce plant growth hormones, and some species are reported to improve nutrient uptake and increase plant tolerance against biotic and abiotic stresses. Thus, this particular type of plant-bacteria association consists of a natural beneficial system to be explored; however, the regulatory mechanisms involved are still not clear. Plant N status might act as a key signal, regulating and integrating various metabolic processes that occur during association with diazotrophic bacteria. This review will focus on the recent progress in understanding plant association with associative and endophytic diazotrophic bacteria, particularly on the knowledge of the N networks involved in BNF and in the promotion of plant growth.

Lag phase-associated iron accumulation is likely a microbial counter-strategy to host iron sequestration: role of the ferric uptake regulator (fur)

Iron is an essential metal for almost all forms of life, but potentiates oxidative stress via Fenton catalysis. During microbial lag phase there is a rapid influx of iron with concomitant oxidative hypersensitivity. How and why iron accumulation occurs remains to be elucidated. Iron homeostasis in prokaryotes is mediated by the ferric uptake regulator (Fur), an iron-activated global regulator that controls intracellular iron levels by feedback inhibition with the metal. Herein it is postulated, based on the expression profiles of antioxidant enzymes within the Fur regulon as observed in wild type and Δfur mutants, that iron accumulation is mediated by a transitively low concentration of the Fur protein during lag phase. Vertebrate hosts sequester iron upon 'sensing' an infection in order to retard microbial proliferation through a process known as 'nutritional immunity'. It is herein argued that the purpose of iron accumulation is not principally a preparative step for the replicative phase, as suggested elsewhere, but an evolved behavior that counteracts host iron sequestration. This interpretation is supported by multiple clinical and animal studies that demonstrate that iron surplus in hosts advances progression and susceptibility to infection, and vice versa. Contextualizing iron accumulation as a counter-immune behavior adds impetus to the development of antibiotics targeting pathogenic modes of iron acquisition.

In and out: an analysis of epibiotic vs periplasmic bacterial predators

Bdellovibrio and like organisms (BALO) are obligate predators of Gram-negative bacteria, belonging to the α- and δ-proteobacteria. BALO prey using either a periplasmic or an epibiotic predatory strategy, but the genetic background underlying these phenotypes is not known. Here we compare the epibiotic Bdellovibrio exovorus and Micavibrio aeruginosavorus to the periplasmic B. bacteriovorus and Bacteriovorax marinus. Electron microscopy showed that M. aeruginosavorus, but not B. exovorus, can attach to prey cells in a non-polar manner through its longitudinal side. Both these predators were resistant to a surprisingly high number of antibiotic compounds, possibly via 26 and 19 antibiotic-resistance genes, respectively, most of them encoding efflux pumps. Comparative genomic analysis of all the BALOs revealed that epibiotic predators have a much smaller genome (ca. 2.5 Mbp) than the periplasmic predators (ca. 3.5 Mbp). Additionally, periplasmic predators have, on average, 888 more proteins, at least 60% more peptidases, and one more rRNA operon. Fifteen and 219 protein families were specific to the epibiotic and the periplasmic predators, respectively, the latter clearly forming the core of the periplasmic 'predatome', which is upregulated during the growth phase. Metabolic deficiencies of epibiotic genomes include the synthesis of inosine, riboflavin, vitamin B6 and the siderophore aerobactin. The phylogeny of the epibiotic predators suggests that they evolved by convergent evolution, with M. aeruginosavorus originating from a non-predatory ancestor while B. exovorus evolved from periplasmic predators by gene loss.

Genome-wide analysis of copper, iron and zinc transporters in the arbuscular mycorrhizal fungus Rhizophagus irregularis

Arbuscular mycorrhizal fungi (AMF), belonging to the Glomeromycota, are soil microorganisms that establish mutualistic symbioses with the majority of higher plants. The efficient uptake of low mobility mineral nutrients by the fungal symbiont and their further transfer to the plant is a major feature of this symbiosis. Besides improving plant mineral nutrition, AMF can alleviate heavy metal toxicity to their host plants and are able to tolerate high metal concentrations in the soil. Nevertheless, we are far from understanding the key molecular determinants of metal homeostasis in these organisms. To get some insights into these mechanisms, a genome-wide analysis of Cu, Fe and Zn transporters was undertaken, making use of the recently published whole genome of the AMF Rhizophagus irregularis. This in silico analysis allowed identification of 30 open reading frames in the R. irregularis genome, which potentially encode metal transporters. Phylogenetic comparisons with the genomes of a set of reference fungi showed an expansion of some metal transporter families. Analysis of the published transcriptomic profiles of R. irregularis revealed that a set of genes were up-regulated in mycorrhizal roots compared to germinated spores and extraradical mycelium, which suggests that metals are important for plant colonization.

Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo

The recently developed transparent soil consists of particles of Nafion, a polymer with a low refractive index (RI), which is prepared by milling and chemical treatment for use as a soil analog. After the addition of a RI-matched solution, confocal imaging can be carried out in vivo and without destructive sampling. In a previous study, we showed that the new substrate provides a good approximation of plant growth conditions found in natural soils. In this paper, we present further development of the techniques for detailed quantitative analysis of images of root-microbe interactions in situ. Using this system it was possible for the first time to analyze bacterial distribution along the roots and in the bulk substrate in vivo. These findings indicate that the coupling of transparent soil with light microscopy is an important advance toward the discovery of the mechanisms of microbial colonisation of the rhizosphere.

