Correction to: Alignment of Biological Sequences with Jalview

Procter, James B.; Carstairs, G. Mungo; Soares, Ben; Mourão, Kira; Ofoegbu, Tochukwu C.; Barton, Daniel L.; Lui, Lauren M.; Menard, Anne; Sherstnev, Natasha; Roldan-Martinez, David; Duce, Suzanne L.; Martin, David; Barton, Geoffrey J.

doi:10.1007/978-1-0716-1036-7_18

Cited by 8 publications

(6 citation statements)

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“… Amino acid conservation between the NT-C2 domains and N-terminal parts of the coiled-coil region of RPG and homologous proteins from rice (Os) and Arabidopsis (At). Sequence alignment was performed using MUSCLE and visualized with Jalview to calculate conservation scores ( Procter et al, 2021 ). Amino acids are colored according to Clustal X Colour Scheme.…”

Section: Resultsmentioning

confidence: 99%

RPG acts as a central determinant for infectosome formation and cellular polarization during intracellular rhizobial infections

Lace

Perez

et al. 2023

eLife

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Host-controlled intracellular accommodation of nitrogen-fixing bacteria is essential for the establishment of a functional Root Nodule Symbiosis (RNS). In many host plants, this occurs via transcellular tubular structures (infection threads - ITs) that extend across cell layers via polar tip-growth. Comparative phylogenomic studies have identified RPG (RHIZOBIUM-DIRECTED POLAR GROWTH) among the critical genetic determinants for bacterial infection. In Medicago truncatula, RPG is required for effective IT progression within root hairs but the cellular and molecular function of the encoded protein remains elusive. Here, we show that RPG resides in the protein complex formed by the core endosymbiotic components VAPYRIN (VPY) and LUMPY INFECTION (LIN) required for IT polar growth, co-localizes with both VPY and LIN in IT tip- and perinuclear-associated puncta of M. truncatula root hairs undergoing infection and is necessary for VPY recruitment into these structures. Fluorescence Lifetime Imaging Microscopy (FLIM) of phosphoinositide species during bacterial infection revealed that functional RPG is required to sustain strong membrane polarization at the advancing tip of the IT. In addition, loss of RPG functionality alters the cytoskeleton-mediated connectivity between the IT tip and the nucleus and affects polar secretion of the cell wall modifying enzyme NODULE PECTATE LYASE (NPL). Our results integrate RPG into a core host machinery required to support symbiont accommodation, suggesting that its occurrence in plant host genomes is essential to co-opt a multimeric protein module committed to endosymbiosis to sustain IT-mediated bacterial infection.

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Section: Resultsmentioning

confidence: 99%

RPG acts as a central determinant for infectosome formation and cellular polarization during intracellular rhizobial infections

Lace

Perez

et al. 2023

eLife

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“…To better understand the plasticity of σ3 divergence, the σ3 polymorphic residues were mapped onto amino acid conservation data and the 3D structure of the protein ( 60 ). The full-length σ3 amino acid sequence of 58 reovirus isolates available on the NCBI GenBank and our naturally derived reoviruses were used to calculate conservation scores for each residue with Jalview ( 77 , 78 ). Furthermore, the aggregation propensity of each σ3 residue was calculated using Aggrescan3D 2.0 (A3D) and the σ3-μ1C complex 3D structure as an estimation of surface exposure ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Reovirus genomic diversity confers plasticity for protease utility during adaptation to intracellular uncoating

