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1. Transcriptome profiling of type VI secretion system core gene tssM mutant of Xanthomonas perforans highlights regulators controlling diverse functions ranging from virulence to metabolism

   https://doi.org/10.1128/spectrum.02852-23  

   Ramamoorthy, Sivakumar ; Pena, Michelle ; Ghosh, Palash ; Liao, Ying-Yu ; Paret, Mathews ; Jones, Jeffrey B. ; Potnis, Neha ( January 2024 , Microbiology Spectrum)

   Burbank, Lindsey Price (Ed.)

   Type VI secretion system (T6SS) is a versatile, contact-dependent contractile nano-weapon in Gram-negative bacteria that fires proteinaceous effector molecules directly into prokaryotic and eukaryotic cells aiding in manipulation of the host and killing of competitors in complex niches. In plant pathogenic xanthomonads, T6SS has been demonstrated to play these diverse roles in individual pathosystems. However, the molecular network underlying the regulation of T6SS is still elusive inXanthomonasspp. To bridge this knowledge gap, we conducted anin vitrotranscriptome screen using plant apoplast mimicking minimal medium, XVM2 medium, to decipher the effect oftssMdeletion, a core gene belonging to T6SS-cluster i3*, on the regulation of gene expression inXanthomonas perforansstrain AL65. Transcriptomic data revealed that a total of 277 and 525 genes were upregulated, while 307 and 392 genes were downregulated in the mutant strain after 8 and 16 hours of growth in XVM2 medium. The transcript abundance of several genes associated with flagellum and pilus biogenesis as well as type III secretion system was downregulated in the mutant strain. Deletion oftssMof cluster-i3* resulted in upregulation of several T6SS genes belonging to cluster-i3*** and genes involved in biofilm and cell wall biogenesis. Similarly, transcription regulators likerpoN, Pho regulon,rpoE, andcsrAwere identified to be upregulated in the mutant strain. Our results suggest that T6SS modulates the expression of global regulators likecsrA,rpoN, andphoregulons, triggering a signaling cascade, and co-ordinates the expression of suite of virulence factors, stress response genes, and metabolic genes.

   T6SS has received attention due to its significance in mediating interorganismal competition through contact-dependent release of effector molecules into prokaryotic and eukaryotic cells. Reverse-genetic studies have indicated the role of T6SS in virulence in a variety of plant pathogenic bacteria, including the one studied here,Xanthomonas. However, it is not clear whether such effect on virulence is merely due to a shift in the microbiome-mediated protection or if T6SS is involved in a complex virulence regulatory network. In this study, we conducted in vitro transcriptome profiling in minimal medium to decipher the signaling pathways regulated by tssM-i3* inX. perforansAL65. We show that TssM-i3* regulates the expression of a suite of genes associated with virulence and metabolism either directly or indirectly by altering the transcription of several regulators. These findings further expand our knowledge on the intricate molecular circuits regulated by T6SS in phytopathogenic bacteria.

    

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2. Host‐dependent contributions of the Cfcdp1 protease gene to virulence in the entomopathogenic fungus Cordyceps fumosorosea

   https://doi.org/10.1002/ps.5549  

   Huang, Wenyou ; Huang, Yü ; Hao, Yongfen ; Huang, Song ; Gao, Tianni ; Keyhani, Nemat O. ; Huang, Zhen ( August 2019 , Pest Management Science)

   The genomes of broad host range insect pathogenic fungi, includingCordyceps fumosorosea, encode for a suite of secreted proteases implicated in targeting, penetration, and degradation of the host exoskeleton or cuticle. These cuticle‐degrading proteases act as critical virulence factors, but their functions within the biological context, particularly in relation to host specificity, remain poorly characterized.

