Virulence Regulator EspR of Mycobacterium tuberculosis Is a Nucleoid-Associated Protein

The principal virulence determinant of Mycobacterium tuberculosis (Mtb), the ESX-1 protein secretion system, is positively controlled at the transcriptional level by EspR. Depletion of EspR reportedly affects a small number of genes, both positively or negatively, including a key ESX-1 component, the espACD operon. EspR is also thought to be an ESX-1 substrate. Using EspR-specific antibodies in ChIP-Seq experiments (chromatin immunoprecipitation followed by ultra-high throughput DNA sequencing) we show that EspR binds to at least 165 loci on the Mtb genome. Included in the EspR regulon are genes encoding not only EspA, but also EspR itself, the ESX-2 and ESX-5 systems, a host of diverse cell wall functions, such as production of the complex lipid PDIM (phenolthiocerol dimycocerosate) and the PE/PPE cell-surface proteins. EspR binding sites are not restricted to promoter regions and can be clustered. This suggests that rather than functioning as a classical regulatory protein EspR acts globally as a nucleoid-associated protein capable of long-range interactions consistent with a recently established structural model. EspR expression was shown to be growth phase-dependent, peaking in the stationary phase. Overexpression in Mtb strain H37Rv revealed that EspR influences target gene expression both positively or negatively leading to growth arrest. At no stage was EspR secreted into the culture filtrate. Thus, rather than serving as a specific activator of a virulence locus, EspR is a novel nucleoid-associated protein, with both architectural and regulatory roles, that impacts cell wall functions and pathogenesis through multiple genes

Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs

Life-threatening `breakthrough' cases of critical COVID-19 are attributed to poor or waning antibody response to the SARS- CoV-2 vaccine in individuals already at risk. Pre-existing autoantibodies (auto-Abs) neutralizing type I IFNs underlie at least 15% of critical COVID-19 pneumonia cases in unvaccinated individuals; however, their contribution to hypoxemic breakthrough cases in vaccinated people remains unknown. Here, we studied a cohort of 48 individuals ( age 20-86 years) who received 2 doses of an mRNA vaccine and developed a breakthrough infection with hypoxemic COVID-19 pneumonia 2 weeks to 4 months later. Antibody levels to the vaccine, neutralization of the virus, and auto- Abs to type I IFNs were measured in the plasma. Forty-two individuals had no known deficiency of B cell immunity and a normal antibody response to the vaccine. Among them, ten (24%) had auto-Abs neutralizing type I IFNs (aged 43-86 years). Eight of these ten patients had auto-Abs neutralizing both IFN-a2 and IFN-., while two neutralized IFN-omega only. No patient neutralized IFN-ss. Seven neutralized 10 ng/mL of type I IFNs, and three 100 pg/mL only. Seven patients neutralized SARS-CoV-2 D614G and the Delta variant (B.1.617.2) efficiently, while one patient neutralized Delta slightly less efficiently. Two of the three patients neutralizing only 100 pg/mL of type I IFNs neutralized both D61G and Delta less efficiently. Despite two mRNA vaccine inoculations and the presence of circulating antibodies capable of neutralizing SARS-CoV-2, auto-Abs neutralizing type I IFNs may underlie a significant proportion of hypoxemic COVID-19 pneumonia cases, highlighting the importance of this particularly vulnerable population

Does hippocampal size correlate with the degree of caching specialization?

A correlation between the degree of specialization for food hoarding and the volume of the hippocampal formation in passerine birds has been accepted for over a decade. The relationship was first demonstrated in family-level comparisons, and subsequently in species comparisons within two families containing a large number of hoarding species, the Corvidae and the Paridae. Recently, this approach has been criticized as invalid and excessively adaptationist. A recent test of the predicted trends with data pooled from previous studies found no evidence for such a correlation in either of these two families. This result has been interpreted as support for the critique. Here we reanalyse the original dataset and also include additional new data on several parid species. Our results show a surprising difference between continents, with North American species possessing significantly smaller hippocampi than Eurasian ones. Controlling for the continent effect makes the hoarding capacity/hippocampal formation correlation clearly significant in both families. We discuss possible reasons for the continent effect

Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays.

