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1. GRASSY TILLERS1 ( GT1 ) and SIX-ROWED SPIKE1 ( VRS1 ) homologs share conserved roles in growth repression

   https://doi.org/10.1073/pnas.2311961120  

   Gallagher, Joseph P; Man, Jarrett; Chiaramida, Adriana; Rozza, Isabella K; Patterson, Erin L; Powell, Morgan M; Schrager-Lavelle, Amanda; Multani, Dilbag S; Meeley, Robert B; Bartlett, Madelaine E (December 2023, Proceedings of the National Academy of Sciences)

   Crop engineering and de novo domestication using gene editing are new frontiers in agriculture. However, outside of well-studied crops and model systems, prioritizing engineering targets remains challenging. Evolution can guide us, revealing genes with deeply conserved roles that have repeatedly been selected in the evolution of plant form. Homologs of the transcription factor genesGRASSY TILLERS1(GT1) andSIX-ROWED SPIKE1(VRS1) have repeatedly been targets of selection in domestication and evolution, where they repress growth in many developmental contexts. This suggests a conserved role for these genes in regulating growth repression. To test this, we determined the roles ofGT1andVRS1homologs in maize (Zea mays) and the distantly related grass brachypodium (Brachypodium distachyon) using gene editing and mutant analysis. In maize,gt1; vrs1-like1(vrl1) mutants have derepressed growth of floral organs. In addition,gt1; vrl1mutants bore more ears and more branches, indicating broad roles in growth repression. In brachypodium,Bdgt1;Bdvrl1mutants have more branches, spikelets, and flowers than wild-type plants, indicating conserved roles forGT1andVRS1homologs in growth suppression overca.59 My of grass evolution. Importantly, many of these traits influence crop productivity. Notably, maizeGT1can suppress growth in arabidopsis (Arabidopsis thaliana) floral organs, despiteca. 160 My of evolution separating the grasses and arabidopsis. Thus,GT1andVRS1maintain their potency as growth regulators across vast timescales and in distinct developmental contexts. This work highlights the power of evolution to inform gene editing in crop improvement. 

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2. The impacts of cytoplasmic incompatibility factor ( cifA and cifB ) genetic variation on phenotypes

   https://doi.org/10.1093/genetics/iyaa007  

   Shropshire, J Dylan; Rosenberg, Rachel; Bordenstein, Seth R (January 2021, Genetics)

   Presgraves, D (Ed.)

   Abstract Wolbachia are maternally transmitted, intracellular bacteria that can often selfishly spread through arthropod populations via cytoplasmic incompatibility (CI). CI manifests as embryonic death when males expressing prophage WO genes cifA and cifB mate with uninfected females or females harboring an incompatible Wolbachia strain. Females with a compatible cifA-expressing strain rescue CI. Thus, cif-mediated CI confers a relative fitness advantage to females transmitting Wolbachia. However, whether cif sequence variation underpins incompatibilities between Wolbachia strains and variation in CI penetrance remains unknown. Here, we engineer Drosophila melanogaster to transgenically express cognate and non-cognate cif homologs and assess their CI and rescue capability. Cognate expression revealed that cifA;B native to D. melanogaster causes strong CI, and cognate cifA;B homologs from two other Drosophila-associated Wolbachia cause weak transgenic CI, including the first demonstration of phylogenetic type 2 cifA;B CI. Intriguingly, non-cognate expression of cifA and cifB alleles from different strains revealed that cifA homologs generally contribute to strong transgenic CI and interchangeable rescue despite their evolutionary divergence, and cifB genetic divergence contributes to weak or no transgenic CI. Finally, we find that a type 1 cifA can rescue CI caused by a genetically divergent type 2 cifA;B in a manner consistent with unidirectional incompatibility. By genetically dissecting individual CI functions for type 1 and 2 cifA and cifB, this work illuminates new relationships between cif genotype and CI phenotype. We discuss the relevance of these findings to CI’s genetic basis, phenotypic variation patterns, and mechanism. 

