Essentiality of c-di-AMP in Bacillus subtilis: Bypassing mutations converge in potassium and glutamate homeostasis

In order to adjust to changing environmental conditions, bacteria use nucleotide second messengers to transduce external signals and translate them into a specific cellular response. Cyclic di-adenosine monophosphate (c-di-AMP) is the only known essential nucleotide second messenger. In addition to the well-established role of this second messenger in the control of potassium homeostasis, we observed that glutamate is as toxic as potassium for a c-di-AMP-free strain of the Gram-positive model bacterium Bacillus subtilis. In this work, we isolated suppressor mutants that allow growth of a c-di-AMP-free strain under these toxic conditions. Characterization of glutamate resistant suppressors revealed that they contain pairs of mutations, in most cases affecting glutamate and potassium homeostasis. Among these mutations, several independent mutations affected a novel glutamate transporter, AimA (Amino acid importer A, formerly YbeC). This protein is the major transporter for glutamate and serine in B. subtilis. Unexpectedly, some of the isolated suppressor mutants could suppress glutamate toxicity by a combination of mutations that affect phospholipid biosynthesis and a specific gain-of-function mutation of a mechanosensitive channel of small conductance (YfkC) resulting in the acquisition of a device for glutamate export. Cultivation of the c-di-AMP-free strain on complex medium was an even greater challenge because the amounts of potassium, glutamate, and other osmolytes are substantially higher than in minimal medium. Suppressor mutants viable on complex medium could only be isolated under anaerobic conditions if one of the two c-di-AMP receptor proteins, DarA or DarB, was absent. Also on complex medium, potassium and osmolyte toxicity are the major bottlenecks for the growth of B. subtilis in the absence of c-di-AMP. Our results indicate that the essentiality of c-di-AMP in B. subtilis is caused by the global impact of the second messenger nucleotide on different aspects of cellular physiology.     

An ultrapotent pan-β-coronavirus lineage B (β-CoV-B) neutralizing antibody locks the receptor-binding domain in closed conformation by targeting its conserved epitope

New threats posed by the emerging circulating variants of SARS-CoV-2 highlight the need to find conserved neutralizing epitopes for therapeutic antibodies and efficient vaccine design. Here, we identified a receptor-binding domain (RBD)-binding antibody, XG014, which potently neutralizes β-coronavirus lineage B (β-CoV-B), including SARS-CoV-2, its circulating variants, SARS-CoV and bat SARSr-CoV WIV1. Interestingly, antibody family members competing with XG014 binding show reduced levels of cross-reactivity and induce antibody-dependent SARS-CoV-2 spike (S) protein-mediated cell-cell fusion, suggesting a unique mode of recognition by XG014. Structural analyses reveal that XG014 recognizes a conserved epitope outside the ACE2 binding site and completely locks RBD in the non-functional “down” conformation, while its family member XG005 directly competes with ACE2 binding and position the RBD “up”. Single administration of XG014 is effective in protection against and therapy of SARS-CoV-2 infection in vivo. Our findings suggest the potential to develop XG014 as pan-β-CoV-B therapeutics and the importance of the XG014 conserved antigenic epitope for designing broadly protective vaccines against β-CoV-B and newly emerging SARS-CoV-2 variants of concern.Supplementary InformationThe online version contains supplementary material available at 10.1007/s13238-021-00871-6.     

Area and Age of Secondary Forests in Brazilian Amazonia 1978–2002: An Empirical Estimate

In quantifying the carbon budget of the Amazon region, temporal estimates of the extent and age of regenerating tropical forests are fundamental. However, retrieving such information from remote-sensing data is difficult, largely because of spectral similarities between different successional stages and variations in the reflectance of forests following different pathways of regeneration. In this study, secondary-forest dynamics in Brazilian Amazonia were modeled for the 1978–2002 period to determine area and age on a grid basis. We modeled the area, age, and age class distribution of secondary forests using empirical relationships with the percentage of remaining primary forest, as determined from large-area remote-sensing campaigns (the Pathfinder and Prodes projects). The statistical models were calibrated using detailed maps of secondary-forest age generated for seven sites in the Brazilian Legal Amazon. The area–age distribution was then specified from mean age by a distribution assumption. Over the period 1978–2002, secondary-forest area was shown to have increased from 29,000 to 161,000 km² (that is, by a factor of 5). The mean age increased from 4.4 to 4.8 years. We generated a time series of secondary-forest area fractions and successional stages that provides wall-to-wall coverage of the Brazilian Amazon at a spatial resolution of 0.1 decimal degrees (approximately 11 km). Validation against reference data yielded root mean squared errors of 8% of the total area for estimate of secondary-forest area and 2.4 years for mean secondary-forest age. Using this approach, we provide the first published update on the state of secondary forests in Amazonia since the early 1990s and a time series of secondary-forest area over the 25-year period.     

Degradation of 4-fluorobiphenyl by mycorrhizal fungi as determined by (19)F nuclear magnetic resonance spectroscopy and (14)C radiolabelling analysis.

The pathways of biotransformation of 4-fluorobiphenyl (4FBP) by the ectomycorrhizal fungus Tylospora fibrilosa and several other mycorrhizal fungi were investigated by using (19)F nuclear magnetic resonance (NMR) spectroscopy in combination with (14)C radioisotope-detected high-performance liquid chromatography ((14)C-HPLC). Under the conditions used in this study T. fibrillosa and some other species degraded 4FBP. (14)C-HPLC profiles indicated that there were four major biotransformation products, whereas (19)F NMR showed that there were six major fluorine-containing products. We confirmed that 4-fluorobiphen-4'-ol and 4-fluorobiphen-3'-ol were two of the major products formed, but no other products were conclusively identified. There was no evidence for the expected biotransformation pathway (namely, meta cleavage of the less halogenated ring), as none of the expected products of this route were found. To the best of our knowledge, this is the first report describing intermediates formed during mycorrhizal degradation of halogenated biphenyls.     

ASSESSMENT OF VIABILITY OF FROZEN BONE MARROW CELLS USING A CELL-CULTURE METHOD

The survival of mouse bone marrow after freezing and thawing was assessed using two methods: the spleen-colony technique; and a cell-culture method. The results of these experiments indicate that both methods yield similar estimates of marrow cell viability. It is suggested that the cell-culture method be used as an assay of marrow-cell viability in situations where the spleen-colony technique is not applicable.