Regulatory rewiring through global gene regulations by PhoB and alarmone (p)ppGpp under various stress conditions

Jha, Varsha; Dafale, Nishant A.; Purohit, Hemant J.

doi:10.1016/j.micres.2019.126309

Cited by 18 publications

(5 citation statements)

References 102 publications

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“…Phosphate salts are present in a variety of soil and aquatic environment, but its concentration in different habitats is very diverse. Sometimes phosphate is present in insoluble form (so called rocks phosphate) that is difficult to metabolize and requires its solubilization by microorganisms [3,4]. In addition, organophosphates are abundant in some particular habitats as products of decay of plant and animal tissues.…”

Section: Introductionmentioning

confidence: 99%

Molecular Mechanisms of Phosphate Sensing, Transport and Signalling in Streptomyces and Related Actinobacteria

Martı́n

Liras

2021

IJMS

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Phosphorous, in the form of phosphate, is a key element in the nutrition of all living beings. In nature, it is present in the form of phosphate salts, organophosphates, and phosphonates. Bacteria transport inorganic phosphate by the high affinity phosphate transport system PstSCAB, and the low affinity PitH transporters. The PstSCAB system consists of four components. PstS is the phosphate binding protein and discriminates between arsenate and phosphate. In the Streptomyces species, the PstS protein, attached to the outer side of the cell membrane, is glycosylated and released as a soluble protein that lacks its phosphate binding ability. Transport of phosphate by the PstSCAB system is drastically regulated by the inorganic phosphate concentration and mediated by binding of phosphorylated PhoP to the promoter of the PstSCAB operon. In Mycobacterium smegmatis, an additional high affinity transport system, PhnCDE, is also under PhoP regulation. Additionally, Streptomyces have a duplicated low affinity phosphate transport system encoded by the pitH1–pitH2 genes. In this system phosphate is transported as a metal-phosphate complex in simport with protons. Expression of pitH2, but not that of pitH1 in Streptomyces coelicolor, is regulated by PhoP. Interestingly, in many Streptomyces species, three gene clusters pitH1–pstSCAB–ppk (for a polyphosphate kinase), are linked in a supercluster formed by nine genes related to phosphate metabolism. Glycerol-3-phosphate may be transported by the actinobacteria Corynebacterium glutamicum that contains a ugp gene cluster for glycerol-3-P uptake, but the ugp cluster is not present in Streptomyces genomes. Sugar phosphates and nucleotides are used as phosphate source by the Streptomyces species, but there is no evidence of the uhp gene involved in the transport of sugar phosphates. Sugar phosphates and nucleotides are dephosphorylated by extracellular phosphatases and nucleotidases. An isolated uhpT gene for a hexose phosphate antiporter is present in several pathogenic corynebacteria, such as Corynebacterium diphtheriae, but not in non-pathogenic ones. Phosphonates are molecules that contains phosphate linked covalently to a carbon atom through a very stable C–P bond. Their utilization requires the phnCDE genes for phosphonates/phosphate transport and genes for degradation, including those for the subunits of the C–P lyase. Strains of the Arthrobacter and Streptomyces genera were reported to degrade simple phosphonates, but bioinformatic analysis reveals that whole sets of genes for putative phosphonate degradation are present only in three Arthrobacter species and a few Streptomyces species. Genes encoding the C–P lyase subunits occur in several Streptomyces species associated with plant roots or with mangroves, but not in the laboratory model Streptomyces species; however, the phnCDE genes that encode phosphonates/phosphate transport systems are frequent in Streptomyces species, suggesting that these genes, in the absence of C–P lyase genes, might be used as surrogate phosphate transporters. In summary, Streptomyces and related actinobacteria seem to be less versatile in phosphate transport systems than Enterobacteria.

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Section: Introductionmentioning

confidence: 99%

Molecular Mechanisms of Phosphate Sensing, Transport and Signalling in Streptomyces and Related Actinobacteria

Martı́n

Liras

2021

IJMS

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“…The activation of phytase activity in our isolates, particularly in the absence of alternative carbon or phosphorus sources, suggests adaptive gene regulation, likely involving mechanisms akin to the Pho regulon. This regulatory response, triggered by phosphorus scarcity, may also induce enzymes to release myo-inositol from phytate, similar to processes observed in Bacillus subtilis (Jha et al, 2019).…”

Section: Discussionmentioning

confidence: 65%

Exploring the biotechnological potential of novel soil-derived Klebsiella sp. and Chryseobacterium sp. strains using phytate as sole carbon source

Maldonado-Pava,

Tapia-Perdomo,

Estupinan-Cardenas

et al. 2024

Front. Bioeng. Biotechnol.

