Genetics of Metabolic Variations between Yersinia pestis Biovars and the Proposal of a New Biovar, microtus

ABSTRACT Yersinia pestis has been historically divided into three biovars: antiqua, mediaevalis, and orientalis. On the basis of this study, strains from Microtus-related plague foci are proposed to constitute a new biovar, microtus. Based on the ability to ferment glycerol and arabinose and to reduce nitrate, Y. pestis strains can be assigned to one of four biovars: antiqua (glycerol positive, arabinose positive, and nitrate positive), mediaevalis (glycerol positive, arabinose positive, and nitrate negative), orientalis (glycerol negative, arabinose positive, and nitrate positive), and microtus (glycerol positive, arabinose negative, and nitrate negative). A 93-bp in-frame deletion in glpD gene results in the glycerol-negative characteristic of biovar orientalis strains. Two kinds of point mutations in the napA gene may cause the nitrate reduction-negative characteristic in biovars mediaevalis and microtus, respectively. A 122-bp frameshift deletion in the araC gene may lead to the arabinose-negative phenotype of biovar microtus strains. Biovar microtus strains have a unique genomic profile of gene loss and pseudogene distribution, which most likely accounts for the human attenuation of this new biovar. Focused, hypothesis-based investigations on these specific genes will help delineate the determinants that enable this deadly pathogen to be virulent to humans and give insight into the evolution of Y. pestis and plague pathogenesis. Moreover, there may be the implications for development of biovar microtus strains as a potential vaccine.

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A family of T6SS antibacterial effectors related to L,D-transpeptidases targets the Peptidoglycan

Access Microbiology ◽

10.1099/acmi.ac2020.po0033 ◽

2020 ◽

Vol 2 (7A) ◽

Author(s):

Stephanie Sibinelli de Sousa ◽

Julia Takuno Hespanhol ◽

Bruno Matsuyama ◽

Stephane Mesnage ◽

Gianlucca Nicastro ◽

...

Keyword(s):

Cell Envelope ◽

Point Mutations ◽

Time Lapse ◽

Secretion Systems ◽

Bacterial Antagonism ◽

New Family ◽

Type Vi Secretion ◽

Altered Cell ◽

Bacterial Effectors ◽

Insight Into

Type VI secretion systems (T6SSs) are contractile nanomachines widely used by bacteria to intoxicate competitors. Salmonella Typhimurium encodes a T6SS within the Salmonella pathogenicity island 6 (SPI-6) that is used during competition against species of the gut microbiota. We characterized a new SPI-6 T6SS antibacterial effector named Tlde1 (type VI L,D-transpeptidase effector 1). Tlde1 is toxic in target-cell periplasm and its toxicity is neutralized by co-expression with immunity protein Tldi1 (type VI L,D-transpeptidase immunity 1). Time-lapse microscopy revealed that intoxicated cells display altered cell division and lose cell envelope integrity. Bioinformatics analysis showed that Tlde1 is evolutionarily related to L,D-transpeptidases. Point mutations on conserved histidine121 and cysteine131 residues eliminated toxicity. Co-incubation of purified recombinant Tlde1 and peptidoglycan tetrapeptides showed that Tlde1 displays both L,D-carboxypeptidase activity by cleaving GM-tetrapeptides between meso-diaminopimelic acid3 and D-alanine4, and L,D-transpeptidase exchange activity by replacing D-alanine4 for a non-canonical D-amino acid. Tlde1 constitutes a new family of T6SS effectors widespread in Proteobacteria. This work increases our knowledge about the bacterial effectors used in interbacterial competitions and provides molecular insight into a new mechanism of bacterial antagonism.

