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1. Cooperation loci are more pleiotropic than private loci in the bacterium Pseudomonas aeruginosa

   https://doi.org/10.1073/pnas.2214827119  

   Scott, Trey J. (October 2022, Proceedings of the National Academy of Sciences)

   Pleiotropy may affect the maintenance of cooperation by limiting cheater mutants if such mutants lose other important traits. If pleiotropy limits cheaters, selection may favor cooperation loci that are more pleiotropic. However, the same should not be true for private loci with functions unrelated to cooperation. Pleiotropy in cooperative loci has mostly been studied with single loci and has not been measured on a wide scale or compared to a suitable set of control loci with private functions. I remedy this gap by comparing genomic measures of pleiotropy in previously identified cooperative and private loci in Pseudomonas aeruginosa. I found that cooperative loci in P. aeruginosa tended to be more pleiotropic than private loci according to the number of protein–protein interactions, the number of gene ontology terms, and gene expression specificity. These results show that pleiotropy may be a general way to limit cheating and that cooperation may shape pleiotropy in the genome. 

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2. Reproductive phasiRNA loci and DICER-LIKE5, but not microRNA loci, diversified in monocotyledonous plants

   https://doi.org/10.1093/plphys/kiab001  

   Patel, Parth; Mathioni, Sandra M; Hammond, Reza; Harkess, Alex E; Kakrana, Atul; Arikit, Siwaret; Dusia, Ayush; Meyers, Blake C (January 2021, Plant Physiology)

   null (Ed.)

   Abstract In monocots other than maize (Zea mays) and rice (Oryza sativa), the repertoire and diversity of microRNAs (miRNAs) and the populations of phased, secondary, small interfering RNAs (phasiRNAs) are poorly characterized. To remedy this, we sequenced small RNAs (sRNA) from vegetative and dissected inflorescence tissue in 28 phylogenetically diverse monocots and from several early-diverging angiosperm lineages, as well as publicly available data from 10 additional monocot species. We annotated miRNAs, small interfering RNAs (siRNAs) and phasiRNAs across the monocot phylogeny, identifying miRNAs apparently lost or gained in the grasses relative to other monocot families, as well as a number of transfer RNA fragments misannotated as miRNAs. Using our miRNA database cleaned of these misannotations, we identified conservation at the 8th, 9th, 19th, and 3′-end positions that we hypothesize are signatures of selection for processing, targeting, or Argonaute sorting. We show that 21-nucleotide (nt) reproductive phasiRNAs are far more numerous in grass genomes than other monocots. Based on sequenced monocot genomes and transcriptomes, DICER-LIKE5, important to 24-nt phasiRNA biogenesis, likely originated via gene duplication before the diversification of the grasses. This curated database of phylogenetically diverse monocot miRNAs, siRNAs, and phasiRNAs represents a large collection of data that should facilitate continued exploration of sRNA diversification in flowering plants. 

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3. BPS Jumping Loci are Automorphic

   https://doi.org/10.1007/s00220-018-3090-3  

   Kachru, Shamit; Tripathy, Arnav (June 2018, Communications in Mathematical Physics)
4. Exceptional loci in Lefschetz theory

   https://doi.org/10.1112/blms.12663  

   Raskin, Sam; Smith, Geoffrey (October 2022, Bulletin of the London Mathematical Society)
5. Atypical Carboxysome Loci: JEEPs or Junk?

   https://doi.org/10.3389/fmicb.2022.872708  

   Sutter, Markus; Kerfeld, Cheryl A.; Scott, Kathleen M. (May 2022, Frontiers in Microbiology)

   Carboxysomes, responsible for a substantial fraction of CO 2 fixation on Earth, are proteinaceous microcompartments found in many autotrophic members of domain Bacteria , primarily from the phyla Proteobacteria and Cyanobacteria . Carboxysomes facilitate CO 2 fixation by the Calvin-Benson-Bassham (CBB) cycle, particularly under conditions where the CO 2 concentration is variable or low, or O 2 is abundant. These microcompartments are composed of an icosahedral shell containing the enzymes ribulose 1,5-carboxylase/oxygenase (RubisCO) and carbonic anhydrase. They function as part of a CO 2 concentrating mechanism, in which cells accumulate HCO 3 − in the cytoplasm via active transport, HCO 3 − enters the carboxysomes through pores in the carboxysomal shell proteins, and carboxysomal carbonic anhydrase facilitates the conversion of HCO 3 − to CO 2 , which RubisCO fixes. Two forms of carboxysomes have been described: α-carboxysomes and β-carboxysomes, which arose independently from ancestral microcompartments. The α-carboxysomes present in Proteobacteria and some Cyanobacteria have shells comprised of four types of proteins [CsoS1 hexamers, CsoS4 pentamers, CsoS2 assembly proteins, and α-carboxysomal carbonic anhydrase (CsoSCA)], and contain form IA RubisCO (CbbL and CbbS). In the majority of cases, these components are encoded in the genome near each other in a gene locus, and transcribed together as an operon. Interestingly, genome sequencing has revealed some α-carboxysome loci that are missing genes encoding one or more of these components. Some loci lack the genes encoding RubisCO, others lack a gene encoding carbonic anhydrase, some loci are missing shell protein genes, and in some organisms, genes homologous to those encoding the carboxysome-associated carbonic anhydrase are the only carboxysome-related genes present in the genome. Given that RubisCO, assembly factors, carbonic anhydrase, and shell proteins are all essential for carboxysome function, these absences are quite intriguing. In this review, we provide an overview of the most recent studies of the structural components of carboxysomes, describe the genomic context and taxonomic distribution of atypical carboxysome loci, and propose functions for these variants. We suggest that these atypical loci are JEEPs, which have modified functions based on the presence of Just Enough Essential Parts. 

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