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Phosphorus (P) is essential for biological systems, playing a pivotal role in energy metabolism and forming crucial structural components of DNA and RNA. Yet its bioavailable forms are scarce. Phytate, a major form of stored phosphorus in cereals and soils, is poorly bioavailable due to its complex structure. Phytases, enzymes that hydrolyze phytate to release useable phosphorus, are vital in overcoming this limitation and have significant biotechnological applications. This study employed novel method to isolate and characterize bacterial strains capable of metabolizing phytate as the sole carbon and phosphorus source from the Andes mountains soils. Ten strains from the genera Klebsiella and Chryseobacterium were isolated, with Chryseobacterium sp. CP-77 and Klebsiella pneumoniae CP-84 showing specific activities of 3.5 ± 0.4 nkat/mg and 40.8 ± 5 nkat/mg, respectively. Genomic sequencing revealed significant genetic diversity, suggesting CP-77 may represent a novel Chryseobacterium species. A fosmid library screening identified several phytase genes, including a 3-phytase in CP-77 and a glucose 1-phosphatase and 3-phytase in CP-84. Phylogenetic analysis confirmed the novelty of these enzymes. These findings highlight the potential of phytase-producing bacteria in sustainable agriculture by enhancing phosphorus bioavailability, reducing reliance on synthetic fertilizers, and contributing to environmental management. This study expands our biotechnological toolkit for microbial phosphorus management and underscores the importance of exploring poorly characterized environments for novel microbial functions. The integration of direct cultivation with metagenomic screening offers robust approaches for discovering microbial biocatalysts, promoting sustainable agricultural practices, and advancing environmental conservation.

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“…PhoB is involved in the regulation of inorganic phosphate (Pi) homeostasis 59 ; it can positively or negatively regulate phosphate uptake in the presence of excess or limited Pi 60 . Disrupting this transcriptional activator causes cells to lose the ability to modulate the phosphate regulon, which proves to be advantageous during bioleaching in phosphate-rich environments.…”

Section: Discussionmentioning

confidence: 99%

Direct Genome-Scale Screening ofGluconobacter oxydansB58 for Rare Earth Element Bioleaching

Marecos,

Pian,

Medin

et al. 2024

Preprint

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The transition to a sustainable energy economy will require an enormous increase in the supply of rare earth elements (REE). Bioleaching offers a promising alternative to conventional hydrometallurgical methods for REE extraction from low-grade ores. However, exploiting this potential remains challenging due to large gaps in our understanding of the genetics involved, and inadequate biological tools to address them. We generated a highly non-redundant whole genome knockout collection for the bioleaching microbeGluconobacter oxydansB58, reducing redundancy by 85% compared to the previous best collection. This new collection was directly screened for bioleaching neodymium from a synthetic monazite powder, identifying 89 genes important for bioleaching, 68 of which have not previously been associated with this mechanism. We conducted bench-scale experiments to validate the extraction efficiency of promising strains: 8 demonstrated significant increases in bioleaching by up to 111% (G. oxydansδGO_1598, a disruption of the gene encoding the orotate phosphoribosyltransferase enzyme PyrE), and one strain significantly reduced it by 97% (δGO_1096, a disruption of the gene encoding the GTP-binding protein TypA). Notable changes in biolixiviant pH were only observed for 3 strains, suggesting an important role for non-acid mechanisms in bioleaching. These findings provide valuable insights into further enhancing REE-bioleaching byG. oxydans’ through targeted genetic engineering.

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Regulatory rewiring through global gene regulations by PhoB and alarmone (p)ppGpp under various stress conditions

Cited by 18 publications

References 102 publications

Molecular Mechanisms of Phosphate Sensing, Transport and Signalling in Streptomyces and Related Actinobacteria

Molecular Mechanisms of Phosphate Sensing, Transport and Signalling in Streptomyces and Related Actinobacteria

Exploring the biotechnological potential of novel soil-derived Klebsiella sp. and Chryseobacterium sp. strains using phytate as sole carbon source

Direct Genome-Scale Screening ofGluconobacter oxydansB58 for Rare Earth Element Bioleaching

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