The contribution of nutrient metal acquisition and metabolism to Acinetobacter baumannii survival within the host

Acinetobacter baumannii is a significant contributor to intensive care unit (ICU) mortality causing numerous types of infection in this susceptible ICU population, most notably ventilator-associated pneumonia. The substantial disease burden attributed to A. baumannii and the rapid acquisition of antibiotic resistance make this bacterium a serious health care threat. A. baumannii is equipped to tolerate the hostile host environment through modification of its metabolism and nutritional needs. Among these adaptations is the evolution of mechanisms to acquire nutrient metals that are sequestered by the host as a defense against infection. Although all bacteria require nutrient metals, there is diversity in the particular metal needs among species and within varying tissue types and bacterial lifecycles. A. baumannii is well-equipped with the metal homeostatic systems required for the colonization of a diverse array of tissues. Specifically, iron and zinc homeostasis is important for A. baumannii interactions with biotic surfaces and for growth within vertebrates. This review discusses what is currently known regarding the interaction of A. baumannii with vertebrate cells with a particular emphasis on the contributions of metal homeostasis systems. Overall, published research supports the utility of exploiting these systems as targets for the development of much-needed antimicrobials against this emerging infectious threat.

Mammalian iron homeostasis in health and disease: uptake, storage, transport, and molecular mechanisms of action

Iron is a crucial factor for life. However, it also has the potential to cause the formation of noxious free radicals. These double-edged sword characteristics demand a tight regulation of cellular iron metabolism. In this review, we discuss the various pathways of cellular iron uptake, cellular iron storage, and transport. Recent advances in understanding the reduction and uptake of non-transferrin-bound iron are discussed. We also discuss the recent progress in the understanding of transcriptional and translational regulation by iron. Furthermore, we discuss recent advances in the understanding of the regulation of cellular and systemic iron homeostasis and several key diseases resulting from iron deficiency and overload. We also discuss the knockout mice available for studying iron metabolism and the related human conditions.

Iron and cancer: more ore to be mined

Iron is an essential nutrient that facilitates cell proliferation and growth. However, iron also has the capacity to engage in redox cycling and free radical formation. Therefore, iron can contribute to both tumour initiation and tumour growth; recent work has also shown that iron has a role in the tumour microenvironment and in metastasis. Pathways of iron acquisition, efflux, storage and regulation are all perturbed in cancer, suggesting that reprogramming of iron metabolism is a central aspect of tumour cell survival. Signalling through hypoxia-inducible factor (HIF) and WNT pathways may contribute to altered iron metabolism in cancer. Targeting iron metabolic pathways may provide new tools for cancer prognosis and therapy.

Filamentous fungi from Plantago lanceolata L. leaves: contribution to the pattern and stability of bioactive metabolites

The aim of this study was to test contribution of plant-associated microorganism (PAMs) to metabolite stability/instability in a medicinal plant matrix. Therefore, PAM strains were isolated and identified based on relevant DNA sequences from Plantago lanceolata leaves. Sterile water extracts of P. lanceolata were incubated with the isolated strains and antioxidants (ascorbic acid (AA), and EDTA) for 15 days, and changes in the concentrations of chief bioactive constituents (aucubin, catalpol, acteoside (=verbascoside)) were quantified by capillary electrophoresis. Phenolic breakdown-products were identified by GC-MS. PAMs were identified from the genera Epicoccum, Bipolaris, Cladosporium, Leptosphaerulina, Aspergillus, Eurotium and Penicillium (pathongens, endophytes, and other species). Some fungi caused significant decomposition of the chief constituents (p<0.001). Surprisingly, some strains inhibited breakdown of acteoside (p<0.001). Meanwhile, concentration of several phenolic acids increased in fungi-infested extracts (p<0.001). Gentisic acid, 4-hydroxyphenyl acetic acid, 4-hydroxybenzoic acid and hydroxytyrosol were only present when the extract was infested with a PAM. The products are powerful antioxidants and chelators. Concentrations of phenolic acids influenced acteoside stability significantly (p<0.01), as shown by basic data-mining techniques. AA and EDTA also significantly inhibited acteoside breakdown in sterile model solutions (p<0.05). Our results suggest that the phenolic acid mixture (produced during the fungal proliferation) protected acteoside from breakdown, possibly via its antioxidant activity and metal complexing ability. It was shown that PAMs can increase or decrease the stability of chief metabolites in herbal matrices, and can significantly alter the chemical pattern of the plant matrix.

The transferrin-iron import system from pathogenic Neisseria species

Two pathogenic species within the genus Neisseria cause the diseases gonorrhoea and meningitis. While vaccines are available to protect against four N. meningitidis serogroups, there is currently no commercial vaccine to protect against serogroup B or against N. gonorrhoeae. Moreover, the available vaccines have significant limitations and with antibiotic resistance becoming an alarming issue, the search for effective vaccine targets to elicit long-lasting protection against Neisseria species is becoming more urgent. One strategy for vaccine development has targeted the neisserial iron import systems. Without iron, the Neisseriae cannot survive and, therefore, these iron import systems tend to be relatively well conserved and are promising vaccine targets, having the potential to offer broad protection against both gonococcal and meningococcal infections. These efforts have been boosted by recent reports of the crystal structures of the neisserial receptor proteins TbpA and TbpB, each solved in complex with human transferrin, an iron binding protein normally responsible for delivering iron to human cells. Here, we review the recent structural reports and put them into perspective with available functional studies in order to derive the mechanism(s) for how the pathogenic Neisseriae are able to hijack human iron transport systems for their own survival and pathogenesis.