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Compatibility of the movement protein and the coat protein of cucumoviruses is required for cell-to-cell movement

Journal of General Virology ◽

10.1099/vir.0.19687-0 ◽

2004 ◽

Vol 85 (4) ◽

pp. 1039-1048 ◽

Cited By ~ 18

Author(s):

Katalin Salánki ◽

Ákos Gellért ◽

Emese Huppert ◽

Gábor Náray-Szabó ◽

Ervin Balázs

Keyword(s):

Coat Protein ◽

Movement Protein ◽

Point Mutations ◽

Cell Movement ◽

Virus Movement ◽

Tomato Aspermy Virus ◽

Sequence Encoding ◽

Surface Electrostatic Potential ◽

Test Plants ◽

Insight Into

For the cell-to-cell movement of cucumoviruses both the movement protein (MP) and the coat protein (CP) are required. These are not reversibly exchangeable between Cucumber mosaic virus (CMV) and Tomato aspermy virus (TAV). The MP of CMV is able to function with the TAV CP (chimera RT), but TAV MP is unable to promote the cell-to-cell movement in the presence of CMV CP (chimera TR). To gain further insight into the non-infectious nature of the TR recombinant, RNA 3 chimeras were constructed with recombinant MPs and CPs. The chimeric MP and one of the CP recombinants were infectious. The other recombinant CP enabled virus movement only after the introduction of two point mutations (Glu→Lys and Lys→Arg at aa 62 and 65, respectively). The mutations served to correct the CP surface electrostatic potential that was altered by the recombination. The infectivity of the TR virus on different test plants was restored by replacing the sequence encoding the C-terminal 29 aa of the MP with the corresponding sequence of the CMV MP gene or by exchanging the sequence encoding the C-terminal 15 aa of the CP with the same region of TAV. The analysis of the recombinant clones suggests a requirement for compatibility between the C-terminal 29 aa of the MP and the C-terminal two-thirds of the CP for cell-to-cell movement of cucumoviruses.

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A bipartite operator interacts with a heat shock element to mediate early meiotic induction of Saccharomyces cerevisiae HSP82.

Molecular and Cellular Biology ◽

10.1128/mcb.15.12.6754 ◽

1995 ◽

Vol 15 (12) ◽

pp. 6754-6769 ◽

Cited By ~ 23

Author(s):

C Szent-Gyorgyi

Keyword(s):

Saccharomyces Cerevisiae ◽

Heat Shock ◽

Point Mutations ◽

Early Step ◽

Heat Shock Element ◽

Cis Acting ◽

Major Mode ◽

Dna Elements ◽

Insight Into ◽

Activation Sequence

Although key genetic regulators of early meiotic transcription in Saccharomyces cerevisiae have been well characterized, the activation of meiotic genes is still poorly understood in terms of cis-acting DNA elements and their associated factors. I report here that induction of HSP82 is regulated by the early meiotic IME1-IME2 transcriptional cascade. Vegetative repression and meiotic induction depend on interactions of the promoter-proximal heat shock element (HSE) with a nearby bipartite repression element, composed of the ubiquitous early meiotic motif, URS1 (upstream repression sequence 1), and a novel ancillary repression element. The ancillary repression element is required for efficient vegetative repression, is spatially separable from URS1, and continues to facilitate repression during sporulation. In contrast, URS1 also functions as a vegetative repression element but is converted early in meiosis into an HSE-dependent activation element. An early step in this transformation may be the antagonism of URS1-mediated repression by IME1. The HSE also nonspecifically supports a second major mode of meiotic activation that does not require URS1 but does require expression of IME2 and concurrent starvation. Interestingly, increased rather than decreased URS1-mediated vegetative transcription can be artificially achieved by introducing rare point mutations into URS1 or by deleting the UME6 gene. These lesions offer insight into mechanisms of URS-dependent repression and activation. Experiments suggest that URS1-bound factors functionally modulate heat shock factor during vegetative transcription and early meiotic induction but not during heat shock. The loss of repression and activation observed when the IME2 activation element, T4C, is substituted for the HSE suggests specific requirements for URS1-upstream activation sequence interactions.