Proteins represent the most sophisticated building blocks available to an organism and to the laboratory chemist. Yet, in contrast to nearly all other types of molecular building blocks, the designed self-assembly of proteins has largely been inaccessible because of the chemical and structural heterogeneity of protein surfaces. To circumvent the challenge of programming extensive non-covalent interactions to control protein self-assembly, we have previously exploited the directionality and strength of metal coordination interactions to guide the formation of closed, homoligomeric protein assemblies. Here, we extend this strategy to the generation of periodic protein arrays. We show that a monomeric protein with properly oriented coordination motifs on its surface can arrange, on metal binding, into one-dimensional nanotubes and two- or three-dimensional crystalline arrays with dimensions that collectively span nearly the entire nano- and micrometre scale. The assembly of these arrays is tuned predictably by external stimuli, such as metal concentration and pH

In Vitro and Cellular Self-Assembly of a Zn-Binding Protein Cryptand via Templated Disulfide Bonds

Simultaneously strong and reversible through redox chemistry, disulfide bonds play a unique and often irreplaceable role in the formation of biological and synthetic assemblies. In an approach inspired by supramolecular chemistry, we report here that engineered noncovalent interactions on the surface of a monomeric protein can template its assembly into a unique cryptand-like protein complex (^C81/C96RIDC1₄) by guiding the selective formation of multiple disulfide bonds across different interfaces. Owing to its highly interconnected framework, ^C81/C96RIDC1₄ is well preorganized for metal coordination in its interior, can support a large internal cavity surrounding the metal sites, and can withstand significant alterations in inner-sphere metal coordination. ^C81/C96RIDC1₄ self-assembles with high fidelity and yield in the periplasmic space of <i>E. coli</i> cells, where it can successfully compete for Zn­(II) binding

In Vitro and Cellular Self-Assembly of a Zn-Binding Protein Cryptand via Templated Disulfide Bonds

Simultaneously strong and reversible through redox chemistry, disulfide bonds play a unique and often irreplaceable role in the formation of biological and synthetic assemblies. In an approach inspired by supramolecular chemistry, we report here that engineered noncovalent interactions on the surface of a monomeric protein can template its assembly into a unique cryptand-like protein complex (^C81/C96RIDC1₄) by guiding the selective formation of multiple disulfide bonds across different interfaces. Owing to its highly interconnected framework, ^C81/C96RIDC1₄ is well preorganized for metal coordination in its interior, can support a large internal cavity surrounding the metal sites, and can withstand significant alterations in inner-sphere metal coordination. ^C81/C96RIDC1₄ self-assembles with high fidelity and yield in the periplasmic space of <i>E. coli</i> cells, where it can successfully compete for Zn­(II) binding

In Vitro and Cellular Self-Assembly of a Zn-Binding Protein Cryptand via Templated Disulfide Bonds

Simultaneously strong and reversible through redox chemistry, disulfide bonds play a unique and often irreplaceable role in the formation of biological and synthetic assemblies. In an approach inspired by supramolecular chemistry, we report here that engineered noncovalent interactions on the surface of a monomeric protein can template its assembly into a unique cryptand-like protein complex (^C81/C96RIDC1₄) by guiding the selective formation of multiple disulfide bonds across different interfaces. Owing to its highly interconnected framework, ^C81/C96RIDC1₄ is well preorganized for metal coordination in its interior, can support a large internal cavity surrounding the metal sites, and can withstand significant alterations in inner-sphere metal coordination. ^C81/C96RIDC1₄ self-assembles with high fidelity and yield in the periplasmic space of <i>E. coli</i> cells, where it can successfully compete for Zn­(II) binding

Designed, Helical Protein Nanotubes with Variable Diameters from a Single Building Block

Due to their structural and mechanical properties, 1D helical protein assemblies represent highly attractive design targets for biomolecular engineering and protein design. Here we present a designed, tetrameric protein building block, Zn₈R₄, which assembles via Zn coordination interactions into a series of crystalline, helical nanotubes whose widths can be controlled by solution conditions. X-ray crystallography and transmission electron microscopy (TEM) measurements indicate that all classes of protein nanotubes are constructed through the same 2D arrangement of Zn₈R₄ tetramers held together by Zn coordination. The mechanical properties of these nanotubes are correlated with their widths. All Zn₈R₄ nanotubes are found to be highly flexible despite possessing crystalline order, owing to their minimal interbuilding-block interactions mediated solely by metal coordination