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3. The Iron-Responsive Genome of the Chiton Acanthopleura granulata

   https://doi.org/10.1093/gbe/evaa263  

   Varney, Rebecca M; Speiser, Daniel I; McDougall, Carmel; Degnan, Bernard M; Kocot, Kevin M (January 2021, Genome Biology and Evolution)

   Venkatesh, B (Ed.)

   Abstract Molluscs biomineralize structures that vary in composition, form, and function, prompting questions about the genetic mechanisms responsible for their production and the evolution of these mechanisms. Chitons (Mollusca, Polyplacophora) are a promising system for studies of biomineralization because they build a range of calcified structures including shell plates and spine- or scale-like sclerites. Chitons also harden the calcified teeth of their rasp-like radula with a coat of iron (as magnetite). Here we present the genome of the West Indian fuzzy chiton Acanthopleura granulata, the first from any aculiferan mollusc. The A. granulata genome contains homologs of many genes associated with biomineralization in conchiferan molluscs. We expected chitons to lack genes previously identified from pathways conchiferans use to make biominerals like calcite and nacre because chitons do not use these materials in their shells. Surprisingly, the A. granulata genome has homologs of many of these genes, suggesting that the ancestral mollusc may have had a more diverse biomineralization toolkit than expected. The A. granulata genome has features that may be specialized for iron biomineralization, including a higher proportion of genes regulated directly by iron than other molluscs. A. granulata also produces two isoforms of soma-like ferritin: one is regulated by iron and similar in sequence to the soma-like ferritins of other molluscs, and the other is constitutively translated and is not found in other molluscs. The A. granulata genome is a resource for future studies of molluscan evolution and biomineralization. 

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4. Shared cis -regulatory modules control expression of the tandem paralogs midline and H15 in the follicular epithelium

   https://doi.org/10.1242/dev.201016  

   Stevens, Cody A.; Stott, Helen L.; Desai, Shreya V.; Yakoby, Nir (November 2022, Development)

   ABSTRACT The posterior end of the follicular epithelium is patterned by midline (MID) and its paralog H15, the Drosophila homologs of the mammalian Tbx20 transcription factor. We have previously identified two cis-regulatory modules (CRMs) that recapitulate the endogenous pattern of mid in the follicular epithelium. Here, using CRISPR/Cas9 genome editing, we demonstrate redundant activity of these mid CRMs. Although the deletion of either CRM alone generated marginal change in mid expression, the deletion of both CRMs reduced expression by 60%. Unexpectedly, the deletion of the 5′ proximal CRM of mid eliminated H15 expression. Interestingly, expression of these paralogs in other tissues remained unaffected in the CRM deletion backgrounds. These results suggest that the paralogs are regulated by a shared CRM that coordinates gene expression during posterior fate determination. The consistent overlapping expression of mid and H15 in various tissues may indicate that the paralogs could also be under shared regulation by other CRMs in these tissues. 

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5. Precursor-directed biosynthesis of catechol compounds in Acinetobacter bouvetii DSM 14964

   https://doi.org/10.1039/D0CC04171H  

   Reitz, Zachary L.; Butler, Alison (October 2020, Chemical Communications)

   null (Ed.)

   Genome mining for VibH homologs reveals several species of Acinetobacter with a gene cluster that putatively encodes the biosynthesis of catechol siderophores with an amine core. A. bouvetii DSM 14964 produces three novel biscatechol siderophores: propanochelin ( 1 ), butanochelin ( 2 ), and pentanochelin ( 3 ). This strain has a relaxed specificity for the amine substrate, allowing for the biosynthesis of a variety of non-natural siderophore analogs by precursor directed biosynthesis. Of potential synthetic utility, A. bouvetii DSM 14964 condenses 2,3-dihydroxybenzoic acid (2,3-DHB) to allylamine and propargylamine, producing catecholic compounds which bind iron( iii ) and may be further modified via thiol–ene or azide–alkyne click chemistry. 

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