A thorough analysis and categorization of bacterial interrupted adenylation domains, including previously unidentified families

Interrupted adenylation (A) domains are key to the immense structural diversity seen in the nonribosomal peptide (NRP) class of natural products (NPs). Interrupted A domains are A domains that contain within them the catalytic portion of another domain, most commonly a methylation (M) domain. It has been well documented that methylation events occur with extreme specificity on either the backbone (N-) or side chain (O- or S-) of the amino acid (or amino acid-like) building blocks of NRPs. Here, through taxonomic and phylogenetic analyses as well as multiple sequence alignments, we evaluated the similarities and differences between interrupted A domains. We probed their taxonomic distribution amongst bacterial organisms, their evolutionary relatedness, and described conserved motifs of each type of M domain found to be embedded in interrupted A domains. Additionally, we categorized interrupted A domains and the M domains within them into a total of seven distinct families and six different types, respectively. The families of interrupted A domains include two new families, 6 and 7, that possess new architectures. Rather than being interrupted between the previously described a2–a3 or a8–a9 of the ten conserved A domain sequence motifs (a1–a10), family 6 contains an M domain between a6–a7, a previously unknown interruption site. Family 7 demonstrates that di-interrupted A domains exist in Nature, containing an M domain between a2–a3 as well as one between a6–a7, displaying a novel arrangement. These in-depth investigations of amino acid sequences deposited in the NCBI database highlighted the prevalence of interrupted A domains in bacterial organisms, with each family of interrupted A domains having a different taxonomic distribution. They also emphasized the importance of utilizing a broad range of bacteria for NP discovery. Categorization of the families of interrupted A domains and types of M domains allowed for a better understanding of the trends of naturally occurring interrupted A domains, which illuminated patterns and insights on how to harness them for future engineering studies.

In-depth study of intriguing bacterial interrupted adenylation domains from seven distinct families and six different types.

Characterization of a Unique Interrupted Adenylation Domain That Can Catalyze Three Reactions

Interrupted adenylation (A) domains contain auxiliary domains within their structure and are a subject of growing interest in the field of nonribosomal peptide biosynthesis. They have been shown to possess intriguing functions and structure as well as promising engineering potential. Here, we present the characterization of an unprecedented type of interrupted A domain from the columbamides biosynthetic pathway, ColG(AM_sM_bA). This interrupted A domain contains two back-to-back methylation (M) domains within the same interruption site in the A domain, whereas previously, naturally occurring reported and characterized interrupted A domains harbored only one M domain. By a series of radiometric and mass spectrometry assays, we show that the first and second M domains site specifically methylate the side-chain oxygen and backbone nitrogen of l-Ser after the substrate is transferred onto a carrier thiolation domain, ColG(T). This is the first reported characterization of a dimethylating back-to-back interrupted A domain. The insights gained by this work lay the foundation for future combinatorial biosynthesis of site specifically methylated nonribosomal peptides.

Lessons learned in engineering interrupted adenylation domains when attempting to create trifunctional enzymes from three independent monofunctional ones

Interrupted adenylation (A) domains are fascinating examples of multifunctional enzymes. They are found in nonribosomal peptide synthetases (NRPSs), which biosynthesize nonribosomal peptides (NRPs), a major class of medically relevant natural products (NPs). Interrupted A domains contain the catalytic portion of another domain within them, typically a methylation (M) domain, thus combining both adenylation and methylation capabilities. In recent years, interrupted A domains have demonstrated tremendous enzyme engineering potential as they are able to be constructed artificially in a laboratory setting by combining the A and M domains of two separate NRPS proteins. A recent discovery and characterization of a naturally occurring interrupted A domain that harbored two M domains back-to-back, a trifunctional protein, showed the ingenuity of Nature to both N- and O-methylate amino acids, the building blocks of NRPs. Since we have shown that a single M domain could be added to an uninterrupted A domain to create an artificial interrupted A domain, we set out to investigate if: (i) an A domain could be engineered to contain two back-to-back M domains and (ii) the added M domains would have to reflect the pattern in Nature, a side chain (O-) methylating M domain (M_s) followed by a backbone (N-) methylating M domain (M_b), or if the order of the M domains could be reversed. To address these questions, we set out to create our own AM_sM_bA and AM_bM_sA engineered interrupted A domains. We evaluated these engineered proteins connected (in cis) and/or disconnected (in trans) from the native thiolation (T) domain, through a series of radiometric assays, high performance liquid chromatography (HPLC), and mass spectrometry (MS) for adenylation, loading, and methylation ability. We found that although adenylation activity was preserved in both versions (AM_sM_bA and AM_bM_sA), addition of the M domains, in natural and unnatural order, did not result in the desired added methylation capability. This study offers valuable insights into the limits of constructing engineered interrupted A domains as potential tools for modifications of NRPs.