   AC. fumosoroseaprotease gene,Cfcdp1, was identified and a targeted gene‐knockout strain constructed. Minor growth defects were observed for theΔCfcdp1strain when compared to the wild‐type parent and complemented (ΔCfcdp1::Cfcdp1) strains, with delayed and decreased sporulation noted for the mutant. Decreased subtilisin‐like protease activity was seen for theΔCfcdp1strain, although total secreted protease activity was similar between the mutant and wild‐type strains. Insect bioassays using whitefly,Bemisia tabaci, and cabbageworm,Pieris rapae, showed decreased infectivity, i.e. 2.4–3.4‐fold increase in lethal dose (LC₅₀) and an increased time to death (LT₅₀), for theΔCfcdp1strain. In contrast, insect bioassays using the diamondback moth,Plutella xylostella, or the brown planthopper,Nilaparvata lugens, showed increased infectivity, i.e. a 3–5‐fold decrease in LC₅₀, and a decreased LT₅₀. Differential effects were also seen on the fecundity ofB. tabaciinfected by the different fungal strains.

   These data reveal host‐dependent effects of a protease implicated in cuticle degradation onC. fumosoroseavirulence. The implications of these findings in suggesting context‐dependent requirements of cuticle‐degrading enzymes and their potentially differential roles in mediating virulence towards different hosts are discussed. © 2019 Society of Chemical Industry

    

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3. Aseismic Deformation During the 2014 M w 5.2 Karonga Earthquake, Malawi, From Satellite Interferometry and Earthquake Source Mechanisms

   https://doi.org/10.1029/2020GL090930  

   Zheng, Whyjay ; Oliva, Sarah Jaye ; Ebinger, Cynthia ; Pritchard, Matthew E. ( November 2020 , Geophysical Research Letters)

   Aseismic deformation has been suggested as a mechanism to release the accumulated strain in rifts. However, the fraction and the spatial distribution of the aseismic strain are poorly constrained during amagmatic episodes. Using Sentinel‐1 interferograms, we identify the surface deformation associated with the 2014M_w5.2 Karonga earthquake, Malawi, and perform inversions for fault geometry. We also analyze aftershocks and find a variety of source mechanisms within short timescales. A significant discrepancy in the earthquake depth determined by geodesy (3–6 km) and seismology (11–13 km) exists, although both methods indicateM_w5.2. We propose that the surface deformation is caused by aseismic slip from a shallow depth. This vertical partitioning from seismic to aseismic strain is accommodated by intersecting dilatational faults in the shallow upper crust and sedimentary basin, highlighting the importance of considering aseismic deformation in active tectonics and time‐averaged strain patterns, even in rifts with little volcanism.

    

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4. Compensatory trans -regulatory alleles minimizing variation in TDH3 expression are common within Saccharomyces cerevisiae

   https://doi.org/10.1002/evl3.137  

   Metzger, Brian P. H. ; Wittkopp, Patricia J. ( October 2019 , Evolution Letters)

   Heritable variation in gene expression is common within species. Much of this variation is due to genetic differences outside of the gene with altered expression and is trans-acting. This trans-regulatory variation is often polygenic, with individual variants typically having small effects, making the genetic architecture and evolution of trans-regulatory variation challenging to study. Consequently, key questions about trans-regulatory variation remain, including the variability of trans-regulatory variation within a species, how selection affects trans-regulatory variation, and how trans-regulatory variants are distributed throughout the genome and within a species. To address these questions, we isolated and measured trans-regulatory differences affecting TDH3 promoter activity among 56 strains of Saccharomyces cerevisiae, finding that trans-regulatory backgrounds varied approximately twofold in their effects on TDH3 promoter activity. Comparing this variation to neutral models of trans-regulatory evolution based on empirical measures of mutational effects revealed that despite this variability in the effects of trans-regulatory backgrounds, stabilizing selection has constrained trans-regulatory differences within this species. Using a powerful quantitative trait locus mapping method, we identified ∼100 trans-acting expression quantitative trait locus in each of three crosses to a common reference strain, indicating that regulatory variation is more polygenic than previous studies have suggested. Loci altering expression were located throughout the genome, and many loci were strain specific. This distribution and prevalence of alleles is consistent with recent theories about the genetic architecture of complex traits. In all mapping experiments, the nonreference strain alleles increased and decreased TDH3 promoter activity with similar frequencies, suggesting that stabilizing selection maintained many trans-acting variants with opposing effects. This variation may provide the raw material for compensatory evolution and larger scale regulatory rewiring observed in developmental systems drift among species.

