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1. Bioinformatic discovery of type 11 secretion system (T11SS) cargo across the Proteobacteria

   https://doi.org/10.1099/mgen.0.001406  

   Grossman, Alex S; Mucci, Nicholas C; Kauffman, Sarah J; Rafi, Jahirul; Goodrich-Blair, Heidi (May 2025, Microbial Genomics)

   Type 11 secretion systems (T11SS) are broadly distributed among proteobacteria, with more than 3000 T11SS family outer membrane proteins (OMPs) comprising 10 major sequence similarity network (SSN) clusters. Of these, only 7, all from animal-associated cluster 1, have been experimentally verified as secretins of cargo, including adhesins, hemophores, and metal binding proteins. To identify novel cargo of a more diverse set of T11SS, we identified gene families co-occurring in gene neighborhoods with either cluster 1 or marine microbe-associated cluster 3 T11SS OMP genes. We developed bioinformatic controls to ensure perceived co-occurrences are specific to T11SS, and not general to OMPs. We found that both cluster 1 and cluster 3 T11SS OMPs frequently co-occur with single carbon metabolism and nucleotide synthesis pathways, but that only cluster 1 T11SS OMPs had significant co-occurrence with metal and heme pathways, as well as with mobile genetic islands, potentially indicating diversified function of this cluster. Cluster 1 T11SS co-occurrences included 2556 predicted cargo proteins, unified by the presence of a C-terminal β-barrel domain, which fall into 141 predicted UniRef50 clusters and approximately 10 different architectures: 4 similar to known cargo and 6 uncharacterized types. We experimentally demonstrate T11SS-dependent secretion of an uncharacterized cargo type with homology to Plasmin sensitive protein (Pls). Unexpectedly, genes encoding marine cluster 3 T11SS OMPs only rarely co-occurred with the C-terminal β-barrel domain and instead frequently co-occurred with DUF1194-containing genes. Overall, our results show that with sufficiently large-scale and controlled genomic data, T11SS-dependent cargo proteins can be accurately predicted. 

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2. The complete mitochondrial genomes of two imperiled species endemic to the Southwestern United States: Peppered Chub ( Macrhybopsis tetranema ) and Gila Trout ( Oncorhynchus gilae )

   https://doi.org/10.1080/23802359.2023.2241658  

   Osborne, Megan J; Barela_Hudgell, Megan A; Caeiro-Dias, Guilherme; Turner, Thomas F (August 2023, Mitochondrial DNA Part B)

   Macrhybopsis tetranema and Oncorhynchus gilae are fish species endemic to the Southwestern United States. We present the complete mitochondrial genomes for these species. Each genome consisted of 13 protein-coding genes, two ribosomal (rRNA) genes, 22 transfer RNA (tRNA) genes, and the control region (D-loop). Mitogenome lengths were 16,916 base pairs (bp) for M. tetranema, and 16,976 bp for O. gilae. The GC content was 41% for M. tetranema and 46% for O. gilae. The relationships of M. tetranema and O. gilae were consistent with previous phylogenetic analyses. 

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3. Selecting genes for analysis using historically contingent progress: from RNA changes to protein-protein interactions

   https://doi.org/10.1101/2024.05.01.592119  

   Lalit, Farhaan; Jose, Antony M (May 2024, bioRxiv)

   SUMMARY Progress in biology has generated numerous lists of genes that share some property. But, advancing from these lists of genes to understanding their roles is slow and unsystematic. Here we use RNA silencing inC. elegansto illustrate an approach for prioritizing genes for detailed study given limited resources. The partially subjective relationships between genes forged by both deduced functional relatedness and biased progress in the field was captured as mutual information and used to cluster genes that were frequently identified yet remain understudied. Studied genes in these clusters suggest regulatory links connecting RNA silencing with other processes like the cell cycle. Many proteins encoded by the understudied genes are predicted to physically interact with known regulators of RNA silencing. These predicted influencers of RNA-regulated expression could be used for feedback regulation, which is essential for the homeostasis observed in all living systems. Thus, among the gene products altered when a process is perturbed are regulators of that process, providing a way to use RNA sequencing to identify candidate protein-protein interactions. Together, the analysis of perturbed transcripts and potential interactions of the proteins they encode could help prioritize candidate regulators of any process. 