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Attenuated Bioluminescent Brucella melitensis Mutants GR019 (virB4), GR024 (galE), and GR026 (BMEI1090-BMEI1091) Confer Protection in Mice

Infection and Immunity ◽

10.1128/iai.74.5.2925-2936.2006 ◽

2006 ◽

Vol 74 (5) ◽

pp. 2925-2936 ◽

Cited By ~ 21

Author(s):

Gireesh Rajashekara ◽

David A. Glover ◽

Menachem Banai ◽

David O'Callaghan ◽

Gary A. Splitter

Keyword(s):

Bioluminescence Imaging ◽

Brucella Melitensis ◽

Direct Visualization ◽

Interferon Regulatory Factor 1 ◽

In Vivo Bioluminescence Imaging ◽

Virulent Challenge ◽

Potential Vaccine ◽

Insight Into

ABSTRACT In vivo bioluminescence imaging is a persuasive approach to investigate a number of issues in microbial pathogenesis. Previously, we have applied bioluminescence imaging to gain greater insight into Brucella melitensis pathogenesis. Endowing Brucella with bioluminescence allowed direct visualization of bacterial dissemination, pattern of tissue localization, and the contribution of Brucella genes to virulence. In this report, we describe the pathogenicity of three attenuated bioluminescent B. melitensis mutants, GR019 (virB4), GR024 (galE), and GR026 (BMEI1090-BMEI1091), and the dynamics of bioluminescent virulent bacterial infection following vaccination with these mutants. The virB4, galE, and BMEI1090-BMEI1091 mutants were attenuated in interferon regulatory factor 1-deficient (IRF-1−/−) mice; however, only the GR019 (virB4) mutant was attenuated in cultured macrophages. Therefore, in vivo imaging provides a comprehensive approach to identify virulence genes that are relevant to in vivo pathogenesis. Our results provide greater insights into the role of galE in virulence and also suggest that BMEI1090 and downstream genes constitute a novel set of genes involved in Brucella virulence. Survival of the vaccine strain in the host for a critical period is important for effective Brucella vaccines. The galE mutant induced no changes in liver and spleen but localized chronically in the tail and protected IRF-1−/− and wild-type mice from virulent challenge, implying that this mutant may serve as a potential vaccine candidate in future studies and that the direct visualization of Brucella may provide insight into selection of improved vaccine candidates.

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Structural insight into the thermostable NADP+-dependentmeso-diaminopimelate dehydrogenase fromUreibacillus thermosphaericus

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s1399004715003673 ◽

2015 ◽

Vol 71 (5) ◽

pp. 1136-1146 ◽

Cited By ~ 10

Author(s):

Hironaga Akita ◽

Tomonari Seto ◽

Toshihisa Ohshima ◽

Haruhiko Sakuraba

Keyword(s):

Main Chain ◽

Hydrophobic Interactions ◽

Point Mutations ◽

Key Factors ◽

Structural Comparison ◽

Amino Acid Dehydrogenase ◽

Large Numbers ◽

Ureibacillus Thermosphaericus ◽

Main Factors ◽

Insight Into

Crystal structures of the thermostablemeso-diaminopimelate dehydrogenase (DAPDH) fromUreibacillus thermosphaericuswere determined for the enzyme in the apo form and in complex with NADP+andN-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid. The main-chain coordinates of the enzyme showed notable similarity to those ofSymbiobacterium thermophilumDAPDH. However, the subunit arrangement ofU. thermosphaericusDAPDH (a dimer) was totally different from that of theS. thermophilumenzyme (a hexamer). Structural comparison with the dimeric enzyme from the mesophileCorynebacterium glutamicumrevealed that the presence of large numbers of intrasubunit and intersubunit hydrophobic interactions, as well as the extensive formation of intersubunit ion-pair networks, were likely to be the main factors contributing to the higher thermostability ofU. thermosphaericusDAPDH. This differs fromS. thermophilumDAPDH, within which the unique hexameric assembly is likely to be responsible for its high thermostability. Analysis of the active site ofU. thermosphaericusDAPDH revealed the key factors responsible for the marked difference in substrate specificity between DAPDH and the D-amino acid dehydrogenase recently created from DAPDH by introducing five point mutations [Akitaet al.(2012).Biotechnol. Lett.34, 1693–1699; 1701–1702].

