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1. Target Enrichment and Extensive Population Sampling Help Untangle the Recent, Rapid Radiation of Oenothera Sect. Calylophus

   https://doi.org/10.1093/sysbio/syac032  

   Cooper, Benjamin J.; Moore, Michael J.; Douglas, Norman A.; Wagner, Warren L.; Johnson, Matthew G.; Overson, Rick P.; Kinosian, Sylvia P.; McDonnell, Angela J.; Levin, Rachel A.; Raguso, Robert A.; et al (May 2022, Systematic Biology)

   Abstract Oenothera sect. Calylophus is a North American group of 13 recognized taxa in the evening primrose family (Onagraceae) with an evolutionary history that may include independent origins of bee pollination, edaphic endemism, and permanent translocation heterozygosity. Like other groups that radiated relatively recently and rapidly, taxon boundaries within Oenothera sect. Calylophus have remained challenging to circumscribe. In this study, we used target enrichment, flanking noncoding regions, gene tree/species tree methods, tests for gene flow modified for target-enrichment data, and morphometric analysis to reconstruct phylogenetic hypotheses, evaluate current taxon circumscriptions, and examine character evolution in Oenothera sect. Calylophus. Because sect. Calylophus comprises a clade with a relatively restricted geographic range, we were able to extensively sample across the range of geographic, edaphic, and morphological diversity in the group. We found that the combination of exons and flanking noncoding regions led to improved support for species relationships. We reconstructed potential hybrid origins of some accessions and note that if processes such as hybridization are not taken into account, the number of inferred evolutionary transitions may be artificially inflated. We recovered strong evidence for multiple evolutionary origins of bee pollination from ancestral hawkmoth pollination, edaphic specialization on gypsum, and permanent translocation heterozygosity. This study applies newly emerging techniques alongside dense infraspecific sampling and morphological analyses to effectively reconstruct the recalcitrant history of a rapid radiation. [Gypsum endemism; Oenothera sect. Calylophus; Onagraceae; phylogenomics; pollinator shift; recent radiation; target enrichment.] 

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2. Light-guided intrabodies for on-demand in situ target recognition in human cells

   https://doi.org/10.1039/D1SC01331A  

   Joest, Eike F.; Winter, Christian; Wesalo, Joshua S.; Deiters, Alexander; Tampé, Robert (April 2021, Chemical Science)

   null (Ed.)

   Due to their high stability and specificity in living cells, fluorescently labeled nanobodies are perfect probes for visualizing intracellular targets at an endogenous level. However, intrabodies bind unrestrainedly and hence may interfere with the target protein function. Here, we report a strategy to prevent premature binding through the development of photo-conditional intrabodies. Using genetic code expansion, we introduce photocaged amino acids within the nanobody-binding interface, which, after photo-activation, show instantaneous binding of target proteins with high spatiotemporal precision inside living cells. Due to the highly stable binding, light-guided intrabodies offer a versatile platform for downstream imaging and regulation of target proteins. 

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3. Indole‐3‐Glycerol Phosphate Synthase From Mycobacterium tuberculosis : A Potential New Drug Target

   https://doi.org/10.1002/cbic.202100314  

   Esposito, Nikolas; Konas, David_W; Goodey, Nina_M (September 2021, ChemBioChem)

   Abstract Tuberculosis (TB), caused by the pathogenMycobacterium tuberculosis, affects millions of people worldwide. Several TB drugs have lost efficacy due to emerging drug resistance and new anti‐TB targets are needed. Recent research suggests that indole‐3‐glycerol phosphate synthase (IGPS) inM. tuberculosis(MtIGPS) could be such a target. IGPS is a (β/α)₈‐barrel enzyme that catalyzes the conversion of 1‐(o‐carboxyphenylamino)‐1‐deoxyribulose 5’‐phosphate (CdRP) into indole‐glycerol‐phosphate (IGP) in the bacterial tryptophan biosynthetic pathway.M. tuberculosisover expresses the tryptophan pathway genes during an immune response and inhibition ofMtIGPS allows CD4 T‐cells to more effectively fight againstM. tuberculosis. Here we review the published data onMtIGPS expression, kinetics, mechanism, and inhibition. We also discussMtIGPS crystal structures and compare them to other IGPS structures to reveal potential structure‐function relationships of interest for the purposes of drug design and biocatalyst engineering. 