Interrupted adenylation (A) domains are fascinating examples of multifunctional enzymes with high potential for engineering. Here, limits were established in engineering trifunctional interrupted A domains.

P5022Dual-energy CT was effective to evaluate of microvasculopathy in chronic thromboembolic pulmonary hypertension

Background

The existence of microvasculopathy in patients with chronic thromboembolic pulmonary hypertension (CTEPH) had been suggested. However, the impact of microvasculopathy for pathophysiology had been unknown. Recently dual-energy CT (DECT) can produce a sensitive iodine distribution map as blood perfusion in lung fields to quantify lung perfusion, also can suggest the existence of microvasculopathy according to poor subpleural perfusion which was published previously.

Methods

We retrospectively reviewed poor subpleural perfusion (defined as subpleural spaces either not or minimally perfused in all segments) and hemodynamics of 83 treatment-naïve CTEPH patients who underwent DECT from February 2014 to Jan 2019. Patients were divided according to poor subpleural perfusion: a microvasculopathy group (n=44) or a non-microvasculopathy group (n=39).

We assessed cardiopulmonary exercise test, right heart catheterization and DECT parameters as quantitative evaluation of pulmonary blood volume (PBV). PBV was calculated as the average of entire lung iodine density.

Results

PBV value in non-microvasculopathy group showed significant inverse correlation with pulmonary vascular resistance (PVR) (y = 14236 x-1.028 r=−0.530, p<0.01).

PBV, SvO2, and %DLCO/VA were significantly lower (22.0 vs. 26.4, p<0.01, 61.3 vs. 66.0, p<0.01, and 59.2 vs 75.9 p<0.01), and systolic pulmonary arterial pressure, PVR, VE/VCO2 slope, BNP were higher (69.3 vs 60.6 p=0.04, 834 vs 586 p<0.01, 45.5 vs. 37.8, p=0.02, and 440 vs 122 p=0.04) in microvasculopathy group, while the other parameters were similar between the two groups.

Multivariate analysis revealed that %DLCO/VA was the only predictor of microvasculopathy (OR,0.895 [95% CI, 0.835 - 0.960]; P<0.01).

Conclusion

Pulmonary blood flow of patients in non-micorvasculopathy group showed inverse correlation with PVR. DECT was effective to assess the microvasculopathy in CTEPH. In our experience, less than 60% of non-operable CTEPH patients have microvasculopathy.

Mechanical regulation of bone homeostasis through p130Cas-mediated alleviation of NF-κB activity

Mechanical loading plays an important role in bone homeostasis. However, molecular mechanisms behind the mechanical regulation of bone homeostasis are poorly understood. We previously reported p130Cas (Cas) as a key molecule in cellular mechanosensing at focal adhesions. Here, we demonstrate that Cas is distributed in the nucleus and supports mechanical loading-mediated bone homeostasis by alleviating NF-κB activity, which would otherwise prompt inflammatory processes. Mechanical unloading modulates Cas distribution and NF-κB activity in osteocytes, the mechanosensory cells in bones. Cas deficiency in osteocytes increases osteoclastic bone resorption associated with NF-κB-mediated RANKL expression, leading to osteopenia. Upon shear stress application on cultured osteocytes, Cas translocates into the nucleus and down-regulates NF-κB activity. Collectively, fluid shear stress-dependent Cas-mediated alleviation of NF-κB activity supports bone homeostasis. Given the ubiquitous expression of Cas and NF-κB together with systemic distribution of interstitial fluid, the Cas-NF-κB interplay may also underpin regulatory mechanisms in other tissues and organs.

Immunogenomic profiles associated with response to neoadjuvant chemoradiotherapy in patients with rectal cancer

BACKGROUND

Accumulating evidence suggests that radiotherapy success has an immune-associated component. The immunogenomic profiles associated with responses to chemoradiotherapy (CRT) were assessed in patients with locally advanced rectal cancer in this study.