Lin,

Wong,

Eaton

et al. 2023

J Virol

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Mammalian orthoreoviruses (reoviruses) infect many mammals and provide a safe model to study enteric viruses. Knowledge of reoviruses is derived from prototypic lab strains, notably T1L and T3D. Based on these prototypic strains, reoviruses can efficiently utilize gut or lysosomal proteases for uncoating and penetration into host cytoplasm. To discover natural reovirus characteristics, we isolated four genetically diverse wastewater reovirus samples and compared their genetic and phenotypic characteristics to those of T1L/T3D. On L929 cells, the most commonly used model for reovirus studies, naturally derived reoviruses displayed lower fitness than T1L/T3D, evident from smaller plaques and higher relative particle-to-PFU ratios. In contrast to T1L/T3D, which are uncoated efficiently by lysosomal-mediated proteolysis, naturally derived reoviruses displayed poor uncoating kinetics. Exposure of naturally derived reoviruses to gut proteases led to rapid extracellular uncoating and significantly improved infectivity relative to T1L/T3D, indicating that wild reoviruses depended more on extracellular gut proteases. To discover if reovirus can adapt to new host proteases, naturally derived samples were passaged on L929 cells, and large and small plaque-forming isolates were evaluated. Larger plaque sizes correlate with faster intracellular uncoating. Whole-genome sequencing identified the outer capsid σ3 protein as the determinant of uncoating proficiency between wild reoviruses. Interestingly, mutations that permitted intracellular uncoating were found in 0.01% of the parental quasispecies, suggesting that variants with altered protease sensitivity were rapidly selected for during cell culture propagation. Altogether, these findings indicate that naturally circulating reoviruses are more reliant on gut proteases, but the genetic diversity of reovirus quasispecies bestows tremendous plasticity toward protease utility. IMPORTANCE Reoviruses infect many mammals and are widely studied as a model system for enteric viruses. However, most of our reovirus knowledge comes from laboratory strains maintained on immortalized L929 cells. Herein, we asked whether naturally circulating reoviruses possess the same genetic and phenotypic characteristics as laboratory strains. Naturally circulating reoviruses obtained from sewage were extremely diverse genetically. Moreover, sewage reoviruses exhibited poor fitness on L929 cells and relied heavily on gut proteases for viral uncoating and productive infection compared to laboratory strains. We then examined how naturally circulating reoviruses might adapt to cell culture conditions. Within three passages, virus isolates from the parental sewage population were selected, displaying improved fitness and intracellular uncoating in L929 cells. Remarkably, selected progeny clones were present at 0.01% of the parental population. Altogether, using reovirus as a model, our study demonstrates how the high genetic diversity of naturally circulating viruses results in rapid adaptation to new environments.

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“…The phylogenetic tree was displayed using iqtree v2.2.0.3 [ 19 ]. Jalview v2.11.2.2 [ 20 , 21 ] was used for alignment display, and a comparison of KL47 and KL64 representative strains with wzc genes was performed using blast v2.13.0, and visualized by CGview [ 22 ].…”

Section: Methodsmentioning

confidence: 99%

Genomic Evolution of ST11 Carbapenem-Resistant Klebsiella pneumoniae from 2011 to 2020 Based on Data from the Pathosystems Resource Integration Center

Zhang

Tang²,

Yang

et al. 2022

Genes

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(1) Objective: ST11 carbapenem-resistant Klebsiella pneumoniae (CRKP) is widespread throughout the world, and the mechanisms for the transmission and evolution of major serotypes, ST11-KL47 and ST11-KL64, were analyzed to investigate the global distribution and evolutionary characteristics of ST11 CRKP; (2) Methods: The Pathosystems Resource Integration Center (PATRIC) database was downloaded and all K. pneumoniae from 2011 to 2020 were screened to obtain ST11 CRKP genome assemblies with basic information. The relationship of serotype evolution between KL47 and KL64 was then investigated using statistical and bioinformatic analysis; (3) Results: In total, 386 ST11 CRKP isolates were included for analysis. Blood (31.09%, 120/386), respiratory tract (23.06%, 89/386), and feces (20.21%, 78/386) were the major sources of samples. China was the leading country where ST11 CRKP was isolated. KL47 and KL64 were found to be the most prevalent serotypes. ST11-KL64 CRKP [median 78(P25-P75: 72~79.25)] had remarkably more virulence genes than the KL47 [median 63(P25~P75: 63~69)], and the distinction was statistically significant (p < 0.001). A differential comparison of virulence genes between KL47 and KL64 revealed 35 differential virulence genes, including rmpA/rmpA2, iucABCD, iutA, etc. The comparison of the recombination of serotype-determining regions between the two serotypes revealed that KL64 CRKP carried more nucleotide sequences in the CD1-VR2-CD2 region than KL47 CRKP. More nucleotide sequences added approximately 303 base pairs (bp) with higher GC content (58.14%), which might facilitate the evolution of the serotype toward KL64; (4) Conclusions: KL47 and KL64 have become the predominant serotypes of ST11 CRKP. KL64 CRKP carries more virulence genes than KL47 and has increased by approximately 303 bp through recombinant mutations, thus facilitating the evolution of KL47 to KL64. Stricter infection prevention and control measures should be developed to deal with the epidemic transmission of ST11-KL64 CRKP.

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Correction to: Alignment of Biological Sequences with Jalview

Cited by 8 publications

References 0 publications

RPG acts as a central determinant for infectosome formation and cellular polarization during intracellular rhizobial infections

RPG acts as a central determinant for infectosome formation and cellular polarization during intracellular rhizobial infections

Reovirus genomic diversity confers plasticity for protease utility during adaptation to intracellular uncoating

Genomic Evolution of ST11 Carbapenem-Resistant Klebsiella pneumoniae from 2011 to 2020 Based on Data from the Pathosystems Resource Integration Center

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