    

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5. Genomics and cellulolytic, hemicellulolytic, and amylolytic potential of Iocasia fonsfrigidae strain SP3-1 for polysaccharide degradation

   https://doi.org/10.7717/peerj.14211  

   Heng, Sobroney ; Sutheeworapong, Sawannee ; Champreda, Verawat ; Uke, Ayaka ; Kosugi, Akihiko ; Pason, Patthra ; Waeonukul, Rattiya ; Ceballos, Ruben Michael ; Ratanakhanokchai, Khanok ; Tachaapaikoon, Chakrit ( January 2022 , PeerJ)

   Background Cellulolytic, hemicellulolytic, and amylolytic (CHA) enzyme-producing halophiles are understudied. The recently defined taxon Iocasia fonsfrigidae consists of one well-described anaerobic bacterial strain: NS-1 T . Prior to characterization of strain NS-1 T , an isolate designated Halocella sp. SP3-1 was isolated and its genome was published. Based on physiological and genetic comparisons, it was suggested that Halocella sp. SP3-1 may be another isolate of I. fronsfrigidae . Despite being geographic variants of the same species, data indicate that strain SP3-1 exhibits genetic, genomic, and physiological characteristics that distinguish it from strain NS-1 T . In this study, we examine the halophilic and alkaliphilic nature of strain SP3-1 and the genetic substrates underlying phenotypic differences between strains SP3-1 and NS-1 T with focus on sugar metabolism and CHA enzyme expression. Methods Standard methods in anaerobic cell culture were used to grow strains SP3-1 as well as other comparator species. Morphological characterization was done via electron microscopy and Schaeffer-Fulton staining. Data for sequence comparisons ( e.g. , 16S rRNA) were retrieved via BLAST and EzBioCloud. Alignments and phylogenetic trees were generated via CLUTAL_X and neighbor joining functions in MEGA (version 11). Genomes were assembled/annotated via the Prokka annotation pipeline. Clusters of Orthologous Groups (COGs) were defined by eegNOG 4.5. DNA-DNA hybridization calculations were performed by the ANI Calculator web service. Results Cells of strain SP3-1 are rods. SP3-1 cells grow at NaCl concentrations of 5-30% (w/v). Optimal growth occurs at 37 °C, pH 8.0, and 20% NaCl (w/v). Although phylogenetic analysis based on 16S rRNA gene indicates that strain SP3-1 belongs to the genus Iocasia with 99.58% average nucleotide sequence identity to Iocasia fonsfrigida NS-1 T , strain SP3-1 is uniquely an extreme haloalkaliphile. Moreover, strain SP3-1 ferments D-glucose to acetate, butyrate, carbon dioxide, hydrogen, ethanol, and butanol and will grow on L-arabinose, D-fructose, D-galactose, D-glucose, D-mannose, D-raffinose, D-xylose, cellobiose, lactose, maltose, sucrose, starch, xylan and phosphoric acid swollen cellulose (PASC). D-rhamnose, alginate, and lignin do not serve as suitable culture substrates for strain SP3-1. Thus, the carbon utilization profile of strain SP3-1 differs from that of I. fronsfrigidae strain NS-1 T . Differences between these two strains are also noted in their lipid composition. Genomic data reveal key differences between the genetic profiles of strain SP3-1 and NS-1 T that likely account for differences in morphology, sugar metabolism, and CHA-enzyme potential. Important to this study, I. fonsfrigidae SP3-1 produces and extracellularly secretes CHA enzymes at different levels and composition than type strain NS-1 T . The high salt tolerance and pH range of SP3-1 makes it an ideal candidate for salt and pH tolerant enzyme discovery. 

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