METHODS

CD8+ tumour-infiltrating lymphocyte (TIL) and stromal lymphocyte densities were assessed by immunohistochemistry using pretreatment biopsies from patients with advanced rectal cancer who had preoperative CRT. Whole-exome sequencing and gene expression microarray analysis were conducted to investigate the genomic properties associated with the response to CRT and CD8+ TIL density. Response to CRT was determined based on Dworak tumour regression grade (TRG); tumours with complete (TRG 4) or near-complete (TRG 3) regression were grouped as good responders, and those with TRG 1 as non-responders.

RESULTS

Immunohistochemical examinations (275 patients) showed that pre-CRT CD8+ TIL density was associated with better response to CRT and improved recurrence-free survival, whereas pre-CRT stromal CD8+ cell density was not associated with either response to CRT or recurrence-free survival. Whole-exome sequencing (74 patients) showed that the numbers of single-nucleotide variations (SNVs) and neoantigens predicted from SNVs were higher in good responders than in non-responders, and these correlated positively with CD8+ TIL density (r_S  = 0·315 and r_S  = 0·334 respectively). Gene expression microarray (90 patients) showed that CD8A expression correlated positively with the expression of programmed cell death 1 (PDCD1) (r_S  = 0·264) and lymphocyte-activation gene 3 (LAG3) (r_S  = 0·507).

CONCLUSION

Pre-CRT neoantigen-specific CD8+ T cell priming may be a key event in CRT responses where immune checkpoint molecules could be useful targets to enhance tumour regression.

Probing the limits of interrupted adenylation domains by engineering a trifunctional enzyme capable of adenylation, N-, and S-methylation

The adenylation (A) domains found in nonribosomal peptide synthetases (NRPSs) exhibit tremendous plasticity. Some A domains have been shown to display the ability to contain within them the catalytic portion of an auxiliary domain, most commonly that of a methyltransferase (M) enzyme. This unique feature of A domains interrupted by M domains allows them to possess bifunctionality, where they can both adenylate and methylate an amino acid substrate. Additionally, these types of inserted M domains are able to selectively carry out either backbone or side chain methylation of amino acids. Interruptions with M domains are naturally found to occur either between the a2-a3 or the a8-a9 of the ten conserved motifs of A domains. Herein, we set out to answer the following question: Can one A domain support two different M domain interruptions occurring in two different locations (a2-a3 and a8-a9) of the A domain and possess the ability to adenylate an amino acid and methylate it on both its side chain and backbone? To answer this question we added a backbone methylating M3S domain from TioS(A3aM3SA3b) between the a8-a9 region of a mono-interrupted A domain, TioN(AaMNAb), that already contained a side chain methylating MN domain between its a2-a3 region. We evaluated the di-interrupted A domain TioN(AMNAM3SA) with a series of radiometric and mass spectrometry assays and found that this engineered enzyme was indeed capable of all three activities. These findings show that production of an active trifunctional di-interrupted A domain is possible and represents an exciting new avenue for future nonribosomal peptide (NRP) derivatization.

Beyond the physician's perspective: A review of patient-reported outcomes in dermatologic surgery and cosmetic dermatology

Patient-reported outcome measures (PROMs) are utilized in health care to quantify the patient's perspective of a health condition or treatment on outcomes, such as health-related quality of life (HRQoL) and patient satisfaction. In dermatology, this is particularly relevant because the patient's perspective is critical in evaluating the outcome of cosmetic procedures as well as skin cancer treatment. We review seven validated PROMs that have been reported in the dermatologic surgery and cosmetic dermatology literature. For patients undergoing cosmetic procedures, the use of PROMs provides additional valuable outcome data beyond physician assessment. For patients with skin cancer, women experience a unique and often greater impact on HRQoL during treatment, which has been captured through PROMs. The recent development of multi-module instruments, such as the FACE-Q and FACE-Q Skin Cancer, have facilitated comprehensive assessments of treatment that impact multiple domains of HRQoL. The use of PROMs allows for dermatologists to reliably capture important disease- and treatment-related concerns, thus improving the patient experience.

Using MbtH-Like Proteins to Alter the Substrate Profile of a Nonribosomal Peptide Adenylation Enzyme

MbtH-like proteins (MLPs) are required for soluble expression and/or optimal activity of some adenylation (A) domains of nonribosomal peptide synthetases. Because A domains can interact with noncognate MLP partners, how the function of an A domain, TioK, involved in the biosynthesis of the bisintercalator thiocoraline, is altered by noncognate MLPs has been investigated. Measuring TioK activity with 12 different MLPs from a variety of bacterial species by using a radiometric assay suggested that the A domain substrate promiscuity could be altered by foreign MLPs. Kinetic studies and bioinformatics analysis expanded the complexity of MLP functions and interactions.