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4. The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation

   https://doi.org/10.1038/s41598-023-35246-w  

   Morita, Shinichi; Shibata, Tomoko F; Nishiyama, Tomoaki; Kobayashi, Yuuki; Yamaguchi, Katsushi; Toga, Kouhei; Ohde, Takahiro; Gotoh, Hiroki; Kojima, Takaaki; Weber, Jesse N; et al (December 2023, Scientific Reports)

   Abstract The Japanese rhinoceros beetleTrypoxylus dichotomusis a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male.T. dichotomushas been used as a research model in various fields such as evolutionary developmental biology, ecology, ethology, biomimetics, and drug discovery. In this study, de novo assembly of 615 Mb, representing 80% of the genome estimated by flow cytometry, was obtained using the 10 × Chromium platform. The scaffold N50 length of the genome assembly was 8.02 Mb, with repetitive elements predicted to comprise 49.5% of the assembly. In total, 23,987 protein-coding genes were predicted in the genome. In addition, de novo assembly of the mitochondrial genome yielded a contig of 20,217 bp. We also analyzed the transcriptome by generating 16 RNA-seq libraries from a variety of tissues of both sexes and developmental stages, which allowed us to identify 13 co-expressed gene modules. We focused on the genes related to horn formation and obtained new insights into the evolution of the gene repertoire and sexual dimorphism as exemplified by the sex-specific splicing pattern of thedoublesexgene. This genomic information will be an excellent resource for further functional and evolutionary analyses, including the evolutionary origin and genetic regulation of beetle horns and the molecular mechanisms underlying sexual dimorphism. 

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5. Identification of the Biosynthetic Gene Cluster for the Organoarsenical Antibiotic Arsinothricin

   https://doi.org/10.1128/Spectrum.00502-21  

   Galván, Adriana E.; Paul, Ngozi P.; Chen, Jian; Yoshinaga-Sakurai, Kunie; Utturkar, Sagar M.; Rosen, Barry P.; Yoshinaga, Masafumi (September 2021, Microbiology Spectrum)

   Tang, Xiaoyu (Ed.)

   ABSTRACT The soil bacterium Burkholderia gladioli GSRB05 produces the natural compound arsinothricin [2-amino-4-(hydroxymethylarsinoyl) butanoate] (AST), which has been demonstrated to be a broad-spectrum antibiotic. To identify the genes responsible for AST biosynthesis, a draft genome sequence of B. gladioli GSRB05 was constructed. Three genes, arsQML , in an arsenic resistance operon were found to be a biosynthetic gene cluster responsible for synthesis of AST and its precursor, hydroxyarsinothricin [2-amino-4-(dihydroxyarsinoyl) butanoate] (AST-OH). The arsL gene product is a noncanonical radical S -adenosylmethionine (SAM) enzyme that is predicted to transfer the 3-amino-3-carboxypropyl (ACP) group from SAM to the arsenic atom in inorganic arsenite, forming AST-OH, which is methylated by the arsM gene product, a SAM methyltransferase, to produce AST. Finally, the arsQ gene product is an efflux permease that extrudes AST from the cells, a common final step in antibiotic-producing bacteria. Elucidation of the biosynthetic gene cluster for this novel arsenic-containing antibiotic adds an important new tool for continuation of the antibiotic era. IMPORTANCE Antimicrobial resistance is an emerging global public health crisis, calling for urgent development of novel potent antibiotics. We propose that arsinothricin and related arsenic-containing compounds may be the progenitors of a new class of antibiotics to extend our antibiotic era. Here, we report identification of the biosynthetic gene cluster for arsinothricin and demonstrate that only three genes, two of which are novel, are required for the biosynthesis and transport of arsinothricin, in contrast to the phosphonate counterpart, phosphinothricin, which requires over 20 genes. Our discoveries will provide insight for the development of more effective organoarsenical antibiotics and illustrate the previously unknown complexity of the arsenic biogeochemical cycle, as well as bring new perspective to environmental arsenic biochemistry. 

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