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Specificity of the Protective Antibody Response to Apical Membrane Antigen 1

Infection and Immunity ◽

10.1128/iai.69.5.3286-3294.2001 ◽

2001 ◽

Vol 69 (5) ◽

pp. 3286-3294 ◽

Cited By ~ 223

Author(s):

Anthony N. Hodder ◽

Pauline E. Crewther ◽

Robin F. Anders

Keyword(s):

Apical Membrane ◽

Affinity Purification ◽

Point Mutations ◽

Apical Membrane Antigen 1 ◽

Apical Membrane Antigen ◽

Potential Vaccine ◽

Inhibitory Antibodies ◽

Domain I ◽

The Impact

ABSTRACT Apical membrane antigen 1 (AMA1) is considered one of the leading candidates for inclusion in a vaccine against blood stages ofPlasmodium falciparum. Although the ama1 gene is relatively conserved compared to those for some other potential vaccine components, numerous point mutations have resulted in amino acid substitutions at many sites in the polypeptide. The polymorphisms in AMA1 have been attributed to the diversifying selection pressure of the protective immune responses. It was therefore of interest to investigate the impact of sequence diversity in P. falciparum AMA1 on the ability of anti-AMA1 antibodies to inhibit the invasion of erythrocytes in vitro by P. falciparummerozoites. For these studies, we used antibodies to recombinantP. falciparum 3D7 AMA1 ectodomain, which was prepared for testing in early clinical trials. Antibodies were raised in rabbits to the antigen formulated in Montanide ISA720, and human antibodies to AMA1 were isolated by affinity purification from the plasma of adults living in regions of Papua New Guinea where malaria is endemic. Both rabbit and human anti-AMA1 antibodies were found to be strongly inhibitory to the invasion of erythrocytes by merozoites from both the homologous and two heterologous lines of P. falciparum. The inhibitory antibodies targeted both conserved and strain-specific epitopes within the ectodomain of AMA1; however, it appears that the majority of these antibodies reacted with strain-specific epitopes in domain I, the N-terminal disulfide-bonded domain, which is the most polymorphic region of AMA1.

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Typing Methods for the Plague Pathogen, Yersinia pestis

Journal of AOAC International ◽

10.1093/jaoac/92.4.1174 ◽

2009 ◽

Vol 92 (4) ◽

pp. 1174-1183 ◽

Cited By ~ 10

Author(s):

Luther E Lindler

Keyword(s):

Yersinia Pestis ◽

Nitrate Reduction ◽

Yersinia Pseudotuberculosis ◽

Western Hemisphere ◽

Glycerol Fermentation ◽

Classification Schemes ◽

Typing Methods ◽

Phenotypic Methods ◽

Human Infections

Abstract Phenotypic and genotypic methodologies have been used to differentiate the etiological agent of plague, Yersinia pestis. Historically, phenotypic methods were used to place isolates into one of three biovars based on nitrate reduction and glycerol fermentation. Classification of Y. pestis into genetic subtypes is problematic due to the relative monomorphic nature of the pathogen. Resolution into groups is dependent on the number and types of loci used in the analysis. The last 510 years of research and analysis in the field of Y. pestis genotyping have resulted in a recognition by Western scientists that two basic types of Y. pestis exist. One type, considered to be classic strains that are able to cause human plague transmitted by the normal flea vector, is termed epidemic strains. The other type does not typically cause human infections by normal routes of infection, but is virulent for rodents and is termed endemic strains. Previous classification schemes used outside the Western hemisphere referred to these latter strains as Pestoides varieties of Y. pestis. Recent molecular analysis has definitely shown that both endemic and epidemic strains arose independently from a common Yersinia pseudotuberculosis ancestor. Currently, 11 major groups of Y. pestis are defined globally.

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Widespread convergence in toxin resistance by predictable molecular evolution

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1511706112 ◽

2015 ◽

Vol 112 (38) ◽

pp. 11911-11916 ◽

Cited By ~ 69

Author(s):

Beata Ujvari ◽

Nicholas R. Casewell ◽

Kartik Sunagar ◽

Kevin Arbuckle ◽

Wolfgang Wüster ◽

...