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4. Repurposing of intestinal defensins as multi-target, dual-function amyloid inhibitors via cross-seeding

   https://doi.org/10.1039/D2SC01447E  

   Tang, Yijing; Zhang, Dong; Gong, Xiong; Zheng, Jie (June 2022, Chemical Science)

   Amyloid formation and microbial infection are the two common pathological causes of neurogenerative diseases, including Alzheimer's disease (AD), type II diabetes (T2D), and medullary thyroid carcinoma (MTC). While significant efforts have been made to develop different prevention strategies and preclinical hits for these diseases, conventional design strategies of amyloid inhibitors are mostly limited to either a single prevention mechanism (amyloid cascade vs. microbial infection) or a single amyloid protein (Aβ, hIAPP, or hCT), which has prevented the launch of any successful drug on the market. Here, we propose and demonstrate a new “anti-amyloid and anti-bacteria” strategy to repurpose two intestinal defensins, human α-defensin 6 (HD-6) and human β-defensin 1 (HBD-1), as multiple-target, dual-function, amyloid inhibitors. Both HD-6 and HBD-1 can cross-seed with three amyloid peptides, Aβ (associated with AD), hIAPP (associated with T2D), and hCT (associated with MTC), to prevent their aggregation towards amyloid fibrils from monomers and oligomers, rescue SH-SY5Y and RIN-m5F cells from amyloid-induced cytotoxicity, and retain their original antimicrobial activity against four common bacterial strains at sub-stoichiometric concentrations. Such sequence-independent anti-amyloid and anti-bacterial functions of intestinal defensins mainly stem from their cross-interactions with amyloid proteins through amyloid-like mimicry of β-sheet associations. In a broader view, this work provides a new out-of-the-box thinking to search and repurpose a huge source of antimicrobial peptides as amyloid inhibitors, allowing the blocking of the two interlinked pathological pathways and bidirectional communication between the central nervous system and intestines via the gut–brain axis associated with neurodegenerative diseases. 

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5. MotifAnalyzer‐PDZ : A computational program to investigate the evolution of PDZ‐binding target specificity

   https://doi.org/10.1002/pro.3741  

   Valgardson, Jordan; Cosbey, Robin; Houser, Paul; Rupp, Milo; Van Bronkhorst, Raiden; Lee, Michael; Jagodzinski, Filip; Amacher, Jeanine F. (November 2019, Protein Science)

   Abstract Recognition of short linear motifs (SLiMs) or peptides by proteins is an important component of many cellular processes. However, due to limited and degenerate binding motifs, prediction of cellular targets is challenging. In addition, many of these interactions are transient and of relatively low affinity. Here, we focus on one of the largest families of SLiM‐binding domains in the human proteome, the PDZ domain. These domains bind the extreme C‐terminus of target proteins, and are involved in many signaling and trafficking pathways. To predict endogenous targets of PDZ domains, we developedMotifAnalyzer‐PDZ, a program that filters and compares all motif‐satisfying sequences in any publicly available proteome. This approach enables us to determine possible PDZ binding targets in humans and other organisms. Using this program, we predicted and biochemically tested novel human PDZ targets by looking for strong sequence conservation in evolution. We also identified three C‐terminal sequences in choanoflagellates that bind a choanoflagellate PDZ domain, theMonsiga brevicollisSHANK1 PDZ domain (mbSHANK1), with endogenously‐relevant affinities, despite a lack of conservation with the targets of a homologous human PDZ domain, SHANK1. All three are predicted to be signaling proteins, with strong sequence homology to cytosolic and receptor tyrosine kinases. Finally, we analyzed and compared the positional amino acid enrichments in PDZ motif‐satisfying sequences from over a dozen organisms. Overall,MotifAnalyzer‐PDZis a versatile program to investigate potential PDZ interactions. This proof‐of‐concept work is poised to enable similar types of analyses for other SLiM‐binding domains (e.g.,MotifAnalyzer‐Kinase).MotifAnalyzer‐PDZis available athttp://motifAnalyzerPDZ.cs.wwu.edu. 

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