Keyword(s):

Molecular Evolution ◽

Cardiac Glycoside ◽

Convergent Evolution ◽

Point Mutations ◽

Sodium Potassium ◽

Toxin Resistance ◽

The Subject ◽

Taxonomic Groups ◽

Core Part ◽

Insight Into

The question about whether evolution is unpredictable and stochastic or intermittently constrained along predictable pathways is the subject of a fundamental debate in biology, in which understanding convergent evolution plays a central role. At the molecular level, documented examples of convergence are rare and limited to occurring within specific taxonomic groups. Here we provide evidence of constrained convergent molecular evolution across the metazoan tree of life. We show that resistance to toxic cardiac glycosides produced by plants and bufonid toads is mediated by similar molecular changes to the sodium-potassium-pump (Na+/K+-ATPase) in insects, amphibians, reptiles, and mammals. In toad-feeding reptiles, resistance is conferred by two point mutations that have evolved convergently on four occasions, whereas evidence of a molecular reversal back to the susceptible state in varanid lizards migrating to toad-free areas suggests that toxin resistance is maladaptive in the absence of selection. Importantly, resistance in all taxa is mediated by replacements of 2 of the 12 amino acids comprising the Na+/K+-ATPase H1–H2 extracellular domain that constitutes a core part of the cardiac glycoside binding site. We provide mechanistic insight into the basis of resistance by showing that these alterations perturb the interaction between the cardiac glycoside bufalin and the Na+/K+-ATPase. Thus, similar selection pressures have resulted in convergent evolution of the same molecular solution across the breadth of the animal kingdom, demonstrating how a scarcity of possible solutions to a selective challenge can lead to highly predictable evolutionary responses.

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New Insight into Bacterial Interaction with the Matrix of Plant-Based Fermented Foods

Foods ◽

10.3390/foods10071603 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1603

Author(s):

Klaudia Gustaw ◽

Iwona Niedźwiedź ◽

Kamila Rachwał ◽

Magdalena Polak-Berecka

Keyword(s):

Gene Loss ◽

Bacterial Species ◽

Evolutionary Process ◽

Fermented Foods ◽

Deep Insight ◽

Chemical Profile ◽

Organoleptic Properties ◽

Bacterial Interaction ◽

The Matrix ◽

Insight Into

Microorganisms have been harnessed to process raw plants into fermented foods. The adaptation to a variety of plant environments has resulted in a nearly inseparable association between the bacterial species and the plant with a characteristic chemical profile. Lactic acid bacteria, which are known for their ability to adapt to nutrient-rich niches, have altered their genomes to dominate specific habitats through gene loss or gain. Molecular biology approaches provide a deep insight into the evolutionary process in many bacteria and their adaptation to colonize the plant matrix. Knowledge of the adaptive characteristics of microorganisms facilitates an efficient use thereof in fermentation to achieve desired final product properties. With their ability to acidify the environment and degrade plant compounds enzymatically, bacteria can modify the textural and organoleptic properties of the product and increase the bioavailability of plant matrix components. This article describes selected microorganisms and their competitive survival and adaptation in fermented fruit and vegetable environments. Beneficial changes in the plant matrix caused by microbial activity and their beneficial potential for human health are discussed as well.

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Structural dynamics is a determinant of the functional significance of missense variants

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1715896115 ◽

2018 ◽

Vol 115 (16) ◽

pp. 4164-4169 ◽

Cited By ~ 29

Author(s):

Luca Ponzoni ◽

Ivet Bahar

Keyword(s):

Structural Dynamics ◽

Protein Function ◽

Biological Function ◽

Point Mutations ◽

Computational Tools ◽

Missense Variants ◽

Pathogenicity Prediction ◽

Cancer Types ◽

The Impact ◽

Insight Into

Accurate evaluation of the effect of point mutations on protein function is essential to assessing the genesis and prognosis of many inherited diseases and cancer types. Currently, a wealth of computational tools has been developed for pathogenicity prediction. Two major types of data are used to this aim: sequence conservation/evolution and structural properties. Here, we demonstrate in a systematic way that another determinant of the functional impact of missense variants is the protein’s structural dynamics. Measurable improvement is shown in pathogenicity prediction by taking into consideration the dynamical context and implications of the mutation. Our study suggests that the class of dynamics descriptors introduced here may be used in conjunction with existing features to not only increase the prediction accuracy of the impact of variants on biological function, but also gain insight into the physical basis of the effect of missense variants.

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